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    HAPLN3 hyaluronan and proteoglycan link protein 3 [ Homo sapiens (human) ]

    Gene ID: 145864, updated on 3-Apr-2024

    Summary

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    Official Symbol
    HAPLN3provided by HGNC
    Official Full Name
    hyaluronan and proteoglycan link protein 3provided by HGNC
    Primary source
    HGNC:HGNC:21446
    See related
    Ensembl:ENSG00000140511 AllianceGenome:HGNC:21446
    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
    EXLD1; HsT19883
    Summary
    This gene belongs to the hyaluronan and proteoglycan binding link protein gene family. The protein encoded by this gene may function in hyaluronic acid binding and cell adhesion. [provided by RefSeq, Jul 2008]
    Expression
    Broad expression in lymph node (RPKM 11.8), appendix (RPKM 10.0) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    Location:
    15q26.1
    Exon count:
    9
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (88877294..88895544, complement)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (86631937..86650187, complement)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (89420525..89438775, complement)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 1748 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89181184-89182162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89182163-89183141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10033 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89191225-89191986 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10034 Neighboring gene interferon stimulated exonuclease gene 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10035 Neighboring gene uncharacterized LOC105370960 Neighboring gene aggrecan Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89390146-89390646 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89390647-89391147 Neighboring gene ReSE screen-validated silencer GRCh37_chr15:89391205-89391372 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89421781-89422356 Neighboring gene H3K27ac hESC enhancer GRCh37_chr15:89428493-89429204 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89438001-89438612 Neighboring gene Sharpr-MPRA regulatory region 11373 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 6792 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:89450127-89451112 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr15:89455820-89456351 Neighboring gene CRISPRi-validated cis-regulatory element chr15.3122 Neighboring gene CRISPRi-validated cis-regulatory element chr15.3123 Neighboring gene CRISPRi-validated cis-regulatory element chr15.3124 Neighboring gene milk fat globule EGF and factor V/VIII domain containing Neighboring gene non-histone chromosomal protein HMG-14-like Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10037 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 10038

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • 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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    Related articles in PubMed

    1. Significant elevation of CLDN16 and HAPLN3 gene expression in human breast cancer. Kuo SJ, et al. Oncol Rep, 2010 Sep. PMID 20664984
    2. A three-gene DNA methylation biomarker accurately classifies early stage prostate cancer. Patel PG, et al. Prostate, 2019 Oct. PMID 31433512
    3. A hyaluronan binding link protein gene family whose members are physically linked adjacent to chondroitin sulfate proteoglycan core protein genes: the missing links. Spicer AP, et al. J Biol Chem, 2003 Jun 6. PMID 12663660
    4. Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area. Kähler AK, et al. Biol Psychiatry, 2011 Jan 1. PMID 20950796
    5. Human colostrum: identification of minor proteins in the aqueous phase by proteomics. Palmer DJ, et al. Proteomics, 2006 Apr. PMID 16502470

    See all (14) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. DNA methylation levels at GAS6(growth arrest specific 6)/GSTP1(glutathione S-transferase pi 1)/HAPLN3(hyaluronan and proteoglycan link protein 3) genomic loci showed large differences between cancer and benign samples
      Title: A three-gene DNA methylation biomarker accurately classifies early stage prostate cancer.
    2. Observational study and meta-analysis of gene-disease association. (HuGE Navigator)
      Title: Candidate gene analysis of the human natural killer-1 carbohydrate pathway and perineuronal nets in schizophrenia: B3GAT2 is associated with disease risk and cortical surface area.
    3. Elevated CLDN16 gene expression was suggested to be involved in the development of breast cancer and to be a biomarker and target treatment for breast cancer.
      Title: Significant elevation of CLDN16 and HAPLN3 gene expression in human breast cancer.
    Submit: New GeneRIF Correction

    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

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables hyaluronic acid binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell adhesion IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in central nervous system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in glial cell differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of neuroblast proliferation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in skeletal system development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular space HDA PubMed 
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in perineuronal net IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in synapse IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    hyaluronan and proteoglycan link protein 3
    Names
    extracellular link domain containing, 1
    NP_001294881.1
    NP_839946.1
    XP_011519563.1
    XP_016877423.1
    XP_047288128.1
    XP_047288129.1
    XP_047288130.1
    XP_047288131.1
    XP_054233307.1
    XP_054233308.1
    XP_054233309.1
    XP_054233310.1
    XP_054233311.1
    XP_054233312.1

    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)

    1. NM_001307952.2 → NP_001294881.1  hyaluronan and proteoglycan link protein 3 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
      Source sequence(s)
      AC103982, BC062320
      Consensus CDS
      CCDS76790.1
      UniProtKB/TrEMBL
      A8K7T8, H3BTH8
      Related
      ENSP00000457180.1, ENST00000562889.5
      Conserved Domains (4) summary
      cd05877
      Location:124 → 229
      Ig_LP_like; Immunoglobulin (Ig)-like domain of human cartilage link protein (LP)
      smart00410
      Location:125 → 224
      IG_like; Immunoglobulin like
      cd03518
      Location:228 → 322
      Link_domain_HAPLN_module_1; Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding ...
      cd03519
      Location:329 → 419
      Link_domain_HAPLN_module_2; Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a ...

    2. NM_178232.4 → NP_839946.1  hyaluronan and proteoglycan link protein 3 isoform 2 precursor

      See identical proteins and their annotated locations for NP_839946.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon in the 5' UTR and coding region which results in the use of a dowstream start codon compared to variant 1. The encoded isoform (2) has a shorter N-terminus compared to isoform 1.
      Source sequence(s)
      AK292103, AY262759
      Consensus CDS
      CCDS10346.1
      UniProtKB/Swiss-Prot
      A8K7P0, Q96S86
      UniProtKB/TrEMBL
      A8K7T8
      Related
      ENSP00000352606.4, ENST00000359595.8
      Conserved Domains (3) summary
      cd05877
      Location:62 → 167
      Ig_LP_like; Immunoglobulin (Ig)-like domain of human cartilage link protein (LP)
      cd03518
      Location:166 → 260
      Link_domain_HAPLN_module_1; Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding ...
      cd03519
      Location:267 → 357
      Link_domain_HAPLN_module_2; Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a ...

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      88877294..88895544 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011521261.2 → XP_011519563.1  hyaluronan and proteoglycan link protein 3 isoform X1

      UniProtKB/TrEMBL
      A8K7T8
      Conserved Domains (4) summary
      cd05877
      Location:106 → 211
      Ig_LP_like; Immunoglobulin (Ig)-like domain of human cartilage link protein (LP)
      smart00410
      Location:107 → 206
      IG_like; Immunoglobulin like
      cd03518
      Location:210 → 304
      Link_domain_HAPLN_module_1; Link_domain_HAPLN_module_1; this link domain is found in the first link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a HA-binding ...
      cd03519
      Location:311 → 401
      Link_domain_HAPLN_module_2; Link_domain_HAPLN_module_2; this link domain is found in the second link module of proteins similar to the vertebrate HAPLN (hyaluronan/HA and proteoglycan binding link) protein family which includes cartilage link protein. The link domain is a ...

    2. XM_017021934.3 → XP_016877423.1  hyaluronan and proteoglycan link protein 3 isoform X3

    3. XM_047432172.1 → XP_047288128.1  hyaluronan and proteoglycan link protein 3 isoform X2

      UniProtKB/Swiss-Prot
      A8K7P0, Q96S86

    4. XM_047432173.1 → XP_047288129.1  hyaluronan and proteoglycan link protein 3 isoform X4

    5. XM_047432175.1 → XP_047288131.1  hyaluronan and proteoglycan link protein 3 isoform X6

    6. XM_047432174.1 → XP_047288130.1  hyaluronan and proteoglycan link protein 3 isoform X5

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      86631937..86650187 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054377332.1 → XP_054233307.1  hyaluronan and proteoglycan link protein 3 isoform X1

    2. XM_054377334.1 → XP_054233309.1  hyaluronan and proteoglycan link protein 3 isoform X3

    3. XM_054377333.1 → XP_054233308.1  hyaluronan and proteoglycan link protein 3 isoform X2

      UniProtKB/Swiss-Prot
      A8K7P0, Q96S86

    4. XM_054377335.1 → XP_054233310.1  hyaluronan and proteoglycan link protein 3 isoform X4

    5. XM_054377337.1 → XP_054233312.1  hyaluronan and proteoglycan link protein 3 isoform X6

    6. XM_054377336.1 → XP_054233311.1  hyaluronan and proteoglycan link protein 3 isoform X5

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96S86.1 GenPept UniProtKB/Swiss-Prot:Q96S86

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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