CHRDL2 chordin like 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHRDL2provided by HGNC
Official Full Name: chordin like 2provided by HGNC
Primary source: HGNC:HGNC:24168
See related: Ensembl:ENSG00000054938 MIM:613127; AllianceGenome:HGNC:24168
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: BNF1; CHL2
Summary: This gene encodes a member of the chordin family of proteins. Chordin family members are secreted proteins that share a cysteine-rich pro-collagen repeat domain and associate with members of the transforming growth factor beta superfamily. In vitro assays demonstrate a direct interaction between the encoded protein and human activin A. This gene is expressed in many tissues including osteoblasts, where it is differentially expressed during differentiation. In addition, its expression is upregulated in human osteoarthritic joint cartilage, suggesting a role in adult cartilage regeneration. [provided by RefSeq, Jan 2015]
Expression: Biased expression in gall bladder (RPKM 39.8), appendix (RPKM 39.3) and 4 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 11q13.4

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	11	NC_000011.10 (74696429..74731426, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	11	NC_060935.1 (74625930..74660944, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	11	NC_000011.9 (74407474..74442471, complement)

Chromosome 11 - NC_000011.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

CHRDL2 promotes cell proliferation by activating the YAP/TAZ signaling pathway in gastric cancer.
Title: CHRDL2 promotes cell proliferation by activating the YAP/TAZ signaling pathway in gastric cancer.
CHRDL2 promotes osteosarcoma cell proliferation and metastasis through the BMP-9/PI3K/AKT pathway.
Title: CHRDL2 promotes osteosarcoma cell proliferation and metastasis through the BMP-9/PI3K/AKT pathway.
These results suggest CHRDL2 could serve as a biomarker of poor prognosis in CRC, and provide evidence that CHRDL2 acts as an oncogene in human colorectal cancer
Title: Overexpression of colorectal cancer oncogene CHRDL2 predicts a poor prognosis.
Observational study of gene-disease association. (HuGE Navigator)
Title: High-density association study of 383 candidate genes for volumetric BMD at the femoral neck and lumbar spine among older men.
Differential expression of CHL2 variants was observed during myoblast and osteoblast differentiation, implying a role for this gene in these physiological processes.
Title: hCHL2, a novel chordin-related gene, displays differential expression and complex alternative splicing in human tissues and during myoblast and osteoblast maturation.
CHL2 expression is restricted to chondrocytes of various developing joint cartilage surfaces and connective tissues in reproductive organs
Title: A novel chordin-like BMP inhibitor, CHL2, expressed preferentially in chondrocytes of developing cartilage and osteoarthritic joint cartilage.

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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

EBI GWAS Catalog

Description
Integrated Genome-wide Association, Coexpression Network, and Expression Single Nucleotide Polymorphism Analysis Identifies Novel Pathway in Allergic Rhinitis. 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

NoName (e-PCR)
- UniSTS:481899

L18031 (e-PCR)
- UniSTS:73648

NoName (e-PCR)
- UniSTS:486071

D11S1892 (e-PCR)
- UniSTS:473272

D11S3545 (e-PCR)
- UniSTS:152784

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables BMP binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cartilage development	IEA Inferred from Electronic Annotation more info
involved_in cell differentiation	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of BMP signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in ossification	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in extracellular space	HDA more info	PubMed

General protein information

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Preferred Names: chordin-like protein 2

Names: breast tumor novel factor 1; chordin-related protein 2

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.

mRNA and Protein(s)

NM_001278473.3 → NP_001265402.1 chordin-like protein 2 isoform 2 precursor

See identical proteins and their annotated locations for NP_001265402.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an alternate 3' coding exon, which results in a frameshift compared to variant 1. The encoded isoform (2) has a shorter and distinct C-terminus compared to isoform 1.

Source sequence(s)

AP001324, AY279090, BC142623

Consensus CDS

CCDS60893.1

UniProtKB/Swiss-Prot

A5PKU9, Q6WN30, Q6WN31, Q6WN32, Q6WN34, Q7Z5J3

UniProtKB/TrEMBL

B4E311

Related

ENSP00000365510.3, ENST00000376332.8

Conserved Domains (2) summary

smart00214
Location:252 → 314

VWC; von Willebrand factor (vWF) type C domain

cl17735
Location:111 → 174

VWC; von Willebrand factor type C domain
NM_001304390.2 → NP_001291319.1 chordin-like protein 2 isoform 3

Status: REVIEWED

Description

Transcript Variant: This variant (3) has a distinct 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate codon compared to variant 1. The encoded isoform (3) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AP001324, AY279092, AY358522

UniProtKB/TrEMBL

B4E311

Conserved Domains (2) summary

smart00214
Location:232 → 294

VWC; von Willebrand factor (vWF) type C domain

cl17735
Location:91 → 154

VWC; von Willebrand factor type C domain
NM_001304391.2 → NP_001291320.1 chordin-like protein 2 isoform 4

Status: REVIEWED

Description

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

Source sequence(s)

AP001324, AY279092, AY358522

UniProtKB/Swiss-Prot

Q6WN34

Conserved Domains (3) summary

smart00214
Location:13 → 75

VWC; von Willebrand factor (vWF) type C domain

PHA03307
Location:136 → 354

PHA03307; transcriptional regulator ICP4; Provisional

cl17735
Location:91 → 154

VWC; von Willebrand factor type C domain
NM_001304415.2 → NP_001291344.1 chordin-like protein 2 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) has a distinct 5' UTR, initiates translation at an alternate codon, and has multiple coding region differences compared to variant 1. The encoded isoform (5) has distinct N- and C-termini and is shorter than isoform 1.

Source sequence(s)

AP001324, AY279092, AY358522

UniProtKB/TrEMBL

Q6WN33

Conserved Domains (3) summary

smart00214
Location:13 → 75

VWC; von Willebrand factor (vWF) type C domain

pfam19548
Location:253 → 326

CHRDL_1_2_C; Chordin-like protein 1/2 C-terminal

cl17735
Location:91 → 154

VWC; von Willebrand factor type C domain
NM_001304416.2 → NP_001291345.1 chordin-like protein 2 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) has a distinct 5' UTR, initiates translation at a downstream codon, and has multiple coding region differences compared to variant 1. The encoded isoform (6) has distinct N- and C-termini and is shorter than isoform 1.

Source sequence(s)

AP001324, AY279092

UniProtKB/TrEMBL

Q9BZ90

Conserved Domains (3) summary

smart00214
Location:136 → 198

VWC; von Willebrand factor (vWF) type C domain

pfam19548
Location:222 → 295

CHRDL_1_2_C; Chordin-like protein 1/2 C-terminal

cl17735
Location:19 → 58

VWC; von Willebrand factor type C domain
NM_001304417.2 → NP_001291346.1 chordin-like protein 2 isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (7) has a distinct 5' UTR, lacks a portion of the 5' coding region and initiates translation at an alternate codon compared to variant 1. The encoded isoform (7) has a distinct N-terminus and is shorter than isoform 1.

Source sequence(s)

AP001324, AY358522

UniProtKB/Swiss-Prot

Q6WN34

Conserved Domains (2) summary

smart00214
Location:187 → 249

VWC; von Willebrand factor (vWF) type C domain

cl17735
Location:46 → 109

VWC; von Willebrand factor type C domain
NM_015424.6 → NP_056239.3 chordin-like protein 2 isoform 1 precursor

See identical proteins and their annotated locations for NP_056239.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1).

Source sequence(s)

AP001324, AY279090, AY358522, BC142623

Consensus CDS

CCDS8234.1

UniProtKB/TrEMBL

B4E311

Related

ENSP00000263671.5, ENST00000263671.9

Conserved Domains (2) summary

smart00214
Location:252 → 314

VWC; von Willebrand factor (vWF) type C domain

cl17735
Location:111 → 174

VWC; von Willebrand factor type C domain