COL6A4P2 collagen type VI alpha 4 pseudogene 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL6A4P2provided by HGNC
Official Full Name: collagen type VI alpha 4 pseudogene 2provided by HGNC
Primary source: HGNC:HGNC:38501
See related: MIM:616612; AllianceGenome:HGNC:38501
Gene type: pseudo
RefSeq status: PROVISIONAL
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: COL6A4
Summary: This transcribed pseudogene represents the 3' end of a presumed ortholog to a mouse gene which encodes a collagen VI alpha 4 chain protein (GeneID 68553). The predicted ORF contains multiple premature stop codons. A large chromosome break separates this pseudogene from the 5' end of the presumed ortholog (DVWA, GeneID 344875) which is located upstream at chromosome 3p24.3. [provided by RefSeq, Jun 2009]
Expression: Low expression observed in reference dataset See more
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Genomic context

Location:: 3q22.1

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (130212820..130273806)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (132956497..133017797)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (129931663..129992649)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: HPA RNA-seq normal tissues HPA RNA-seq normal tissues
Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
BioProject: PRJEB4337
Publication: PMID 24309898
Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Due to a chromosome breakage on chromosome 3, the human genome does not have a collagen VI alpha 4 (COL6A4) gene, but have two COL6A4 pseudogenes instead.
Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).
The discovery of three additional collagen VI chains doubles the collagen VI family and adds a layer of complexity to collagen VI assembly and function in the extracellular matrix.
Title: Three novel collagen VI chains, alpha4(VI), alpha5(VI), and alpha6(VI).

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Phenotypes

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Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of d-amphetamine response in healthy volunteers identifies putative associations, including cadherin 13 (CDH13). EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

General gene information

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Markers

RH92350 (e-PCR)
- UniSTS:86279

ha2998 (e-PCR)
- UniSTS:515619

SHGC-79329 (e-PCR)
- UniSTS:103237

SHGC-143562 (e-PCR)
- UniSTS:171955

SHGC-70163 (e-PCR)
- UniSTS:183785

Other Names

alpha collagen containing double von Willebrand factor A domains
collagen VI alpha 4 pseudogene 2
collagen, type VI, alpha 4

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.