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

Gene ID: 81578, updated on 10-Oct-2023

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
NEW
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Genomic context

See COL21A1 in Genome Data Viewer
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_000006.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107986539 Neighboring gene uncharacterized LOC105375100 Neighboring gene Sharpr-MPRA regulatory region 6371 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:56111277-56111778 Neighboring gene OCT4-NANOG-H3K27ac hESC enhancer GRCh37_chr6:56111779-56112278 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56142823-56143330 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56144052-56144553 Neighboring gene dihydrofolate reductase pseudogene 6 Neighboring gene regulator of chromosome condensation 2 pseudogene 7 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56399527-56400028 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56400029-56400528 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:56406989-56407754 Neighboring gene MPRA-validated peak5860 silencer Neighboring gene dystonin Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24702 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24703 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579434-56579994 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56579995-56580556 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:56581759-56582299 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56616684-56617267 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17296 Neighboring gene NANOG hESC enhancer GRCh37_chr6:56624276-56624832 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24704 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr6:56640200-56641045 Neighboring gene MPRA-validated peak5861 silencer Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:56707357-56708225 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr6:56708226-56709093 Neighboring gene Sharpr-MPRA regulatory region 11401 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24705 Neighboring gene DST antisense RNA 1

Genomic regions, transcripts, and products

Bibliography

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Phenotypes

EBI GWAS Catalog

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

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

Markers

Clone Names

  • FLJ39125, FLJ44623, MGC26619, DKFZp564B052

General protein information

Preferred Names
collagen alpha-1(XXI) chain
Names
alpha 1 chain-like collagen
collagen, type XXI, alpha 1

NCBI Reference Sequences (RefSeq)

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)

  1. NM_001318751.2NP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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 ...
  2. NM_001318752.2NP_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
    F5GZK2
    Related
    ENSP00000359855.1, ENST00000370819.5
    Conserved Domains (4) summary
    pfam01391
    Location:446505
    Collagen; Collagen triple helix repeat (20 copies)
    COG2304
    Location:1296
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cl00057
    Location:34254
    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:230412
    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 ...
  3. NM_001318753.2NP_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:3390
    Collagen; Collagen triple helix repeat (20 copies)
  4. NM_001318754.2NP_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:197240
    Collagen; Collagen triple helix repeat (20 copies)
  5. NM_030820.4NP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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

  1. 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
  2. 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
  3. 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

  1. NC_000006.12 Reference GRCh38.p14 Primary Assembly

    Range
    56056590..56394128 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_011514924.3XP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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 ...
  2. XM_006715223.2XP_006715286.1  collagen alpha-1(XXI) chain isoform X2

    UniProtKB/TrEMBL
    B7ZLK3
    Conserved Domains (4) summary
    pfam01391
    Location:449508
    Collagen; Collagen triple helix repeat (20 copies)
    COG2304
    Location:1296
    YfbK; Secreted protein containing bacterial Ig-like domain and vWFA domain [General function prediction only]
    cl00057
    Location:34254
    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:230412
    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 ...
  3. XM_047419383.1XP_047275339.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3
  4. XM_011514925.4XP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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 ...
  5. XM_011514927.1XP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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 ...
  6. XM_011514926.2XP_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:454764
    Glutenin_hmw; High molecular weight glutenin subunit
    cl00057
    Location:34254
    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:230412
    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 ...

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060930.1 Alternate T2T-CHM13v2.0

    Range
    55896186..56235397 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054356488.1XP_054212463.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3
  2. XM_054356493.1XP_054212468.1  collagen alpha-1(XXI) chain isoform X2

    UniProtKB/TrEMBL
    B7ZLK3
  3. XM_054356491.1XP_054212466.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3
  4. XM_054356489.1XP_054212464.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3
  5. XM_054356492.1XP_054212467.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3
  6. XM_054356490.1XP_054212465.1  collagen alpha-1(XXI) chain isoform X1

    UniProtKB/Swiss-Prot
    A6NIX5, B2R8J9, Q49A51, Q71RF4, Q8WXV8, Q96P44, Q9H0V3
    UniProtKB/TrEMBL
    A0A158RFW1, B7ZLK3