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It is now the 2nd CHALLENGE Period for CACAO Spring 2020! It will end on Sunday February 23, 2020 at 11:59 pm CST
This is your chance to challenge other team's annotations. You may also DEFEND or suggest improvements to your own annotations IF they have been challenged. Please note, although we ENCOURAGE challenges, an excess of identical challenges that do not appear to be applicable to the annotation or well thought out will be considered spam and ignored.
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Category:Team Gene String

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StatusPageUserDate/TimeGO Term (Aspect)ReferenceEvidenceNotesLinks
unacceptableARATH:F4JQG2RazMonk, Team Gene String2017-04-23 15:20:27 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge
unacceptableARATH:A8MRI1RazMonk, Team Gene String2017-04-23 15:20:22 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge
unacceptableARATH:Q9LU44RazMonk, Team Gene String2017-04-23 15:20:15 CDTGO:0006913 nucleocytoplasmic transport (P)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 5, the GFP fluorescence of all these proteins in nuclei was strongly reduced during the course of cytoplasmic photobleaching. … These results demonstrate that AtU2AF35, AtU2AF65, and AtSF1 are nucleocytoplasmic shuttling proteins"

challenge
acceptableARATH:Q9LU44RazMonk, Team Gene String2017-04-23 15:12:27 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:Q9LU44RazMonk, Team Gene String2017-04-23 15:12:26 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtSF1 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:A8MRI1RazMonk, Team Gene String2017-04-23 15:10:01 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:A8MRI1RazMonk, Team Gene String2017-04-23 15:10:00 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF35 in A. thaliana. "As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:F4JQG2RazMonk, Team Gene String2017-04-23 15:08:07 CDTGO:0005654 nucleoplasm (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableARATH:F4JQG2RazMonk, Team Gene String2017-04-23 15:08:07 CDTGO:0005730 nucleolus (C)PMID:28432478ECO:0000314 direct assay evidence used in manual assertion

Protein called AtU2AF65 in A. thaliana.

"As shown in Fig. 2, strong nucleoplasm GFP fluorescence was found except the dark circled area which is presumably nucleolus. We performed FRAP analysis of two areas (nucleoplasm and nucleolus). In the nucleolus area, photobleaching was done to expand the dark circled area. Fluorescence recovered rapidly after photobleaching in both areas, indicating that Arabidopsis U2AF and SF1 proteins are highly mobile nuclear proteins, like the RSZp22 protein."

challenge
acceptableHUMAN:DHX29RazMonk, Team Gene String2017-04-23 04:25:35 CDTGO:0042255 ribosome assembly (P)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. In cells with silenced DHX using shRNA, polysome profiles showed a reduction in polysomes with concomitant increases in 40S, 60S, and 80S ribosome fractions (Fig. 3B).

challenge
unacceptableHUMAN:CADH5LoganMcCurry, Team Gene String2017-04-22 22:54:31 CDTGO:0005829 cytosol (C)PMID:28428220ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 Parts L and M details the colocalization of CDH5 with CKLF3 throughout the endothelial cytosol. The organism of the gene used is human, and the gene is referred to as VE-cadherin in the experiment while UniProt refers to it as CDH5. The colocalized protein, CKLF3, is referred to as CMTM3 throughout the experiment and as CKLF3 by UniProt, with accession Q96MX0.

challenge
acceptableHUMAN:CKLF3LoganMcCurry, Team Gene String2017-04-22 22:53:09 CDTGO:0005829 cytosol (C)PMID:28428220ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 Parts C, L and M details the colocalization of CKLF3 with CDH5 throughout the endothelial cytosol. The organism of the gene used is human, and the gene is referred to as CMTM3 in the experiment while UniProt refers to it as CKLF3. The colocalized protein, CDH5, is referred to as VE-cadherin throughout the experiment and as CDH5 by UniProt, with accession P33151.

challenge
acceptableHUMAN:CKLF3LoganMcCurry, Team Gene String2017-04-22 22:38:50 CDTGO:0031410 cytoplasmic vesicle (C)PMID:28428220ECO:0000314 direct assay evidence used in manual assertion

Fig. 5 Part B shows CKLF3 localizing in cytoplasmic vesicle-like structures. The organism is human, and the gene is referred to as CMTM3 throughout the experiment while it is referred to as CKLF3 by UniProt.

challenge
unacceptableDANRE:GLE1LoganMcCurry, Team Gene String2017-04-21 19:01:40 CDTGO:1905046 positive regulation of Schwann cell proliferation involved in axon regeneration (P)PMID:26921650ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 6 Parts A-D shows the requirement of Gle1 for the formation of myelinating Schwann cells with comparison of mutant and wild type axons. Fig. 5 Parts A-B shows the requirement of Gle1 for proper proliferation of Schwann cell precursors, as the mutants showed reduced proliferation. Both the experiment and UniProt refer to the gene as Gle1. The organism is Danio rerio (Zebrafish).

challenge
acceptableDANRE:GLE1LoganMcCurry, Team Gene String2017-04-21 18:48:01 CDTGO:0014044 Schwann cell development (P)PMID:26921650ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 4 Parts A, C, E and G shows defective Schwann cell development in mutants for Gle1 in comparison to Fig. 4 Parts B, D, F and H which consisted of wild type siblings. Both UniProt and the experiment refers to the gene as Gle1, and the organism is Danio rerio (Zebrafish).

challenge
updatedbyinstructorSCHPO:SAP1LoganMcCurry, Team Gene String2017-04-21 17:40:51 CDTGO:1902985 mitotic pre-replicative complex assembly (P)PMID:28223353ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5. Sap1 is required to load Cdc18 onto DNA for pre-RC assembly. Sap1, S. pombe.

challenge
acceptableHUMAN:LN28BRazMonk, Team Gene String2017-04-18 13:56:44 CDTGO:2000632 negative regulation of pre-miRNA processing (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Figure S11B. Shows inhibition of Dicer processings by Lin28 in vitro "(B) In vitro processing of pre-let-7a-1, pre-let-7g and pre-miR-16-1 by Dicer with rLin28b present. "

challenge
acceptableDANRE:GLE1LoganMcCurry, Team Gene String2017-04-18 13:48:57 CDTGO:0060296 regulation of cilium beat frequency involved in ciliary motility (P)PMID:28035044ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 5 Parts A-B shows that a depletion of Gle1 reduces ciliary beating and alters left–right asymmetry in the organism Danio rerio (Zebrafish). An antisense morpholino was used in creating a mutant phenotype with a knockdown Zebrafish Gle1. Both the experiment and Uniprot refer to the gene as Gle1. A new GO term was requested for "positive regulation of cilium beat frequency involved in ciliary motility" at https://github.com/geneontology/go-ontology/issues/13375

challenge
unacceptableHUMAN:DHX29RazMonk, Team Gene String2017-04-18 13:47:07 CDTGO:0008284 positive regulation of cell proliferation (P)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. HeLa cell proliferation was inhibited by almost 3-fold in DHX29 siRNA-silenced cells (Fig. 5A). Cell proliferation also was significantly (3-fold) inhibited by shRNA-mediated silencing of DHX29 after 4 days, compared with a nontargeting shRNA control (Fig. 5B). These results demonstrate that DHX29 is associated for cell proliferation.

challenge
acceptableHUMAN:GLE1LoganMcCurry, Team Gene String2017-04-18 12:59:27 CDTGO:0005813 centrosome (C)PMID:28035044ECO:0000314 direct assay evidence used in manual assertion

Figure 1 Part A shows Gle1 localization at the centrosome indicated by the arrow pointing with "Ce." The organism for the gene is human and was expressed in Danio rerio (Zebrafish). The gene is referred to as Gle1 by both UniProt and the experiment.

challenge
unacceptableARATH:DNAT1RazMonk, Team Gene String2017-04-16 23:42:16 CDTGO:0005777 peroxisome (C)PMID:28352967ECO:0000314 direct assay evidence used in manual assertion

AtDHNAT1 in A. thaliana; has two splice variants including At5g48950.1 (no separate UniProt ID). As predicted, the C-terminal part of At5g48950.1 could target GFP to peroxisomes (Fig. 3b), shown through GFP reporter assay

challenge
unacceptableARATH:DNAT1RazMonk, Team Gene String2017-04-16 23:42:16 CDTGO:0005777 peroxisome (C)PMID:28352967ECO:0000314 direct assay evidence used in manual assertion

AtDHNAT1 in A. thaliana; has two splice variants including At3g50170.1 (no separate UniProt ID). The C-terminal part of At3g50170.1 could target GFP to peroxisomes (Fig. 5b), shown with GFP reporter assay

challenge
acceptableHUMAN:GLE1LoganMcCurry, Team Gene String2017-04-09 00:03:22 CDTGO:0005814 centriole (C)PMID:28035044ECO:0000314 direct assay evidence used in manual assertion

Figure 2 Part A shows localization of Gle1 in centrioles, with brighter CETN signals showing older ("mother") centriole localization. The gene is referred to as Gle1 by both UniProt and the experiment, and the organism for the gene is human and was expressed in Danio rerio (Zebrafish).

challenge
acceptableHUMAN:GLE1LoganMcCurry, Team Gene String2017-04-08 23:59:50 CDTGO:0005635 nuclear envelope (C)PMID:28035044ECO:0000314 direct assay evidence used in manual assertion

Figure 1 Part A shows Gle1 localization at the nuclear envelope indicated by the arrow pointing with "NE." The organism for the gene is human and was expressed in Danio rerio (Zebrafish). The gene is referred to as Gle1 by both UniProt and the experiment.

challenge
acceptableHUMAN:GLE1LoganMcCurry, Team Gene String2017-04-08 23:52:12 CDTGO:0036064 ciliary basal body (C)PMID:28035044ECO:0000314 direct assay evidence used in manual assertion

Figure 1 Part B shows localization of Gle1 to the ciliary base's ciliary basal body. The gene is referred to as Gle1 by both UniProt and the experiment, and the organism for the gene is human and was expressed in Danio rerio (Zebrafish).

challenge
acceptableORYSJ:MEL1LoganMcCurry, Team Gene String2017-04-08 22:26:51 CDTGO:1903343 positive regulation of meiotic DNA double-strand break formation (P)PMID:27521428ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 1 Part D shows a lack of double stand break formation during the meiotic leptotene state in a mel1 mutant. This is in comparison to the wild type cell in Fig. 1 Part A, and indicates a positive regulation of meiotic DNA double stand break formation. The protein is referred to as mel1 by both UniProt and the journal. The organism is Oryza sativa.

challenge
unacceptableSCHPO:RNA14LoganMcCurry, Team Gene String2017-04-08 22:25:31 CDTGO:0051984 positive regulation of chromosome segregation (P)PMID:26581324ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2 part C shows chromosome segregation defects indicated by arrows in the Rna14 mutant. Fig. 3 part B shows the percentage of chromosome loss over time in both the wild type and mutant Rna14 strains, and indicates a 20% chromosome loss with the Rna14 mutant after twelve hours. Fig. 3 part C shows the timed viability of these Rn14 mutants, with only 10% of the Rna14 mutants surviving after 12 hours. These show Rna14 having a positive regulation of chromosome segregation in the organism S. pombe. Both the experiment and UniProt refer to the gene as Rna14.

challenge
acceptableORYSJ:MEL1LoganMcCurry, Team Gene String2017-04-07 13:15:55 CDTGO:0061866 negative regulation of histone H3-S10 phosphorylation (P)PMID:27521428ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 5 Part A-I demonstrates a negative regulation of H3-S10 phosphorylation, where the mel1 mutant showed relatively increased levels of H3-S10 phosphorylation between pre and post leptotene phases. The organism is Oryza sativa and the gene is referred to as mel1 by Uniprot and the experiment. A new term was requested: "negative regulation of histone H3-S10 phosphorylation" at https://github.com/geneontology/go-ontology/issues/13327

challenge
acceptableHUMAN:HNRPURazMonk, Team Gene String2017-04-04 13:49:23 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human hnRNP U. Figure 3, immunofluorescence spectroscopy confirmed localization to the nucleoplasm.

challenge
acceptableHUMAN:DHX9RazMonk, Team Gene String2017-04-04 13:44:17 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human DHX9. Figure 3, immunofluorescence spectroscopy shows localization to the nucleoplasm.

challenge
acceptableHUMAN:NUP98RazMonk, Team Gene String2017-04-04 13:41:14 CDTGO:0005654 nucleoplasm (C)PMID:28221134ECO:0000314 direct assay evidence used in manual assertion

Human nup98. Figure 3, immunofluorescence spectroscopy confirmed localization to the nucleoplasm.

challenge
acceptableARATH:ISE2RazMonk, Team Gene String2017-04-04 13:32:26 CDTGO:0016554 cytidine to uridine editing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 2. Loss of ISE2 compromises C-to-U RNA editing at specific sites. 6 sites known to undergo C-to-U editing are monitored, with a marked decrease in editing in cells with silenced ISE2.

challenge
acceptableARATH:ISE2RazMonk, Team Gene String2017-04-04 13:32:26 CDTGO:0000373 Group II intron splicing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 4. ISE2 is required for splicing of a group II intron in ycf3 transcripts. Verified using qPCR and gel electrophoresis showing an increase in the unspliced variant of the intron.

challenge
acceptableARATH:ISE2RazMonk, Team Gene String2017-04-04 13:32:26 CDTGO:1901259 chloroplast rRNA processing (P)PMID:28346704ECO:0000315 mutant phenotype evidence used in manual assertion

ISE2 in A. thaliana. Figure 5. Loss of ISE2 leads to defects in rRNA processing. With silenced ISE2, aberrant forms of rRNA are visualized with gel electrophoresis when compared to overexpressed ISE2 and control cells.

challenge
acceptableHUMAN:DHX29RazMonk, Team Gene String2017-04-04 13:16:12 CDTGO:0008494 translation activator activity (F)PMID:20018725ECO:0000315 mutant phenotype evidence used in manual assertion

Human DHX29. In control cells, Cdc25C mRNA sedimented predominantly with heavy polysomes, whereas in DHX29-silenced cells, it was shifted to light polysomes, indicating decreased translation initiation of this mRNA (Fig. 4A). In agreement with these findings, Cdc25C protein levels decreased by more than 3-fold on DHX29 silencing (Fig. 4B).

challenge
updatedbyinstructorHUMAN:DHX29RazMonk, Team Gene String2017-04-04 13:16:11 CDTGO:0022627 cytosolic small ribosomal subunit (C)PMID:20018725ECO:0000314 direct assay evidence used in manual assertion

Human DHX29. Figure 1: Immunofluorescence shows DHX29 was enriched in 40S fractions. A low level of DHX29 was associated with 60S and 80S ribosomes.

challenge
unacceptableHUMAN:PACS2RazMonk, Team Gene String2017-04-04 13:00:40 CDTGO:0006915 apoptotic process (P)PMID:15692567ECO:0000315 mutant phenotype evidence used in manual assertion

Human PACS-2 depletion conferred a marked resistance to STS, increasing the percentage of viable cells by nearly four-fold. The antiapoptotic effects of the PACS-2 siRNA were corroborated by analyzing the STS-mediated caspase cleavage of poly-ADP-ribose polymerase (PARP) to generate p85.

challenge
acceptableHUMAN:PACS2RazMonk, Team Gene String2017-04-04 12:56:35 CDTGO:0032469 endoplasmic reticulum calcium ion homeostasis (P)PMID:15692567ECO:0000315 mutant phenotype evidence used in manual assertion

Human PACS-2

Fig. 3C, histamine elicited a two-fold greater increase in calcium released from the ER into the cytosol of PACS-2-depleted cells compared to PACS-1-depleted or control cells.

challenge
acceptableORYSJ:MEL1LoganMcCurry, Team Gene String2017-03-23 10:37:13 CDTGO:1900111 positive regulation of histone H3-K9 dimethylation (P)PMID:27521428ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 3 Part F demonstrates a positive regulation of H3K9 dimethylation in regards to the wildtype MEL1 during pre-leptotene and post-leptotene meiotic phases. The mutant phenotype for MEL1 showed reduced levels of H3K9 dimethylation. The organism is Oryza sativa, and the gene is referred to as mel1 throughout the experiment and by Uniprot.

challenge
acceptableORYSJ:MEL1LoganMcCurry, Team Gene String2017-03-23 10:37:13 CDTGO:2000616 negative regulation of histone H3-K9 acetylation (P)PMID:27521428ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 3 Part L demonstrates a negative regulation of H3-K9 acetylation, where the mel1 mutant showed relatively increased levels of H3-K9 acetylation between pre and post leptotene phases. The organism is Oryza sativa and the gene is referred to as mel1 by Uniprot and the experiment.

challenge
acceptableSCHPO:YPT3LoganMcCurry, Team Gene String2017-03-21 14:33:47 CDTGO:0005737 cytoplasm (C)PMID:27630265ECO:0000314 direct assay evidence used in manual assertion

In Fig. 2A GFP-Ypt3 was observed as numerous dots dispersed throughout the cytoplasm during sporulation. The organism is S. pombe, and the authors refer to the gene as Ypt3.

challenge
acceptableSCHPO:SPO13LoganMcCurry, Team Gene String2017-03-21 13:47:25 CDTGO:0035974 meiotic spindle pole body (C)PMID:27630265ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5C shows how Spo13 is localized at the spindle pole body during Meiosis II. The organism is S. pombe and the protein is referred to as Spo13 throughout the experiment.

challenge
updatedbyinstructorSCHPO:SEC2LoganMcCurry, Team Gene String2017-03-04 20:14:03 CSTGO:0090619 meiotic spindle pole (C)PMID:27630562ECO:0000314 direct assay evidence used in manual assertion

Figure 8B and 8C shows localization of Sec2 to the spindle pole body during Meiosis in the organism S. pombe.

challenge
acceptableSCHPO:YPT3LoganMcCurry, Team Gene String2017-02-19 00:08:03 CSTGO:0035974 meiotic spindle pole body (C)PMID:27630265ECO:0000314 direct assay evidence used in manual assertion

Figure 6A details Ypt3 localization at the meiotic spindle pole body during sporulation. The organism is S. pombe. The authors refer to the protein as Ypt3 throughout the experiment.

challenge
acceptableSCHPO:SPO13LoganMcCurry, Team Gene String2017-02-18 23:52:15 CSTGO:0035974 meiotic spindle pole body (C)PMID:27630265ECO:0000314 direct assay evidence used in manual assertion

Figure 5B shows how Spo13 is localized at the spindle pole body during Meiosis II. The organism is S. pombe and the protein is referred to as Spo13 throughout the experiment.

challenge
acceptableSCHPO:YPT2LoganMcCurry, Team Gene String2017-02-18 23:37:17 CSTGO:0035974 meiotic spindle pole body (C)PMID:27630265ECO:0000315 mutant phenotype evidence used in manual assertion

Figure 5B and 5C shows Ypt2 localizing at the Meiosis II Spindle Pole Body in a Spo13-dependent manner. The organism is S. Pombe. The colocalized protein is Spo13: C6Y4C9.

challenge
unacceptableHUMAN:DHX29RazMonk, Team Gene String2017-02-14 14:39:31 CSTGO:0009615 detection of virus (P)PMID:24821782ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2I, and J show that knockdown DHX29 expression shows a reduced production of immune response peptides IFN-β and IL-6 upon viral stimulation. The protein is referred to as DHX29 in the paper and is specifically mentioned to be human DHX29.

challenge
unacceptableCAEEL:GPDH2RazMonk, Team Gene String2017-02-14 14:24:08 CSTGO:0047484 regulation of response to osmotic stress (P)PMID:28166192ECO:0000315 mutant phenotype evidence used in manual assertion

Fig 2b shows that GPDH-2 is required for parental protection of progeny in response to osmotic stress (i.e. the parental protein is required to regulate response to progeny's osmotic stress). The protein is called GPDH-2 in the paper, used with the organism C. elegans

challenge
unacceptableCAEEL:ILB3RazMonk, Team Gene String2017-02-14 14:17:24 CSTGO:0047484 regulation of response to osmotic stress (P)PMID:28166192ECO:0000315 mutant phenotype evidence used in manual assertion

Supplementary Figs. 1h and 1i: Shows that INS-3 is responsible for developmental arrest in response to osmotic stress. Referred to in paper as INS-3, insulin like peptide, in C. elegans.

challenge
acceptableHUMAN:DHX29RazMonk, Team Gene String2017-02-14 14:09:47 CSTGO:0001731 formation of translation preinitiation complex (P)PMID:23047696ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2E: Lane 2 shows non-canonical toeprints without DHX29, and 2e lane 3 shows canonical toeprints of formation of preinitiation complex with DHX29 in the presence of all other necessary translation initiation components. Lanes 4, 5, and 6 of the same figure show non-canonical toeprints with truncated forms of DHX29

Human DHX29 transfected into E. coli

challenge
acceptableHUMAN:DHX29RazMonk, Team Gene String2017-02-14 14:09:47 CSTGO:0017111 nucleoside-triphosphatase activity (F)PMID:23047696ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 7C shows NTPase activity for human DHX29. Within the paper, the protein is called DHX29 of mammalian DHX29. From fig. 1 and methods, it is said to be human DHX29

challenge
acceptableSCHPO:CUT7LoganMcCurry, Team Gene String2017-02-14 14:01:16 CSTGO:0008574 ATP-dependent microtubule motor activity, plus-end-directed (F)PMID:27834216ECO:0000314 direct assay evidence used in manual assertion

Figure 2. Part C details how ATP added to the Cut7 motor after flush with a buffer reverses a minus-end directed activity into a plus-end directed step. The organism is S. pombe.

challenge
updatedbyinstructorHUMAN:LN28BRazMonk, Team Gene String2017-02-14 13:56:09 CSTGO:0050779 RNA destabilization (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

Figure 4B: Human Lin28b (from recombinant E. coli), when added to cell extract in increasing amounts, increases the amount of uridylated pre-let-7a-1 (up-let-7a-1). Figure 4E: up-let-7a-1 shows decreased stability as compared to pre-let-7a-1. According to the authors, this indicates that "Lin28 mediates the terminal uridylation of pre-let-7 diverting the Dicer processing and irreversibly reroutes pre-let-7 into a decay pathway."

challenge
acceptableHUMAN:LN28BRazMonk, Team Gene String2017-02-14 13:56:09 CSTGO:2000627 positive regulation of miRNA catabolic process (P)PMID:18951094ECO:0000315 mutant phenotype evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Fig. 4b shows "in vitro uridylation of pre-let-7a-1 was carried out with purified recombinant Lin28b protein." Fig. 4e shows a quicker decay of target species, pre-let-7a-1, after uridylation by overexpressed human lin28b; up-let-7a-1 is the product of the uridylation of pre-let-7a-1 by lin28b. Called human lin28b.

challenge
acceptableHUMAN:LN28BRazMonk, Team Gene String2017-02-14 13:56:09 CSTGO:2000635 negative regulation of primary miRNA processing (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

"Lin28b was identified via RNA affinity purification of Huh7 cell extracts with pre-let-7a-1"

Figure S11A. Shows inhibition of Drosha processings by Lin28 in vitro "(A) In vitro processing of pri-let-7a-1, pri-let-7g and pri-miR-16-1 by Drosha with recombinant Lin28b (rLin28b) present" Called Lin28b.

challenge
unacceptableMOUSE:LN28ARazMonk, Team Gene String2017-02-14 13:54:05 CSTGO:2000627 positive regulation of miRNA catabolic process (P)PMID:18951094ECO:0000315 mutant phenotype evidence used in manual assertion

"Protein knockdown was carried out against human Lin28b in Huh7 cells and mouse Lin28a in mouse ESCs" Fig. S3 shows, with knocked down mouse Lin28a, there is a marked increase in accumulation of mature let7a species.

Called mouse Lin28a in paper.

challenge
acceptableMOUSE:LN28ARazMonk, Team Gene String2017-02-14 13:54:05 CSTGO:0071076 RNA 3' uridylation (P)PMID:18951094ECO:0000314 direct assay evidence used in manual assertion

Fig. 3Aa and 3Ab: When comparing Lin28a mutant with wildtype, it can be seen that Lin28a does bind the miRNA species in question, pri-let-7a. With both pri-let-7a and Lin28a present, the sharp band at pre-let-7a produced with mutant lin28a seen on the northern blot is abrogated and instead a smear can be seen in its place. In Fig. 3Ba, these species of varying lengths (cloned from HEK293T cells ectopically expressing pri-let-7a-1 and Lin28a) are sequenced showing 3' uridylation of an average of 14 U nucleotides.

Called Lin28a in paper

challenge
unacceptableSCHPO:YPT2LoganMcCurry, Team Gene String2017-02-03 21:22:07 CSTGO:0051286 cell tip (C)PMID:27082518ECO:0000314 direct assay evidence used in manual assertion

Fig. 8 parts A, B and C details movement of Ypt2 towards the cell tip during cell interphase. The organism is S. pombe.

challenge
updatedbyinstructorSCHPO:YPT3LoganMcCurry, Team Gene String2017-02-03 20:52:07 CSTGO:0035838 growing cell tip (C)PMID:27082518ECO:0000314 direct assay evidence used in manual assertion

Fig. 8B and 8C details that Ypt3 would travel alone or would colocalize with Ypt2 48% of the time in the punctate structures. This occurred mainly at the cell tip during interphase or at the division site during cytokinesis. Organism is S. pombe. "Indeed, those Ypt3-only puncta also traveled to the division site during cytokinesis and to the growing cell tips during interphase (Fig 8C and S5B Fig, arrows)"

challenge
unacceptableSCHPO:YPT3LoganMcCurry, Team Gene String2017-02-03 20:52:06 CSTGO:1905346 protein localization to cleavage furrow rim (P)PMID:27082518ECO:0000314 direct assay evidence used in manual assertion

Fig. 8 part D's lower right panels details the localization of Ypt3 at the cleavage furrow rim during cytokineses, with red arrows indicating longer docking times than yellow arrows for Ypt3 puncta. The organism is S. pombe, and the authors refer to the protein as Ypt3.

challenge
acceptableSCHPO:PIF1LoganMcCurry, Team Gene String2017-01-31 15:35:55 CSTGO:0031297 replication fork processing (P)PMID:22426535ECO:0000315 mutant phenotype evidence used in manual assertion

Fig. 2 B-D states how Pfh1 promotes replication fork progression at a tRNA gene, with it performing a sweepase function in promoting replication fork passage. A child term was created for this regarding progress and tRNA genes. The organism is S. pombe.

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