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    CHRDL1 chordin like 1 [ Homo sapiens (human) ]

    Gene ID: 91851, updated on 23-Nov-2023

    Summary

    Official Symbol
    CHRDL1provided by HGNC
    Official Full Name
    chordin like 1provided by HGNC
    Primary source
    HGNC:HGNC:29861
    See related
    Ensembl:ENSG00000101938 MIM:300350; AllianceGenome:HGNC:29861
    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
    CHL; MGC1; MGCN; VOPT; NRLN1; dA141H5.1
    Summary
    This gene encodes an antagonist of bone morphogenetic protein 4. The encoded protein may play a role in topographic retinotectal projection and in the regulation of retinal angiogenesis in response to hypoxia. Alternatively spliced transcript variants encoding different isoforms have been described. [provided by RefSeq, Jan 2009]
    Expression
    Broad expression in fat (RPKM 100.2), prostate (RPKM 57.9) and 15 other tissues See more
    Orthologs
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See CHRDL1 in Genome Data Viewer
    Location:
    Xq23
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (110673856..110795817, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (109121756..109243896, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (109917084..110039045, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:109763200-109764196 Neighboring gene cripto, EGF-CFC family member 3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:109844205-109844705 Neighboring gene H3K27ac hESC enhancer GRCh37_chrX:109911493-109912258 Neighboring gene M6PR pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29856 Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110065211-110065764 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20942 Neighboring gene H3K4me1 hESC enhancer GRCh37_chrX:110187999-110188834 Neighboring gene OCT4-H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110207796-110208396 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chrX:110254037-110254537 Neighboring gene p21 (RAC1) activated kinase 3 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20943 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29857 Neighboring gene NANOG hESC enhancer GRCh37_chrX:110438658-110439159 Neighboring gene FCF1 pseudogene 4 Neighboring gene glutamate dehydrogenase 1 pseudogene 9

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    Associated conditions

    Description Tests
    Isolated congenital megalocornea
    MedGen: C4518341 OMIM: 309300 GeneReviews: Not available
    Compare labs

    Copy number response

    Description
    Copy number response
    Triplosensitivity

    No evidence available (Last evaluated 2016-12-08)

    ClinGen Genome Curation Page
    Haploinsufficency

    Sufficient evidence for dosage pathogenicity (Last evaluated 2016-12-08)

    ClinGen Genome Curation PagePubMed

    EBI GWAS Catalog

    Description
    A genome-wide association study in Europeans and South Asians identifies five new loci for coronary artery disease.
    EBI GWAS Catalog

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables BMP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    enables transforming growth factor beta binding IEA
    Inferred from Electronic Annotation
    more info
     
    Process Evidence Code Pubs
    involved_in AMPA glutamate receptor clustering IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in BMP signaling pathway IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    involved_in embryonic axis specification IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in excitatory chemical synaptic transmission IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in eye development IMP
    Inferred from Mutant Phenotype
    more info
    PubMed 
    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
     
    involved_in regulation of synaptic plasticity IEA
    Inferred from Electronic Annotation
    more info
     
    involved_in synapse maturation IEA
    Inferred from Electronic Annotation
    more info
     
    Component Evidence Code Pubs
    located_in endoplasmic reticulum lumen TAS
    Traceable Author Statement
    more info
     
    located_in extracellular region TAS
    Traceable Author Statement
    more info
     
    located_in plasma membrane IEA
    Inferred from Electronic Annotation
    more info
     
    located_in synapse IEA
    Inferred from Electronic Annotation
    more info
     

    General protein information

    Preferred Names
    chordin-like protein 1
    Names
    neuralin-1
    neurogenesin-1
    ventroptin

    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.

    Genomic

    1. NG_012816.1 RefSeqGene

      Range
      5242..127203
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001143981.2NP_001137453.1  chordin-like protein 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_001137453.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longest transcript and encodes the longest isoform (1). Variants 1 and 5 both encode the same isoform (1).
      Source sequence(s)
      AK293106, AL049176, AL591489
      Consensus CDS
      CCDS48149.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000361112.1, ENST00000372042.6
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    2. NM_001143982.2NP_001137454.1  chordin-like protein 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001137454.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. The resulting protein (isoform 2) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AK312270, AL049176, BC002909
      Consensus CDS
      CCDS48150.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000399739.2, ENST00000444321.2
      Conserved Domains (1) summary
      cl17735
      Location:115178
      VWC; von Willebrand factor type C domain
    3. NM_001143983.3NP_001137455.2  chordin-like protein 1 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001137455.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks two alternate exons, resulting in the loss of an in-frame segment in the central coding region, compared to variant 1. The resulting protein (isoform 4) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AA057564, AK297563, AL049176
      Consensus CDS
      CCDS48148.2
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000418443.1, ENST00000482160.5
      Conserved Domains (1) summary
      cl17735
      Location:181243
      VWC; von Willebrand factor type C domain
    4. NM_001367204.1NP_001354133.1  chordin-like protein 1 isoform 1 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5), as well as variant 1, encodes isoform 1.
      Source sequence(s)
      AL049176, AL591489
      Consensus CDS
      CCDS48149.1
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    5. NM_001367205.1NP_001354134.1  chordin-like protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6), as well as variant 7, encodes isoform 5.
      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    6. NM_001367206.1NP_001354135.1  chordin-like protein 1 isoform 5 precursor

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7), as well as variant 6, encodes isoform 5.
      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    7. NM_001367207.1NP_001354136.1  chordin-like protein 1 isoform 6 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:115178
      VWC; von Willebrand factor type C domain
    8. NM_001367208.1NP_001354137.1  chordin-like protein 1 isoform 7 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    9. NM_001367209.1NP_001354138.1  chordin-like protein 1 isoform 8 precursor

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:116179
      VWC; von Willebrand factor type C domain
    10. NM_145234.4NP_660277.2  chordin-like protein 1 isoform 3 precursor

      See identical proteins and their annotated locations for NP_660277.2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' UTR and uses alternate in-frame splice sites in the coding region compared to variant 1. The resulting protein (isoform 3) is shorter but has the identical N- and C-termini compared to isoform 1.
      Source sequence(s)
      AL049176, BC002909, BP377491
      Consensus CDS
      CCDS14553.1
      UniProtKB/Swiss-Prot
      B1AKD0, B4DMP3, D3DUY6, E9PGS5, Q539E4, Q9BU40, Q9Y3H7
      UniProtKB/TrEMBL
      A0A452Q6Z9
      Related
      ENSP00000361115.1, ENST00000372045.5
      Conserved Domains (1) summary
      cl17735
      Location:115178
      VWC; von Willebrand factor type C domain

    RNA

    1. NR_159734.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL049176, AL591489

    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_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      110673856..110795817 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005262222.3XP_005262279.1  chordin-like protein 1 isoform X1

      See identical proteins and their annotated locations for XP_005262279.1

      UniProtKB/TrEMBL
      A0A452Q6Z9
      Conserved Domains (1) summary
      cl17735
      Location:115178
      VWC; von Willebrand factor type C domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      109121756..109243896 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328104.1XP_054184079.1  chordin-like protein 1 isoform X1

      UniProtKB/TrEMBL
      A0A452Q6Z9