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

    Gene ID: 56650, updated on 9-Dec-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; CLDN-25; GENX-3745
    Summary
    Located in cell surface. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in brain (RPKM 128.7), testis (RPKM 51.4) and 23 other tissues See more
    Orthologs
    mouse all
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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_2024_08 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (98515483..98522902, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (101219167..101226586, complement)
    RS_2024_09 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. 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
    2. 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
    3. 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
    4. Down Regulation of CLDND1 Induces Apoptosis in Breast Cancer Cells. Achari C, et al. PLoS One, 2015. PMID 26083392, Free PMC Article
    5. 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

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Transcription of CLDND1 in human brain endothelial cells is regulated by the myeloid zinc finger 1.
      Title: Transcription of CLDND1 in human brain endothelial cells is regulated by the myeloid zinc finger 1.
    2. 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.
    3. 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.
    4. 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.
    5. CLDND1 as a novel survival factor in basal-like breast cancer cell lines
      Title: Down Regulation of CLDND1 Induces Apoptosis in Breast Cancer Cells.
    6. 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)

    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_2024_08

    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

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

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