COL11A2 collagen type XI alpha 2 chain [Homo sapiens (human)] - Gene

Summary

Official Symbol: COL11A2provided by HGNC
Official Full Name: collagen type XI alpha 2 chainprovided by HGNC
Primary source: HGNC:HGNC:2187
See related: Ensembl:ENSG00000204248 MIM:120290; AllianceGenome:HGNC:2187
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: HKE5; PARP; STL3; FBCG2; DFNA13; DFNB53; OSMEDA; OSMEDB
Summary: This gene encodes one of the two alpha chains of type XI collagen, a minor fibrillar collagen. It is located on chromosome 6 very close to but separate from the gene for retinoid X receptor beta. Type XI collagen is a heterotrimer but the third alpha chain is a post-translationally modified alpha 1 type II chain. Proteolytic processing of this type XI chain produces PARP, a proline/arginine-rich protein that is an amino terminal domain. Mutations in this gene are associated with type III Stickler syndrome, otospondylomegaepiphyseal dysplasia (OSMED syndrome), Weissenbacher-Zweymuller syndrome, autosomal dominant non-syndromic sensorineural type 13 deafness (DFNA13), and autosomal recessive non-syndromic sensorineural type 53 deafness (DFNB53). Alternative splicing results in multiple transcript variants. A related pseudogene is located nearby on chromosome 6. [provided by RefSeq, Jul 2009]
Expression: Broad expression in testis (RPKM 1.9), brain (RPKM 1.8) and 20 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 6p21.32

Exon count:: 72

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	6	NC_000006.12 (33162694..33193519, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	6	NC_060930.1 (32984047..33014927, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	6	NC_000006.11 (33130471..33161296, complement)

Chromosome 6 - NC_000006.12 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
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?

Autosomal recessive otospondylo-mega-epiphyseal dysplasia: comprehensive clinical review of a pediatric cohort.
Title: Autosomal recessive otospondylo-mega-epiphyseal dysplasia: comprehensive clinical review of a pediatric cohort.
COL11A2 as a candidate gene for vertebral malformations and congenital scoliosis.
Title: COL11A2 as a candidate gene for vertebral malformations and congenital scoliosis.
Association Between COL5a1, COL11a1, and COL11a2 Gene Variations and Rotator Cuff Tendinopathy in Young Athletes.
Title: Association Between COL5a1, COL11a1, and COL11a2 Gene Variations and Rotator Cuff Tendinopathy in Young Athletes.
The Association of Variants within Types V and XI Collagen Genes with Knee Joint Laxity Measurements.
Title: The Association of Variants within Types V and XI Collagen Genes with Knee Joint Laxity Measurements.
Exon-Trapping Assay Improves Clinical Interpretation of COL11A1 and COL11A2 Intronic Variants in Stickler Syndrome Type 2 and Otospondylomegaepiphyseal Dysplasia.
Title: Exon-Trapping Assay Improves Clinical Interpretation of COL11A1 and COL11A2 Intronic Variants in Stickler Syndrome Type 2 and Otospondylomegaepiphyseal Dysplasia.
Genetic variant of COL11A2 gene is functionally associated with developmental dysplasia of the hip in Chinese Han population.
Title: Genetic variant of COL11A2 gene is functionally associated with developmental dysplasia of the hip in Chinese Han population.
Mutation in COL11A2 gene is associated with Stargardt disease as well as Stickler's Syndrome .
Title: The uncommon occurrence of two common inherited disorders in a single patient: a mini case series.
rs986522(C) significantly increased the risk of lumbar disc degeneration in Chinese Han females.
Title: Genetic variants in COL11A2 of lumbar disk degeneration among Chinese Han population.
that the COL11A2 gene, which has previously been associated with familial osteoarthritis, may play a role in pain sensitization after the development of osteoarthritis
Title: Single Nucleotide Polymorphism in the COL11A2 Gene Associated with Heat Pain Sensitivity in Knee Osteoarthritis.
Missense mutations in COL6A1, COL11A2, FGFR1, and BMP2 genetically predispose patients to ossification of posterior longitudinal ligaments.
Title: Targeted next-generation sequencing reveals multiple deleterious variants in OPLL-associated genes.

Submit: New GeneRIF Correction See all GeneRIFs (32)

Phenotypes

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

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description	Tests
Autosomal dominant nonsyndromic hearing loss 13 MedGen: C1866095 OMIM: 601868 GeneReviews: Genetic Hearing Loss Overview	Compare labs
Autosomal recessive nonsyndromic hearing loss 53 MedGen: C1864746 OMIM: 609706 GeneReviews: Not available	Compare labs
Fibrochondrogenesis 2 MedGen: C3281128 OMIM: 614524 GeneReviews: Not available	Compare labs
Otospondylomegaepiphyseal dysplasia, autosomal dominant MedGen: C1848488 OMIM: 184840 GeneReviews: Stickler Syndrome	Compare labs
Otospondylomegaepiphyseal dysplasia, autosomal recessive MedGen: C5551484 OMIM: 215150 GeneReviews: Not available	Compare labs

EBI GWAS Catalog

Description
A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sj&#x000c3;&#x000b6;gren's syndrome at 7q11.23. EBI GWAS Catalog EBI GWAS CatalogPubMed
Association of granulomatosis with polyangiitis (Wegener's) with HLA-DPB1*04 and SEMA6A gene variants: evidence from genome-wide analysis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetically distinct subsets within ANCA-associated vasculitis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Newly identified loci that influence lipid concentrations and risk of coronary artery disease. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

RXRB_2036 (e-PCR)
- UniSTS:280976

SHGC-56505 (e-PCR)
- UniSTS:44179

G10518 (e-PCR)
- UniSTS:32168

RH46226 (e-PCR)
- UniSTS:12484

RH69971 (e-PCR)
- UniSTS:46538

SHGC-35646 (e-PCR)
- UniSTS:18681

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables extracellular matrix structural constituent conferring tensile strength	HDA more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	IBA Inferred from Biological aspect of Ancestor more info
enables extracellular matrix structural constituent conferring tensile strength	NAS Non-traceable Author Statement more info	PubMed
enables extracellular matrix structural constituent conferring tensile strength	RCA inferred from Reviewed Computational Analysis more info	PubMed
enables metal ion binding	IEA Inferred from Electronic Annotation more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein-macromolecule adaptor activity	NAS Non-traceable Author Statement more info	PubMed

Process	Evidence Code	Pubs
involved_in cartilage development	IBA Inferred from Biological aspect of Ancestor more info
involved_in cartilage development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in collagen fibril organization	IBA Inferred from Biological aspect of Ancestor more info
involved_in collagen fibril organization	IDA Inferred from Direct Assay more info	PubMed
involved_in roof of mouth development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IBA Inferred from Biological aspect of Ancestor more info
acts_upstream_of_or_within sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in sensory perception of sound	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	IMP Inferred from Mutant Phenotype more info	PubMed
involved_in skeletal system development	NAS Non-traceable Author Statement more info	PubMed
involved_in soft palate development	IMP Inferred from Mutant Phenotype more info	PubMed

Component	Evidence Code	Pubs
part_of collagen trimer	IBA Inferred from Biological aspect of Ancestor more info
part_of collagen type XI trimer	NAS Non-traceable Author Statement more info	PubMed
located_in collagen-containing extracellular matrix	HDA more info	PubMed
is_active_in collagen-containing extracellular matrix	IBA Inferred from Biological aspect of Ancestor more info
located_in collagen-containing extracellular matrix	NAS Non-traceable Author Statement more info	PubMed
located_in endoplasmic reticulum lumen	TAS Traceable Author Statement more info
located_in extracellular region	TAS Traceable Author Statement more info
is_active_in extracellular space	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: collagen alpha-2(XI) chain

Names: collagen, type XI, alpha 2; pro-a2 chain of collagen type XI

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.

Genomic

NG_011589.1 RefSeqGene

Range

5002..34775

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001163771.2 → NP_001157243.1 collagen alpha-2(XI) chain isoform 4 precursor

See identical proteins and their annotated locations for NP_001157243.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) lacks several exons at the 3' end and has a distinct 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (4) has a distinct C-terminus and is considerably shorter than isoform 1.

Source sequence(s)

AL645940, BC053886

Consensus CDS

CCDS54992.1

UniProtKB/TrEMBL

A0A140T9A1

Related

ENSP00000378620.1, ENST00000395194.1

Conserved Domains (1) summary

smart00210
Location:31 → 213

TSPN; Thrombospondin N-terminal -like domains
NM_001424108.1 → NP_001411037.1 collagen alpha-2(XI) chain isoform 5 preproprotein

Status: REVIEWED

Source sequence(s)

AL645940
NM_001424109.1 → NP_001411038.1 collagen alpha-2(XI) chain isoform 6

Status: REVIEWED

Source sequence(s)

AL645940
NM_001424110.1 → NP_001411039.1 collagen alpha-2(XI) chain isoform 7

Status: REVIEWED

Source sequence(s)

AL645940
NM_001424111.1 → NP_001411040.1 collagen alpha-2(XI) chain isoform 7

Status: REVIEWED

Source sequence(s)

AL645940
NM_001424112.1 → NP_001411041.1 collagen alpha-2(XI) chain isoform 8

Status: REVIEWED

Source sequence(s)

AL645940
NM_080679.3 → NP_542410.2 collagen alpha-2(XI) chain isoform 3 preproprotein

See identical proteins and their annotated locations for NP_542410.2

Status: REVIEWED

Description

Transcript Variant: This variant (3) lacks three alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 3), compared to isoform 1. There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50215.1.

Source sequence(s)

AL645940

UniProtKB/TrEMBL

A0A0G2JL78, A0A140TA54

Conserved Domains (3) summary

pfam01391
Location:547 → 603

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1433 → 1628

COLFI; Fibrillar collagens C-terminal domain

smart00210
Location:31 → 213

TSPN; Thrombospondin N-terminal -like domains
NM_080680.3 → NP_542411.2 collagen alpha-2(XI) chain isoform 1 preproprotein

See identical proteins and their annotated locations for NP_542411.2

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50214.1.

Source sequence(s)

AL645940

UniProtKB/TrEMBL

A0A0C4DFS1, A0A1U9X7J8

Related

ENSP00000339915.2, ENST00000341947.7

Conserved Domains (5) summary

pfam01391
Location:654 → 710

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1540 → 1735

COLFI; Fibrillar collagens C-terminal domain

smart00210
Location:31 → 213

TSPN; Thrombospondin N-terminal -like domains

cl26386
Location:1264 → 1437

DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

cl28033
Location:361 → 703

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
NM_080681.3 → NP_542412.2 collagen alpha-2(XI) chain isoform 2 preproprotein

See identical proteins and their annotated locations for NP_542412.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks two alternate in-frame exons, compared to variant 1, resulting in a shorter protein (isoform 2), compared to isoform 1. There are no publicly available human transcripts representing the full-length exon combination of this variant, but the region of variation is supported by experimental data in PMIDs 8663204 and 8838804, by homology data in mouse, and the full-length sequence is represented in accession U32169.1:AAC50213.1.

Source sequence(s)

AL645940

Consensus CDS

CCDS43452.1

UniProtKB/TrEMBL

A0A140T9N1, Q4VXY6

Related

ENSP00000363840.4, ENST00000374708.8

Conserved Domains (3) summary

pfam01391
Location:568 → 624

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1454 → 1649

COLFI; Fibrillar collagens C-terminal domain

smart00210
Location:31 → 213

TSPN; Thrombospondin N-terminal -like domains

RNA

NR_187605.1 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL645940

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

NC_000006.12 Reference GRCh38.p14 Primary Assembly

Range

33162694..33193519 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047418183.1 → XP_047274139.1 collagen alpha-2(XI) chain isoform X7
XM_017010250.2 → XP_016865739.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A0C4DFS1, A0A1U9X7J8

Conserved Domains (5) summary

pfam01391
Location:654 → 710

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1540 → 1735

COLFI; Fibrillar collagens C-terminal domain

smart00210
Location:31 → 213

TSPN; Thrombospondin N-terminal -like domains

cl26386
Location:1264 → 1437

DNA_pol3_gamma3; DNA polymerase III subunits gamma and tau domain III

cl28033
Location:361 → 703

Herpes_ICP4_C; Herpesvirus ICP4-like protein C-terminal region
XM_011514300.3 → XP_011512602.1 collagen alpha-2(XI) chain isoform X4

See identical proteins and their annotated locations for XP_011512602.1

Conserved Domains (2) summary

pfam01391
Location:356 → 412

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1242 → 1437

COLFI; Fibrillar collagens C-terminal domain
XM_011514299.3 → XP_011512601.1 collagen alpha-2(XI) chain isoform X3

See identical proteins and their annotated locations for XP_011512601.1

UniProtKB/TrEMBL

A0A1U9X7J8

Conserved Domains (2) summary

pfam01391
Location:416 → 472

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1302 → 1497

COLFI; Fibrillar collagens C-terminal domain
XM_017010251.3 → XP_016865740.1 collagen alpha-2(XI) chain isoform X6
XM_011514302.3 → XP_011512604.1 collagen alpha-2(XI) chain isoform X5

See identical proteins and their annotated locations for XP_011512604.1

Conserved Domains (2) summary

pfam01391
Location:283 → 339

Collagen; Collagen triple helix repeat (20 copies)

smart00038
Location:1169 → 1364

COLFI; Fibrillar collagens C-terminal domain

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_113891.3 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

4574202..4605026 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054329736.1 → XP_054185711.1 collagen alpha-2(XI) chain isoform X8

Reference GRCh38.p14 ALT_REF_LOCI_3

Genomic

NT_167245.2 Reference GRCh38.p14 ALT_REF_LOCI_3

Range

4406193..4437018 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330229.1 → XP_054186204.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A0C4DFS1
XM_054330232.1 → XP_054186207.1 collagen alpha-2(XI) chain isoform X4
XM_054330231.1 → XP_054186206.1 collagen alpha-2(XI) chain isoform X3
XM_054330234.1 → XP_054186209.1 collagen alpha-2(XI) chain isoform X6
XM_054330233.1 → XP_054186208.1 collagen alpha-2(XI) chain isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_4

Genomic

NT_167246.2 Reference GRCh38.p14 ALT_REF_LOCI_4

Range

4582167..4613046 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330520.1 → XP_054186495.1 collagen alpha-2(XI) chain isoform X11
XM_054330519.1 → XP_054186494.1 collagen alpha-2(XI) chain isoform X10
XM_054330517.1 → XP_054186492.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A140TA43
XM_054330518.1 → XP_054186493.1 collagen alpha-2(XI) chain isoform X9
XM_054330522.1 → XP_054186497.1 collagen alpha-2(XI) chain isoform X4
XM_054330521.1 → XP_054186496.1 collagen alpha-2(XI) chain isoform X3
XM_054330524.1 → XP_054186499.1 collagen alpha-2(XI) chain isoform X6
XM_054330523.1 → XP_054186498.1 collagen alpha-2(XI) chain isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_5

Genomic

NT_167247.2 Reference GRCh38.p14 ALT_REF_LOCI_5

Range

4598652..4629530 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054330768.1 → XP_054186743.1 collagen alpha-2(XI) chain isoform X14
XM_054330766.1 → XP_054186741.1 collagen alpha-2(XI) chain isoform X13
XM_054330764.1 → XP_054186739.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A0G2JL35
XM_054330765.1 → XP_054186740.1 collagen alpha-2(XI) chain isoform X12
XM_054330770.1 → XP_054186745.1 collagen alpha-2(XI) chain isoform X4
XM_054330769.1 → XP_054186744.1 collagen alpha-2(XI) chain isoform X3
XM_054330772.1 → XP_054186747.1 collagen alpha-2(XI) chain isoform X6
XM_054330771.1 → XP_054186746.1 collagen alpha-2(XI) chain isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_6

Genomic

NT_167248.2 Reference GRCh38.p14 ALT_REF_LOCI_6

Range

4357098..4387977 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054331004.1 → XP_054186979.1 collagen alpha-2(XI) chain isoform X17
XM_054331003.1 → XP_054186978.1 collagen alpha-2(XI) chain isoform X16
XM_054331001.1 → XP_054186976.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A0G2JL35
XM_054331002.1 → XP_054186977.1 collagen alpha-2(XI) chain isoform X15
XM_054331006.1 → XP_054186981.1 collagen alpha-2(XI) chain isoform X4
XM_054331005.1 → XP_054186980.1 collagen alpha-2(XI) chain isoform X3
XM_054331008.1 → XP_054186983.1 collagen alpha-2(XI) chain isoform X6
XM_054331007.1 → XP_054186982.1 collagen alpha-2(XI) chain isoform X5

Reference GRCh38.p14 ALT_REF_LOCI_7

Genomic

NT_167249.2 Reference GRCh38.p14 ALT_REF_LOCI_7

Range

4611340..4639206 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060930.1 Alternate T2T-CHM13v2.0

Range

32984047..33014927 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054354226.1 → XP_054210201.1 collagen alpha-2(XI) chain isoform X20
XM_054354224.1 → XP_054210199.1 collagen alpha-2(XI) chain isoform X19
XM_054354222.1 → XP_054210197.1 collagen alpha-2(XI) chain isoform X1

UniProtKB/TrEMBL

A0A0C4DFS1
XM_054354223.1 → XP_054210198.1 collagen alpha-2(XI) chain isoform X18
XM_054354228.1 → XP_054210203.1 collagen alpha-2(XI) chain isoform X4
XM_054354227.1 → XP_054210202.1 collagen alpha-2(XI) chain isoform X3
XM_054354230.1 → XP_054210205.1 collagen alpha-2(XI) chain isoform X6
XM_054354229.1 → XP_054210204.1 collagen alpha-2(XI) chain isoform X5