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CLDND1 claudin domain containing 1 [ Homo sapiens (human) ]

Gene ID: 56650, updated on 5-Mar-2024

Summary

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Official Symbol
CLDND1provided by HGNC
Official Full Name
claudin domain containing 1provided by HGNC
Primary source
HGNC:HGNC:1322
See related
Ensembl:ENSG00000080822 MIM:619677; AllianceGenome:HGNC:1322
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
Z38; C3orf4; GENX-3745
Summary
Located in cell surface. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in brain (RPKM 128.7), testis (RPKM 51.4) and 23 other tissues See more
Orthologs
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Genomic context

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See CLDND1 in Genome Data Viewer
Location:
3q11.2; 3q12.1
Exon count:
6
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (98515483..98522902, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (101219167..101226586, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (98234327..98241746, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene olfactory receptor family 5 subfamily K member 1 Neighboring gene olfactory receptor family 5 subfamily K member 2 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14555 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14556 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 20137 Neighboring gene NANOG hESC enhancer GRCh37_chr3:98247209-98247752 Neighboring gene RPL38 pseudogene 4 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14557 Neighboring gene G protein-coupled receptor 15

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. Long non-coding RNA Z38 promotes cell proliferation and metastasis in human renal cell carcinoma. He X, et al. Mol Med Rep, 2017 Oct. PMID 28849012
  2. Prognostic significance of long noncoding RNA Z38 as a candidate biomarker in breast cancer. Nie ZL, et al. J Clin Lab Anal, 2018 Jan. PMID 28247935, Free PMC Article
  3. Down Regulation of CLDND1 Induces Apoptosis in Breast Cancer Cells. Achari C, et al. PLoS One, 2015. PMID 26083392, Free PMC Article
  4. Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes. Fayein NA, et al. Gene, 2002 May 1. PMID 12036590
  5. The Genexpress IMAGE knowledge base of the human brain transcriptome: a prototype integrated resource for functional and computational genomics. Piétu G, et al. Genome Res, 1999 Feb. PMID 10022985, Free PMC Article

See all (26) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. suggest that the transient decrease of CLDND1 after cerebellar hemorrhage is responsible for low-molecular-weight selective vascular hyperpermeability
    Title: Claudin domain containing 1 contributing to endothelial cell adhesion decreases in presence of cerebellar hemorrhage.
  2. Z38 was overexpressed in clinical patients with RCC and was associated with RCC stage. Knockdown of Z38 in A498 and ACHIN cells inhibited cell proliferation and metastasis
    Title: Long non-coding RNA Z38 promotes cell proliferation and metastasis in human renal cell carcinoma.
  3. findings strongly suggest that CLDND1 is a direct RORalpha target
    Title: The retinoic acid receptor-related orphan receptor α positively regulates tight junction protein claudin domain-containing 1 mRNA expression in human brain endothelial cells.
  4. CLDND1 as a novel survival factor in basal-like breast cancer cell lines
    Title: Down Regulation of CLDND1 Induces Apoptosis in Breast Cancer Cells.
  5. A cDNA library consisting of 220 upregulated genes in tumour tissue was established and named as LSCC. Differential expression was confirmed in five of these genes, including IGFBP5, SQLE, RAP2B, CLDN1, and TBL1XR1.
    Title: Identification of genes differentially expressed in human primary lung squamous cell carcinoma.
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

HIV-1 interactions

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Replication interactions

Interaction Pubs
Knockdown of claudin domain containing 1 (CLDND1) by siRNA inhibits HIV-1 replication in HeLa-derived TZM-bl 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

  • MGC3316, MGC9861, MGC111162

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Component Evidence Code Pubs
located_in apical plasma membrane IEA
Inferred from Electronic Annotation
more info
  
located_in cell surface HDA PubMed 

General protein information

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Preferred Names
claudin domain-containing protein 1
Names
claudin domain containing 1 protein
membrane protein GENX-3745

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_001040181.2 → NP_001035271.1  claudin domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001035271.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the predominant transcript and encodes isoform a. Variants 1, 2, 3, and 6 all encode the same isoform.
    Source sequence(s)
    AA811441, BC013610, EB386420
    Consensus CDS
    CCDS2930.1
    UniProtKB/Swiss-Prot
    B3KQR1, D3DN36, F2Z2D9, Q502Y8, Q6UVX2, Q9BUZ9, Q9NY35, Q9NZZ5, Q9Y4S9
    UniProtKB/TrEMBL
    D6RCR8
    Related
    ENSP00000340247.6, ENST00000341181.11
    Conserved Domains (1) summary
    cl21598
    Location:17 → 234
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

  2. NM_001040182.2 → NP_001035272.1  claudin domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_001035272.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (4) includes an alternate 5' exon and may initiate transcription at an upstream AUG, compared to variant 1. Variant 4 encodes an isoform with a longer N-terminus (b), compared to isoform a.
    Source sequence(s)
    BC095441, DB461184
    Consensus CDS
    CCDS46877.1
    UniProtKB/TrEMBL
    A0A0R4J2F2, D6RCR8
    Related
    ENSP00000377735.3, ENST00000394181.6
    Conserved Domains (1) summary
    cl21598
    Location:40 → 257
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

  3. NM_001040183.2 → NP_001035273.1  claudin domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001035273.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    AA811441, BU784186, CD520771, DB461184, EB386420
    Consensus CDS
    CCDS2930.1
    UniProtKB/Swiss-Prot
    B3KQR1, D3DN36, F2Z2D9, Q502Y8, Q6UVX2, Q9BUZ9, Q9NY35, Q9NZZ5, Q9Y4S9
    UniProtKB/TrEMBL
    D6RCR8
    Related
    ENSP00000421413.1, ENST00000508902.5
    Conserved Domains (1) summary
    cl21598
    Location:17 → 234
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

  4. NM_001040199.2 → NP_001035289.1  claudin domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001035289.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (6) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    AA811441, AC021660, BC013610, BF967477, BI552824, EB386420
    Consensus CDS
    CCDS2930.1
    UniProtKB/Swiss-Prot
    B3KQR1, D3DN36, F2Z2D9, Q502Y8, Q6UVX2, Q9BUZ9, Q9NY35, Q9NZZ5, Q9Y4S9
    UniProtKB/TrEMBL
    D6RCR8
    Related
    ENSP00000426869.1, ENST00000513287.5
    Conserved Domains (1) summary
    cl21598
    Location:17 → 234
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

  5. NM_001040200.2 → NP_001035290.1  claudin domain-containing protein 1 isoform d

    See identical proteins and their annotated locations for NP_001035290.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (7) lacks an alternate exon in the 5' coding region and uses an upstream start codon, compared to variant 1. Variant 7 encodes an isoform with a distinct N-terminus (d), compared to isoform a.
    Source sequence(s)
    AA811441, AC021660, DB465920
    Consensus CDS
    CCDS43116.1
    UniProtKB/Swiss-Prot
    Q9NY35
    Related
    ENSP00000424669.1, ENST00000511081.5
    Conserved Domains (1) summary
    cl21598
    Location:44 → 139
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

  6. NM_019895.3 → NP_063948.1  claudin domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_063948.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) differs in the 5' UTR compared to variant 1. Variants 1, 2, 3, and 6 encode the same isoform (a).
    Source sequence(s)
    AA811441, BC001757, DB461184, EB386420
    Consensus CDS
    CCDS2930.1
    UniProtKB/Swiss-Prot
    B3KQR1, D3DN36, F2Z2D9, Q502Y8, Q6UVX2, Q9BUZ9, Q9NY35, Q9NZZ5, Q9Y4S9
    UniProtKB/TrEMBL
    D6RCR8
    Related
    ENSP00000377734.2, ENST00000394180.6
    Conserved Domains (1) summary
    cl21598
    Location:17 → 234
    PMP22_Claudin; PMP-22/EMP/MP20/Claudin family

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    98515483..98522902 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    101219167..101226586 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NM_001040184.1: Suppressed sequence

    Description
    NM_001040184.1: This RefSeq was suppressed because its 3' exon aligns to MLT1G1 repeat and the coding region in the 3' exon is not supported.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9NY35.1 GenPept UniProtKB/Swiss-Prot:Q9NY35

Gene LinkOut

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