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    HMCN2 hemicentin 2 [ Homo sapiens (human) ]

    Gene ID: 256158, updated on 27-Nov-2024

    Summary

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    Official Symbol
    HMCN2provided by HGNC
    Official Full Name
    hemicentin 2provided by HGNC
    Primary source
    HGNC:HGNC:21293
    See related
    Ensembl:ENSG00000148357 AllianceGenome:HGNC:21293
    Gene type
    protein coding
    RefSeq status
    INFERRED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Summary
    Predicted to enable axon guidance receptor activity. Predicted to be involved in homophilic cell adhesion via plasma membrane adhesion molecules and synapse organization. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Nov 2024]
    Expression
    Broad expression in small intestine (RPKM 2.1), fat (RPKM 1.8) and 19 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See HMCN2 in Genome Data Viewer
    Location:
    9q34.11
    Exon count:
    102
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130265760..130434123)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142470624..142639100)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133028039..133309510)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20400 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132936047-132936957 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132947945-132948786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132948787-132949629 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132949630-132950471 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132951645-132951994 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132959499-132960000 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:132960001-132960500 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132971269-132971960 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132972653-132973344 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:132976749-132976936 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:132977599-132978255 Neighboring gene Sharpr-MPRA regulatory region 5428 Neighboring gene neuronal calcium sensor 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132981410-132982372 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:132999231-132999790 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29151 Neighboring gene Sharpr-MPRA regulatory region 4503 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr9:133021088-133021842 Neighboring gene uncharacterized LOC124902285 Neighboring gene microRNA 12126 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133030927-133031514 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133051720-133052288 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133063657-133064459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29152 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133234271-133235042 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133257005-133257920 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133263798-133264331 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133265187-133265694 Neighboring gene RNA, 7SL, cytoplasmic 665, pseudogene Neighboring gene uncharacterized LOC107987134 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133296398-133297200 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133297201-133298001 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133302089-133302636 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133303731-133304276 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20401 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133321151-133321818 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133322488-133323155 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 491 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133328870-133329370 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29153 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29154 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133342170-133342798 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133346469-133347206 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133347207-133347943 Neighboring gene VISTA enhancer hs1328 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133355453-133356208 Neighboring gene argininosuccinate synthase 1 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133373167-133373668 Neighboring gene Sharpr-MPRA regulatory region 5386 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:133380533-133381032 Neighboring gene NANOG-H3K27ac hESC enhancer GRCh37_chr9:133381216-133382062 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133394336-133394851 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133397629-133398376 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401147-133401648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133401649-133402148 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133402913-133403413 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr9:133420171-133420671 Neighboring gene uncharacterized LOC100272217

    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. Distribution and evolution of von Willebrand/integrin A domains: widely dispersed domains with roles in cell adhesion and elsewhere. Whittaker CA, et al. Mol Biol Cell, 2002 Oct. PMID 12388743, Free PMC Article
    2. Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication. König R, et al. Cell, 2008 Oct 3. PMID 18854154, Free PMC Article
    3. Extracellular matrix remodelling in response to venous hypertension: proteomics of human varicose veins. Barallobre-Barreiro J, et al. Cardiovasc Res, 2016 Jun 1. PMID 27068509, Free PMC Article
    4. Genome-scale RNAi screen for host factors required for HIV replication. Zhou H, et al. Cell Host Microbe, 2008 Nov 13. PMID 18976975
    5. SR protein kinases promote splicing of nonconsensus introns. Lipp JJ, et al. Nat Struct Mol Biol, 2015 Aug. PMID 26167880

    See all (12) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    Submit: New GeneRIF Correction

    Phenotypes

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    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)

    HIV-1 interactions

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    Replication interactions

    Interaction Pubs
    Knockdown of hemicentin 2 (HMCN2) by siRNA inhibits the early stages of HIV-1 replication in 293T cells infected with VSV-G pseudotyped HIV-1 PubMed
    Knockdown of hemicentin 2 (HMCN2) by siRNA inhibits HIV-1 replication in HeLa P4/R5 cells PubMed

    Go to the HIV-1, Human Interaction Database

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ23816, FLJ46139, FLJ46844, DKFZp434P0216

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables axon guidance receptor activity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables extracellular matrix structural constituent RCA
    inferred from Reviewed Computational Analysis
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in axon guidance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in homophilic cell adhesion via plasma membrane adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in synapse organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in axon IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in basement membrane IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell cortex IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cell junction IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in cleavage furrow IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in collagen-containing extracellular matrix HDA PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in neuronal cell body IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    hemicentin-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)

    1. NM_001291815.2 → NP_001278744.1  hemicentin-2 precursor

      Status: INFERRED

      Source sequence(s)
      ABBA01012042, ABBA01043973, AL354898, AL360004, FP565345, KF458942
      Consensus CDS
      CCDS94512.1
      UniProtKB/Swiss-Prot
      A0A096LP30, A0A804HLC3, Q8N225, Q8NDA2, Q8TCI8
      Related
      ENSP00000508292.2, ENST00000683500.2
      Conserved Domains (11) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:4247 → 4309
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:4883 → 4922
      EGF_CA; Calcium-binding EGF-like domain
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:2954 → 3034
      IG_like; Immunoglobulin like
      pfam07679
      Location:4323 → 4409
      I-set; Immunoglobulin I-set domain
      pfam07474
      Location:4411 → 4593
      G2F; G2F domain
      pfam07645
      Location:4733 → 4774
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      pfam14670
      Location:4652 → 4687
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl11960
      Location:4322 → 4405
      Ig; Immunoglobulin domain

    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

    1. NC_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      130265760..130434123
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_011518466.3 → XP_011516768.1  hemicentin-2 isoform X2

      Conserved Domains (11) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:4247 → 4309
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:4839 → 4878
      EGF_CA; Calcium-binding EGF-like domain
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:2954 → 3034
      IG_like; Immunoglobulin like
      pfam07679
      Location:4323 → 4409
      I-set; Immunoglobulin I-set domain
      pfam07474
      Location:4411 → 4593
      G2F; G2F domain
      pfam07645
      Location:4689 → 4730
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      pfam14670
      Location:4652 → 4687
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl11960
      Location:4322 → 4405
      Ig; Immunoglobulin domain

    2. XM_011518465.3 → XP_011516767.1  hemicentin-2 isoform X1

      Conserved Domains (10) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:4247 → 4309
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:4842 → 4881
      EGF_CA; Calcium-binding EGF-like domain
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:2954 → 3034
      IG_like; Immunoglobulin like
      pfam07679
      Location:4323 → 4409
      I-set; Immunoglobulin I-set domain
      pfam07474
      Location:4411 → 4593
      G2F; G2F domain
      pfam07645
      Location:4692 → 4733
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:4322 → 4405
      Ig; Immunoglobulin domain

    3. XM_011518467.3 → XP_011516769.1  hemicentin-2 isoform X3

      Conserved Domains (11) summary
      cd00096
      Location:715 → 779
      Ig; Immunoglobulin domain
      smart00408
      Location:4188 → 4250
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:4824 → 4863
      EGF_CA; Calcium-binding EGF-like domain
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:1258 → 1340
      IG_like; Immunoglobulin like
      pfam07679
      Location:4264 → 4350
      I-set; Immunoglobulin I-set domain
      pfam07474
      Location:4352 → 4534
      G2F; G2F domain
      pfam07645
      Location:4674 → 4715
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      pfam14670
      Location:4593 → 4628
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl11960
      Location:4263 → 4346
      Ig; Immunoglobulin domain

    4. XM_011518468.3 → XP_011516770.1  hemicentin-2 isoform X4

      Conserved Domains (11) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:4247 → 4309
      IGc2; Immunoglobulin C-2 Type
      smart00179
      Location:4689 → 4732
      EGF_CA; Calcium-binding EGF-like domain
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:3329 → 3410
      IG_like; Immunoglobulin like
      pfam07679
      Location:4323 → 4409
      I-set; Immunoglobulin I-set domain
      pfam07474
      Location:4411 → 4593
      G2F; G2F domain
      pfam07645
      Location:4733 → 4774
      EGF_CA; Calcium-binding EGF domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      pfam14670
      Location:4652 → 4687
      FXa_inhibition; Coagulation Factor Xa inhibitory site
      cl11960
      Location:4322 → 4405
      Ig; Immunoglobulin domain

    5. XM_011518469.3 → XP_011516771.1  hemicentin-2 isoform X6

      Conserved Domains (7) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:1360 → 1423
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:1258 → 1340
      IG_like; Immunoglobulin like
      pfam07679
      Location:3038 → 3129
      I-set; Immunoglobulin I-set domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:2868 → 2942
      Ig; Immunoglobulin domain

    6. XM_011518470.3 → XP_011516772.1  hemicentin-2 isoform X7

      Conserved Domains (7) summary
      cd00096
      Location:1912 → 1975
      Ig; Immunoglobulin domain
      smart00408
      Location:1360 → 1423
      IGc2; Immunoglobulin C-2 Type
      smart00409
      Location:792 → 879
      IG; Immunoglobulin
      smart00410
      Location:2558 → 2638
      IG_like; Immunoglobulin like
      pfam07679
      Location:608 → 692
      I-set; Immunoglobulin I-set domain
      pfam13519
      Location:39 → 209
      VWA_2; von Willebrand factor type A domain
      cl11960
      Location:2868 → 2942
      Ig; Immunoglobulin domain

    7. XM_017014585.2 → XP_016870074.1  hemicentin-2 isoform X5

    8. XM_017014586.1 → XP_016870075.1  hemicentin-2 isoform X8

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      142470624..142639100
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054362616.1 → XP_054218591.1  hemicentin-2 isoform X2

    2. XM_054362615.1 → XP_054218590.1  hemicentin-2 isoform X1

    3. XM_054362617.1 → XP_054218592.1  hemicentin-2 isoform X3

    4. XM_054362618.1 → XP_054218593.1  hemicentin-2 isoform X4

    5. XM_054362620.1 → XP_054218595.1  hemicentin-2 isoform X6

    6. XM_054362621.1 → XP_054218596.1  hemicentin-2 isoform X7

    7. XM_054362619.1 → XP_054218594.1  hemicentin-2 isoform X5

    8. XM_054362622.1 → XP_054218597.1  hemicentin-2 isoform X8

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_144655.1: Suppressed sequence

      Description
      NM_144655.1: This RefSeq was suppressed temporarily based on the calculation that the annotated protein was shorter than a protein or proteins from a putative ortholog.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q8NDA2.4 GenPept UniProtKB/Swiss-Prot:Q8NDA2

    Gene LinkOut

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

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