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HMCN2 hemicentin 2 [ Homo sapiens (human) ]

Gene ID: 256158, updated on 8-Dec-2022

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 calcium ion binding activity. Predicted to be an extracellular matrix structural constituent. Predicted to be involved in cell adhesion. Located in collagen-containing extracellular matrix. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in small intestine (RPKM 2.1), fat (RPKM 1.8) and 19 other tissues See more
Orthologs
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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
110 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130265760..130434123)
110 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142470642..142639100)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133028039..133309510)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene Sharpr-MPRA regulatory region 4503 Neighboring gene microRNA 12126 Neighboring gene uncharacterized LOC124902285 Neighboring gene RNA, 7SL, cytoplasmic 665, pseudogene Neighboring gene uncharacterized LOC107987134 Neighboring gene small nucleolar RNA U13 Neighboring gene Sharpr-MPRA regulatory region 491 Neighboring gene argininosuccinate synthase 1

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

See citations in PubMed for homologs of this gene provided by HomoloGene

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)

Genotypes

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
 PubMed 
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 cell adhesion 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
 PubMed 
involved_in synapse organization IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
Component Evidence Code Pubs
is_active_in axon IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
located_in cleavage furrow IEA
Inferred from Electronic Annotation
more info
  
located_in collagen-containing extracellular matrix HDA PubMed 
is_active_in neuronal cell body IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
 PubMed 

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/TrEMBL
    A0A804HLC3
    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: Homo sapiens Annotation Release 110 details...Open this link in a new tab

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
    142470642..142639100
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

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
Q8NDA2.3 GenPept UniProtKB/Swiss-Prot:Q8NDA2

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