NDLI: Small open reading frames: a comparative genetics approach to validation

Content Provider	Springer Nature : BioMed Central
Author	Jain, Niyati Richter, Felix Adzhubei, Ivan Sharp, Andrew J. Gelb, Bruce D.
Abstract	Open reading frames (ORFs) with fewer than 100 codons are generally not annotated in genomes, although bona fide genes of that size are known. Newer biochemical studies have suggested that thousands of small protein-coding ORFs (smORFs) may exist in the human genome, but the true number and the biological significance of the micropeptides they encode remain uncertain. Here, we used a comparative genomics approach to identify high-confidence smORFs that are likely protein-coding. We identified 3,326 high-confidence smORFs using constraint within human populations and evolutionary conservation as additional lines of evidence. Next, we validated that, as a group, our high-confidence smORFs are conserved at the amino-acid level rather than merely residing in highly conserved non-coding regions. Finally, we found that high-confidence smORFs are enriched among disease-associated variants from GWAS. Overall, our results highlight that smORF-encoded peptides likely have important functional roles in human disease.
Related Links	https://bmcgenomics.biomedcentral.com/counter/pdf/10.1186/s12864-023-09311-7.pdf
Ending Page	11
Page Count	11
Starting Page	1
File Format	HTM / HTML
ISSN	14712164
DOI	10.1186/s12864-023-09311-7
Journal	BMC Genomics
Issue Number	1
Volume Number	24
Language	English
Publisher	BioMed Central
Publisher Date	2023-05-01
Access Restriction	Open
Subject Keyword	Life Sciences Microarrays Proteomics Animal Genetics and Genomics Microbial Genetics and Genomics Plant Genetics and Genomics Micropeptides Small open reading frames Human genetic variation Evolutionary conservation Comparative genetics
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics
Journal Impact Factor	3.5/2023
5-Year Journal Impact Factor	4.1/2023

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

Comparative genomics of Riemerella anatipestifer reveals genetic diversity

Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors

A comparative plastome approach enhances the assessment of genetic variation in the Melilotus genus

sORFdb – a database for sORFs, small proteins, and small protein families in bacteria

Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics

Analysis of structural variation among inbred mouse strains

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

DeepHistone: a deep learning approach to predicting histone modifications

Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle

Small open reading frames: a comparative genetics approach to validation

Similar Documents

Comparative genomics of Riemerella anatipestifer reveals genetic diversity

Mutational constraint analysis workflow for overlapping short open reading frames and genomic neighbors

A comparative plastome approach enhances the assessment of genetic variation in the Melilotus genus

sORFdb – a database for sORFs, small proteins, and small protein families in bacteria

Plant protein peptidase inhibitors: an evolutionary overview based on comparative genomics

Analysis of structural variation among inbred mouse strains

Evidence for conservation and selection of upstream open reading frames suggests probable encoding of bioactive peptides

DeepHistone: a deep learning approach to predicting histone modifications

Comparative genomics of 84 Pectobacterium genomes reveals the variations related to a pathogenic lifestyle

Small open reading frames: a comparative genetics approach to validation