# WormBase **URL:** https://community.alliancegenome.org/c/model-organism-worms/wormbase/24.md [Latest](https://community.alliancegenome.org/latest.md) · [Categories](https://community.alliancegenome.org/categories.md) --- ## [About the WormBase category](https://community.alliancegenome.org/t/about-the-wormbase-category/2664)
**Author:** [@system](https://community.alliancegenome.org/u/system)\ **Replies:** 0
Discuss and report issues concerning WormBase --- ## [ACKnowledge Community Curation Project - Help WormBase!](https://community.alliancegenome.org/t/acknowledge-community-curation-project-help-wormbase/8631)
**Author:** [@Ranjana](https://community.alliancegenome.org/u/Ranjana)\ **Replies:** 0\ **Last updated:** [March 2, 2026, 7:36pm UTC](https://community.alliancegenome.org/t/acknowledge-community-curation-project-help-wormbase/8631 "2026-03-02T19:36:30Z")
The ACKnowledge Community Curation Project is an AI-assisted community curation project in which authors of C. elegans papers can help alert WormBase curators to the data in their papers. Alerting WormBase curators help… --- ## [Error in young adult single-cell data on wormbase](https://community.alliancegenome.org/t/error-in-young-adult-single-cell-data-on-wormbase/8304)
**Author:** [@Abbas\_Ghaddar](https://community.alliancegenome.org/u/Abbas_Ghaddar)\ **Replies:** 0\ **Last updated:** [January 31, 2025, 4:23pm UTC](https://community.alliancegenome.org/t/error-in-young-adult-single-cell-data-on-wormbase/8304 "2025-01-31T16:23:37Z")
UPDATE: The issue has been fixed! Hello, Just wanted to give everyone a heads up. We recently noticed that our single-cell data (Ghaddar et al. 2023) was not properly imported into wormbase. We’re working with wormbase… --- ## [C. elegans CB4856 GTF/GFF file](https://community.alliancegenome.org/t/c-elegans-cb4856-gtf-gff-file/7777)
**Author:** [@Anusha\_Aggarwal](https://community.alliancegenome.org/u/Anusha_Aggarwal)\ **Replies:** 3\ **Last updated:** [August 28, 2024, 1:01pm UTC](https://community.alliancegenome.org/t/c-elegans-cb4856-gtf-gff-file/7777 "2024-08-28T13:01:26Z")
Hi everyone! Does anyone know where I can get access to a GTF/GFF file specific to the CB4856 C. elegans strain? The GTF file posted on WormBase is empty, and the GFF file seems to have very limited & duplicated inform… --- ## [Exporting sequence for a list of genes](https://community.alliancegenome.org/t/exporting-sequence-for-a-list-of-genes/7604)
**Author:** [@kchoe](https://community.alliancegenome.org/u/kchoe)\ **Replies:** 4\ **Last updated:** [April 2, 2024, 7:53pm UTC](https://community.alliancegenome.org/t/exporting-sequence-for-a-list-of-genes/7604 "2024-04-02T19:53:20Z")
Hello, I would like to export DNA sequence for a list of about 100 genes for motif analysis. e.g., 1500 bp upstream for promoter analysis. What tool would be best for this? Thank you, --- ## [C.elegans and human homologous gene](https://community.alliancegenome.org/t/c-elegans-and-human-homologous-gene/6914)
**Author:** [@wangwenya](https://community.alliancegenome.org/u/wangwenya)\ **Replies:** 0\ **Last updated:** [May 8, 2023, 1:03pm UTC](https://community.alliancegenome.org/t/c-elegans-and-human-homologous-gene/6914 "2023-05-08T13:03:14Z")
C.elegans and human homologous gene --- ## [Genbank format downloading from jbrowse1/2](https://community.alliancegenome.org/t/genbank-format-downloading-from-jbrowse1-2/6772)
**Author:** [@lybCNU](https://community.alliancegenome.org/u/lybCNU)\ **Replies:** 13\ **Last updated:** [February 23, 2023, 1:45am UTC](https://community.alliancegenome.org/t/genbank-format-downloading-from-jbrowse1-2/6772 "2023-02-23T01:45:46Z")
As GBrowse is goinig to be retired January 2023, is there anyway to download directly genbank format from jbrowse? Genbank format can be edited with snapgene with gene feature. Manual adding feature to jbrowse sequencing… --- ## [Unusual request for help please!](https://community.alliancegenome.org/t/unusual-request-for-help-please/6347)
**Author:** [@leea](https://community.alliancegenome.org/u/leea)\ **Replies:** 1\ **Last updated:** [January 15, 2022, 6:10am UTC](https://community.alliancegenome.org/t/unusual-request-for-help-please/6347 "2022-01-15T06:10:49Z")
Hi all, I unfortunately am infested with something, and was hoping I could find a person here who would be willing to run my genetic data against the data of WormBase if that is at all possible? I would be happy to comp… --- ## [Introducing the Alliance Community Forum](https://community.alliancegenome.org/t/introducing-the-alliance-community-forum/6184)
**Author:** [@tharris](https://community.alliancegenome.org/u/tharris)\ **Replies:** 2\ **Last updated:** [July 12, 2021, 6:24pm UTC](https://community.alliancegenome.org/t/introducing-the-alliance-community-forum/6184 "2021-07-12T18:24:47Z")
Dear Worm Community Forum Users – As previously discussed, the Worm Community Forum is moving! Today, along with the Alliance of Genome Resources, we are pleased to introduce a new online discussion forum. Alliance Co… --- ## [The Worm Community Forum is MOVING!](https://community.alliancegenome.org/t/the-worm-community-forum-is-moving/6175)
**Author:** [@tharris](https://community.alliancegenome.org/u/tharris)\ **Replies:** 0\ **Last updated:** [May 25, 2021, 10:11pm UTC](https://community.alliancegenome.org/t/the-worm-community-forum-is-moving/6175 "2021-05-25T22:11:00Z")
Hello Worm Community Forum Users: In the coming weeks, the Worm Community Forum will be migrating to a new home and a new platform. As part of the Alliance of Genome Resources (https://alliancegenome.org) project (of w… --- ## [k-rendering error on genome browser tracks ](https://community.alliancegenome.org/t/k-rendering-error-on-genome-browser-tracks/6044)
**Author:** [@psiv](https://community.alliancegenome.org/u/psiv)\ **Replies:** 3\ **Last updated:** [January 27, 2021, 12:00am UTC](https://community.alliancegenome.org/t/k-rendering-error-on-genome-browser-tracks/6044 "2021-01-27T00:00:35Z")
I get an error - 'k rendering error: Can’t call method “values” on an undefined value at /usr/share/perl5/Bio/Graphics/Glyph/wiggle\_data.pm (attached). I’ve tried different browsers. Any advice on how to fix this? Thank… --- ## [identical genomes in wormbase for c elegans](https://community.alliancegenome.org/t/identical-genomes-in-wormbase-for-c-elegans/5505)
**Author:** [@shafferpr](https://community.alliancegenome.org/u/shafferpr)\ **Replies:** 1\ **Last updated:** [March 6, 2017, 4:12pm UTC](https://community.alliancegenome.org/t/identical-genomes-in-wormbase-for-c-elegans/5505 "2017-03-06T16:12:12Z")
Hi all, I’m interested in looking at many different versions of the c elegans genomic data to learn something about the genetic variation in the population. I’ve been exploring the ftp site: ftp://ftp.wormbase.org/pub/w… --- ## [An unusual operon](https://community.alliancegenome.org/t/an-unusual-operon/5498)
**Author:** [@gw3](https://community.alliancegenome.org/u/gw3)\ **Replies:** 0\ **Last updated:** [February 20, 2017, 12:31pm UTC](https://community.alliancegenome.org/t/an-unusual-operon/5498 "2017-02-20T12:31:51Z")
The operon CEOP3188 contains the gene R07E5.10. R07E5.10 has two isoforms R07E5.10b and R07E5.10a. These might be better represented as two individual genes. They each start with a SL1/SL2 trans-splicing site. The SL1/… --- ## [C37C3.8 has a conserved non-canonical initiation codon (probably!)](https://community.alliancegenome.org/t/c37c3-8-has-a-conserved-non-canonical-initiation-codon-probably/5496)
**Author:** [@gw3](https://community.alliancegenome.org/u/gw3)\ **Replies:** 0\ **Last updated:** [February 17, 2017, 5:19pm UTC](https://community.alliancegenome.org/t/c37c3-8-has-a-conserved-non-canonical-initiation-codon-probably/5496 "2017-02-17T17:19:56Z")
C37C3.8 probably has a conserved non-canonical initiation codon. The first exon of orthologs of the CDS C37C3.8c has an ORF with a conserved a coding sequence. It is highly likely that the initiation starts with the fi… --- ## [C34E10.10 has an unusual 5' end](https://community.alliancegenome.org/t/c34e10-10-has-an-unusual-5-end/5495)
**Author:** [@gw3](https://community.alliancegenome.org/u/gw3)\ **Replies:** 0\ **Last updated:** [February 17, 2017, 5:06pm UTC](https://community.alliancegenome.org/t/c34e10-10-has-an-unusual-5-end/5495 "2017-02-17T17:06:35Z")
C34E10.10 is a well-conserved gene. It is an ortholog of human UTP23 (UTP23, small subunit processome component); involved in embryo development. In nematodes, it appears to have a conserved coding exon at the 5’ end of… --- ## [How can I download wormpep208?](https://community.alliancegenome.org/t/how-can-i-download-wormpep208/5457)
**Author:** [@AHeffo](https://community.alliancegenome.org/u/AHeffo)\ **Replies:** 2\ **Last updated:** [October 24, 2016, 1:53am UTC](https://community.alliancegenome.org/t/how-can-i-download-wormpep208/5457 "2016-10-24T01:53:40Z")
I am trying to download wormpep208 with a FTP for peptide/protein identification. When I use the “ftp.sanger.ac.uk/pub/databases/wormpep/wormpep208” directory, the “wormpep” folder is empty and I can’t find the .FASTA f… --- ## [Hawaiian SNPs](https://community.alliancegenome.org/t/hawaiian-snps/5452)
**Author:** [@rbsmit](https://community.alliancegenome.org/u/rbsmit)\ **Replies:** 2\ **Last updated:** [October 13, 2016, 5:53pm UTC](https://community.alliancegenome.org/t/hawaiian-snps/5452 "2016-10-13T17:53:15Z")
With Wormmart I was relatively easily able to get all Hawaiian SNPs from a specified interval that resulted in missense, nonsense or indel mutations in the corresponding proteins. I’ve almost figured out how to get the … --- ## [F26D11.1 has an unusual 5' end](https://community.alliancegenome.org/t/f26d11-1-has-an-unusual-5-end/5434)
**Author:** [@gw3](https://community.alliancegenome.org/u/gw3)\ **Replies:** 0\ **Last updated:** [September 9, 2016, 2:47pm UTC](https://community.alliancegenome.org/t/f26d11-1-has-an-unusual-5-end/5434 "2016-09-09T14:47:14Z")
F26D11.1 is a conserved locus c.f. C. briggsae CBG08614, remanei CRE27490, japonica CJA12219. It has a very high level of expression in the first three exons and expression decreases to moderately high in the last two… --- ## [Cdh-4 (WBGene00000396) Reference issues](https://community.alliancegenome.org/t/cdh-4-wbgene00000396-reference-issues/5046)
**Author:** [@PaulD](https://community.alliancegenome.org/u/PaulD)\ **Replies:** 3\ **Last updated:** [June 9, 2016, 11:05am UTC](https://community.alliancegenome.org/t/cdh-4-wbgene00000396-reference-issues/5046 "2016-06-09T11:05:48Z")
cdh-4 appears to be a well studied C. elegans gene involved in cell migration and fate. The problem is that this loci appears to suffer from 2 issues in what is the current 13th intron (WS246). While there is very good… --- ## [FTP sites down, WormMart down, where do I find gff3 files?](https://community.alliancegenome.org/t/ftp-sites-down-wormmart-down-where-do-i-find-gff3-files/5337)
**Author:** [@LaDu](https://community.alliancegenome.org/u/LaDu)\ **Replies:** 4\ **Last updated:** [February 5, 2016, 6:24pm UTC](https://community.alliancegenome.org/t/ftp-sites-down-wormmart-down-where-do-i-find-gff3-files/5337 "2016-02-05T18:24:56Z")
I’m getting timeouts on both http://caprica.caltech.edu:9002/biomart/martview/ and ftp://ftp.wormbase.org/pub/wormbase/genomes/elegans/genome\_feature\_tables/GFF3 I’d like to simply download gff3 files that tell me wh… --- ## [Announcing WormBase ParaSite 3](https://community.alliancegenome.org/t/announcing-wormbase-parasite-3/5209)
**Author:** [@bruce](https://community.alliancegenome.org/u/bruce)\ **Replies:** 0\ **Last updated:** [July 30, 2015, 2:43pm UTC](https://community.alliancegenome.org/t/announcing-wormbase-parasite-3/5209 "2015-07-30T14:43:25Z")
We are pleased to announce the third release of WormBase ParaSite, the home for parasitic worm draft genomes and genomic data in WormBase. This release includes two new annotated genomes, taking the total number of nema… --- ## [nematode assembly hub - feedback wanted](https://community.alliancegenome.org/t/nematode-assembly-hub-feedback-wanted/5175)
**Author:** [@mh6](https://community.alliancegenome.org/u/mh6)\ **Replies:** 0\ **Last updated:** [June 17, 2015, 1:49pm UTC](https://community.alliancegenome.org/t/nematode-assembly-hub-feedback-wanted/5175 "2015-06-17T13:49:31Z")
reposted here, as UCSC doesn’t allow posts soliciting testers for assembly hubs: Hia, I am working since a bit on creating a nematode assembly hub covering the WormBase core species. While I was passing it around inter… --- ## [Methionine restriction in C. elegans](https://community.alliancegenome.org/t/methionine-restriction-in-c-elegans/5127)
**Author:** [@tn72316](https://community.alliancegenome.org/u/tn72316)\ **Replies:** 1\ **Last updated:** [April 10, 2015, 2:16pm UTC](https://community.alliancegenome.org/t/methionine-restriction-in-c-elegans/5127 "2015-04-10T14:16:24Z")
Hi All, My lab is interested in getting into c. elegans research. However, we would like to perform a particular type of analysis. We would like to restrict the methionine content in these worms (down to 40-80% normal … --- ## [contigs](https://community.alliancegenome.org/t/contigs/5066)
**Author:** [@laura](https://community.alliancegenome.org/u/laura)\ **Replies:** 3\ **Last updated:** [January 7, 2015, 11:33am UTC](https://community.alliancegenome.org/t/contigs/5066 "2015-01-07T11:33:27Z")
Hello everyone, Could someone tell me how do I download the contig where is my gene of interest? Many thanks in advance --- ## [Rpa-4 WS247 Is a complicated loci](https://community.alliancegenome.org/t/rpa-4-ws247-is-a-complicated-loci/5035)
**Author:** [@PaulD](https://community.alliancegenome.org/u/PaulD)\ **Replies:** 1\ **Last updated:** [November 3, 2014, 10:42am UTC](https://community.alliancegenome.org/t/rpa-4-ws247-is-a-complicated-loci/5035 "2014-11-03T10:42:43Z")
Up until WS247 rpa-3 and rpa-4 existed a 2 distinct genes in the WormBase annotation. This was recently revised as it appears that rpa-3 is a partial duplication of rpa-4 but it lacks it’s 5’ end and probably the promot… --- ## [Wormbase blast/blat not accessible ?](https://community.alliancegenome.org/t/wormbase-blast-blat-not-accessible/5009)
**Author:** [@wolfgang](https://community.alliancegenome.org/u/wolfgang)\ **Replies:** 2\ **Last updated:** [September 29, 2014, 1:22pm UTC](https://community.alliancegenome.org/t/wormbase-blast-blat-not-accessible/5009 "2014-09-29T13:22:17Z")
The link http://www.wormbase.org/tools/blast\_blat from the Wormbase main page is not working for me anymore. Anyone else experiencing this problem? --- ## [Wormine for genetic variation](https://community.alliancegenome.org/t/wormine-for-genetic-variation/4968)
**Author:** [@danielecook](https://community.alliancegenome.org/u/danielecook)\ **Replies:** 0\ **Last updated:** [August 23, 2014, 5:57pm UTC](https://community.alliancegenome.org/t/wormine-for-genetic-variation/4968 "2014-08-23T17:57:36Z")
Hello - I’m trying to use Worm Mine to fetch genetic variation data. Specifically, I want to be able to use the API to query and return the data that is available on wormbase as seen in this table. Is this possible wit… --- ## [WormMine - specific cell/tissue expression...](https://community.alliancegenome.org/t/wormmine-specific-cell-tissue-expression/4952)
**Author:** [@Dolphin](https://community.alliancegenome.org/u/Dolphin)\ **Replies:** 0\ **Last updated:** [August 12, 2014, 11:54am UTC](https://community.alliancegenome.org/t/wormmine-specific-cell-tissue-expression/4952 "2014-08-12T11:54:16Z")
Is there a way within WormMine to return genes with expression patterns limited to and specific for a particular cell/tissue only? For example, I’d like to identify reporter strains in which GFP expression is limited to… --- ## [how to predict the transplicing site in c elegan genome](https://community.alliancegenome.org/t/how-to-predict-the-transplicing-site-in-c-elegan-genome/4932)
**Author:** [@capricy](https://community.alliancegenome.org/u/capricy)\ **Replies:** 8\ **Last updated:** [August 4, 2014, 6:45pm UTC](https://community.alliancegenome.org/t/how-to-predict-the-transplicing-site-in-c-elegan-genome/4932 "2014-08-04T18:45:08Z")
Hello, there, I have been reading the articles about the prediction of transpliced genes. They all point to a putative transplicing site. Just wonder if someone would briefly let me know how these transplicing sites are… --- ## [Evolution in action: Y51H4A.22/Y51H4A.23 and T08B6.9](https://community.alliancegenome.org/t/evolution-in-action-y51h4a-22-y51h4a-23-and-t08b6-9/4901)
**Author:** [@gw3](https://community.alliancegenome.org/u/gw3)\ **Replies:** 0\ **Last updated:** [June 17, 2014, 2:54pm UTC](https://community.alliancegenome.org/t/evolution-in-action-y51h4a-22-y51h4a-23-and-t08b6-9/4901 "2014-06-17T14:54:14Z")
T08B6.9 is a well-defined expressed coding gene with 9 exons. It has been duplicated in the at some point in the past to produce Y51H4A.22 and Y51H4A.23. Y51H4A.22 looks like a well-defined expressed coding gene, endin… [Next page](https://community.alliancegenome.org/c/model-organism-worms/wormbase/24.md?page=1)