Description

This hub represents GeneCaRNA, the integrated gene-centric compendium of human ncRNA genes, embedded within GeneCards. The ncRNA compendium was created by integrating data of >460k transcripts genomic locations into a comprehensive non-redundant gene-centric view of human ncRNA genes.

GeneCaRNA track set contains 9 gene tracks and 9 transcript tracks.

Gene tracks:

1. A track including all ncRNA genes
2. One separate gene track for each ncRNA subcategory:
   1. lncRNA - long non-coding RNA
   2. miRNA - micro RNA
   3. rRNA - ribosomal RNA
   4. tRNA - transfer RNA
   5. snoRNA - small nucleolar RNA
   6. SRP RNA - Signal recognition particle RNA
   7. piRNA - piwi-interacting RNA
   8. Other - a track for all other ncRNA subcategories including: guide RNA, misc RNA, ribozyme, Y_RNA, snRNA, vault_RNA, and scRNA

Transcript tracks:

3. A track including all ncRNA transcripts
4. One separate transcript track for each ncRNA subcategory (similar to the gene subcategory tracks)

Display conventions

Each gene in the gene tracks is identified by its GeneCaRNA symbol, and a link to the relevant Card is provided in the details page. Each transcript in the transcript tracks is identified by its transcript identifier (RNAcentral Id). The transcript details page provides links to the respective gene/transcript centric GeneCaRNA/RNAcentral pages.

Colors distinguish genes and transcripts of different subcategories:

Methods

ncRNA records and annotations are integrated from EBI’s RNAcentral, and its 21 primary sources of human ncRNA transcripts, as well as from Ensembl, NCBI Entrez Gene, and HGNC. Using the gene-centric GeneCards model, we clustered overlapping transcript entries from the aforementioned sources, applying an algorithm based on genomic coordinates.

Our unified compilation contains >200k ncRNA gene entries (including ~100,000 Piwi-interacting-RNAs). Each ncRNA gene is featured in GeneCaRNA, with affiliated transcripts and annotations from all relevant sources.

Transcript tracks:

All ncRNA transcripts are shown, colored via the subcategory Transcript color scheme. Transcripts and their exon structure are based on RNAcentral data.

Gene tracks:

All ncRNA genes are shown, colored via the subcategory Gene color scheme. The gene’s territory is defined as the union of all the territories of its associated transcripts. The gene’s exons structure represents all exonic territories of its clustered transcripts.

More details are provided at the GeneCards information page.

Source data for the GeneCards Suite version v5.24 was downloaded during February 2025.

References

Barshir R, Fishilevich F, Iny-Stein T, Zelig O, Mazor Y, Guan-Golan Y, Safran M and Lancet D. GeneCaRNA: a comprehensive gene-centric database of human non-coding RNAs in the GeneCards Suite, Journal of Molecular Biology (2021) 166913. doi: 10.1016. PMID 33676929

Stelzer G, Rosen R, Plaschkes I, Zimmerman S, Twik M, Fishilevich S, Iny Stein T, Nudel R, Lieder I, Mazor Y, Kaplan S, Dahary, D, Warshawsky D, Guan- Golan Y, Kohn A, Rappaport N, Safran M, and Lancet D. The GeneCards Suite: From Gene Data Mining to Disease Genome Sequence Analysis, Current Protocols in Bioinformatics (2016), 54:1.30.1-1.30.33. doi: 10.1002/cpbi.5. PMID 27322403

The RNAcentral Consortium. RNAcentral: a hub of information for non-coding RNA sequences, Nucleic Acids Research, Volume 47, Issue D1, 08 January 2019, Pages D1250–D1251, doi: 10.1093/nar/gky1206. PMID 30535383

Contact

Credits

Supported in part by a grant from LifeMap Sciences Inc.