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SCARNA5 small Cajal body-specific RNA 5 [ Homo sapiens (human) ]

Gene ID: 677775, updated on 17-Sep-2024

Summary

Official Symbol
SCARNA5provided by HGNC
Official Full Name
small Cajal body-specific RNA 5provided by HGNC
Primary source
HGNC:HGNC:32561
See related
Ensembl:ENSG00000252010 MIM:615640; AllianceGenome:HGNC:32561
Gene type
ncRNA
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
U87
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Genomic context

See SCARNA5 in Genome Data Viewer
Location:
2q37.1
Exon count:
1
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 2 NC_000002.12 (233275726..233276003)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 2 NC_060926.1 (233763810..233764087)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 2 NC_000002.11 (234184372..234184649)

Chromosome 2 - NC_000002.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12465 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17328 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12466 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17329 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233926783-233927376 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233927377-233927970 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17330 Neighboring gene neuraminidase 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12468 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233937995-233938700 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17331 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17332 Neighboring gene Sharpr-MPRA regulatory region 10619 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17333 Neighboring gene inositol polyphosphate-5-phosphatase D Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233953501-233954000 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972121-233972622 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233972623-233973122 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17334 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233982267-233982860 Neighboring gene H3K27ac hESC enhancer GRCh37_chr2:233987251-233987751 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233988888-233989435 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr2:233989436-233989982 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:233993677-233994176 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234072305-234072918 Neighboring gene NANOG hESC enhancer GRCh37_chr2:234125377-234125936 Neighboring gene RNA, 7SL, cytoplasmic 32, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234131944-234132095 Neighboring gene ReSE screen-validated silencer GRCh37_chr2:234151441-234151635 Neighboring gene P300/CBP strongly-dependent group 1 enhancer GRCh37_chr2:234155927-234157126 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17335 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17336 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17337 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12469 Neighboring gene autophagy related 16 like 1 Neighboring gene NANOG hESC enhancer GRCh37_chr2:234197330-234197831 Neighboring gene small Cajal body-specific RNA 6 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234227861-234228828 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234228829-234229795 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17338 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234234987-234235964 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr2:234237262-234238093 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr2:234238124-234238905 Neighboring gene S-antigen visual arrestin

Genomic regions, transcripts, and products

Phenotypes

EBI GWAS Catalog

Description
A genome-wide association study on a southern European population identifies a new Crohn's disease susceptibility locus at RBX1-EP300.
EBI GWAS Catalog
A genome-wide scan of Ashkenazi Jewish Crohn's disease suggests novel susceptibility loci.
EBI GWAS Catalog
Fucosyltransferase 2 (FUT2) non-secretor status is associated with Crohn's disease.
EBI GWAS Catalog
Genome-wide association study identifies new susceptibility loci for Crohn disease and implicates autophagy in disease pathogenesis.
EBI GWAS Catalog
Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci.
EBI GWAS Catalog

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Gene Ontology Provided by GOA

Process Evidence Code Pubs
involved_in RNA processing IEA
Inferred from Electronic Annotation
more info
 
Component Evidence Code Pubs
located_in Cajal body IMP
Inferred from Mutant Phenotype
more info
PubMed 
located_in nucleolus IEA
Inferred from Electronic Annotation
more info
 

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

RNA

  1. NR_003008.2 RNA Sequence

    Status: VALIDATED

    Source sequence(s)
    AC013726
    Related
    ENST00000516201.1

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000002.12 Reference GRCh38.p14 Primary Assembly

    Range
    233275726..233276003
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 PATCHES

Genomic

  1. NW_011332690.1 Reference GRCh38.p14 PATCHES

    Range
    221064..221341
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060926.1 Alternate T2T-CHM13v2.0

    Range
    233763810..233764087
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)