COL21A1 collagen type XXI alpha 1 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL21A1provided by HGNC
Official Full Name: collagen type XXI alpha 1 chainprovided by HGNC
Primary source: HGNC:HGNC:17025
See related: Ensembl:ENSG00000124749 MIM:610002; AllianceGenome:HGNC:17025
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: FP633; COLA1L
Summary: This gene encodes the alpha chain of type XXI collagen, a member of the FACIT (fibril-associated collagens with interrupted helices) collagen family. Type XXI collagen is localized to tissues containing type I collagen and maintains the integrity of the extracellular matrix. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Jan 2016]
Expression: Broad expression in placenta (RPKM 9.8), heart (RPKM 8.6) and 16 other tissues See more
Orthologs: all
NEW: Try the new Gene table
Try the new Transcript table

Genomic context

Location:: 6p12.1; 6p12.3-p11.2

Exon count:: 37

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (56056590..56394128, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (55896186..56235397, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (55921388..56258926, complement)

Chromosome 6 - NC_000006.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

Go to the top of the page Help

Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

Go to the top of the page Help

See details

Project title: 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

Go to the top of the page Help

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Prognostic significance of abnormal matrix collagen remodeling in colorectal cancer based on histologic and bioinformatics analysis.
Title: Prognostic significance of abnormal matrix collagen remodeling in colorectal cancer based on histologic and bioinformatics analysis.
Validating candidate biomarkers for different stages of non-alcoholic fatty liver disease.
Title: Validating candidate biomarkers for different stages of non-alcoholic fatty liver disease.
Low copy number of Col21A1 is associated with nonsyndromic cleft lip and/or palate.
Title: Two novel genes TOX3 and COL21A1 in large extended Malay families with nonsyndromic cleft lip and/or palate.
Extracellular matrix proteins expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line.
Title: Extracellular matrix proteins expression profiling in chemoresistant variants of the A2780 ovarian cancer cell line.
Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

Submit: New GeneRIF Correction

Phenotypes

Go to the top of the page Help

Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
Genome-wide association study of atypical psychosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Meta-analysis of genome-wide association studies identifies ten loci influencing allergic sensitization. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

Go to the top of the page Help

See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

Go to the top of the page Help

Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

Go to the top of the page Help

Markers

RH45942 (e-PCR)
- UniSTS:19474

Bdy88c05 (e-PCR)
- UniSTS:27945

D6S2015 (e-PCR)
- UniSTS:17238

RH46582 (e-PCR)
- UniSTS:22108

SHGC-58459 (e-PCR)
- UniSTS:94345

RH118905 (e-PCR)
- UniSTS:138897

SHGC-6162 (e-PCR)
- UniSTS:69323

D6S1870 (e-PCR)
- UniSTS:12243

SHGC-53575 (e-PCR)
- UniSTS:66541

Clone Names

FLJ39125, FLJ44623, MGC26619, DKFZp564B052

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IEA Inferred from Electronic Annotation more info
colocalizes_with collagen-containing extracellular matrix	HDA more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info

General protein information

Go to the top of the page Help

Preferred Names: collagen alpha-1(XXI) chain

Names: alpha 1 chain-like collagen; collagen, type XXI, alpha 1

NCBI Reference Sequences (RefSeq)

Go to the top of the page Help

NEW Try the new Transcript table

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.

mRNA and Protein(s)

NM_001318751.2 → NP_001305680.1 collagen alpha-1(XXI) chain isoform a precursor

Status: REVIEWED

Description

Transcript Variant: This variant (2) includes an alternate exon in the 5' UTR compared to variant 1. Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AF330693, BC143865, BP231679, HY145939

Consensus CDS

CCDS55025.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
NM_001318752.2 → NP_001305681.1 collagen alpha-1(XXI) chain isoform b precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) contains an alternate 5' UTR and lacks an in-frame coding exon compared to variant 1. The encoded isoform (b) is shorter than isoform a.

Source sequence(s)

AF330693, DA856279

Consensus CDS

CCDS83099.1

UniProtKB/TrEMBL

B7ZLK3

Related

ENSP00000359855.1, ENST00000370819.5

Conserved Domains (4) summary

pfam01391
Location:446 → 505

Collagen; Collagen triple helix repeat (20 copies)

COG2304
Location:1 → 296

YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
NM_001318753.2 → NP_001305682.1 collagen alpha-1(XXI) chain isoform c

Status: REVIEWED

Description

Transcript Variant: This variant (4) differs in the 5' UTR, lacks multiple exons in the 5' coding region, and initiates translation at an alternate start codon, compared to variant 1. The encoded isoform (c) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AF330693, AK096444, AL513530, DA826579

UniProtKB/Swiss-Prot

Q96P44

UniProtKB/TrEMBL

B3KU30

Conserved Domains (1) summary

pfam01391
Location:33 → 90

Collagen; Collagen triple helix repeat (20 copies)
NM_001318754.2 → NP_001305683.1 collagen alpha-1(XXI) chain isoform d

Status: REVIEWED

Description

Transcript Variant: This variant (5) differs in the 5' UTR, lacks multiple exons in the 5' coding region, contains an alternate splice site in the 3' coding region, and initiates translation at an alternate start codon compared to variant 1. The encoded isoform (d) has a distinct N-terminus and is shorter than isoform a.

Source sequence(s)

AF330693, AK096444, AL513530

UniProtKB/TrEMBL

B3KU30

Related

ENST00000467045.5

Conserved Domains (1) summary

pfam01391
Location:197 → 240

Collagen; Collagen triple helix repeat (20 copies)
NM_030820.4 → NP_110447.2 collagen alpha-1(XXI) chain isoform a precursor

See identical proteins and their annotated locations for NP_110447.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) encodes the longest isoform (a). Variants 1 and 2 encode the same isoform (a).

Source sequence(s)

AF330693, AL136624, BP231679

Consensus CDS

CCDS55025.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Related

ENSP00000244728.5, ENST00000244728.10

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...

RNA

NR_134849.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate splice site in the 5' region compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF330693, BC045597, BP231679
NR_134850.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate splice site in 5' region and includes an alternate internal exon compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF330693, BC143863, BP231679
NR_134851.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses an alternate splice site in 5' region, includes an alternate internal exon, and lacks an exon in the 3' region, compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF330693, BC143864, BP231679

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

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

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

56056590..56394128 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011514924.3 → XP_011513226.1 collagen alpha-1(XXI) chain isoform X1

See identical proteins and their annotated locations for XP_011513226.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_006715223.2 → XP_006715286.1 collagen alpha-1(XXI) chain isoform X2

UniProtKB/TrEMBL

B7ZLK3

Conserved Domains (4) summary

pfam01391
Location:449 → 508

Collagen; Collagen triple helix repeat (20 copies)

COG2304
Location:1 → 296

YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_047419383.1 → XP_047275339.1 collagen alpha-1(XXI) chain isoform X1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1
XM_011514925.4 → XP_011513227.1 collagen alpha-1(XXI) chain isoform X1

See identical proteins and their annotated locations for XP_011513227.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_011514927.1 → XP_011513229.1 collagen alpha-1(XXI) chain isoform X1

See identical proteins and their annotated locations for XP_011513229.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...
XM_011514926.2 → XP_011513228.1 collagen alpha-1(XXI) chain isoform X1

See identical proteins and their annotated locations for XP_011513228.1

UniProtKB/Swiss-Prot

A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3

UniProtKB/TrEMBL

A0A158RFW1, B7ZLK3

Conserved Domains (3) summary

pfam03157
Location:454 → 764

Glutenin_hmw; High molecular weight glutenin subunit

cl00057
Location:34 → 254

vWFA; Von Willebrand factor type A (vWA) domain was originally found in the blood coagulation protein von Willebrand factor (vWF). Typically, the vWA domain is made up of approximately 200 amino acid residues folded into a classic a/b para-rossmann type of ...

cl22861
Location:230 → 412

LamG; Laminin G domain; Laminin G-like domains are usually Ca++ mediated receptors that can have binding sites for steroids, beta1 integrins, heparin, sulfatides, fibulin-1, and alpha-dystroglycans. Proteins that contain LamG domains serve a variety of ...