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    CDIN1 CDAN1 interacting nuclease 1 [ Homo sapiens (human) ]

    Gene ID: 84529, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CDIN1provided by HGNC
    Official Full Name
    CDAN1 interacting nuclease 1provided by HGNC
    Primary source
    HGNC:HGNC:26929
    See related
    Ensembl:ENSG00000186073 MIM:615626; AllianceGenome:HGNC:26929
    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
    HH114; C15orf41
    Summary
    This gene encodes a protein with two predicted helix-turn-helix domains. Mutations in this gene were found in families with congenital dyserythropoietic anemia type Ib. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Mar 2014]
    Expression
    Broad expression in heart (RPKM 18.6), urinary bladder (RPKM 3.9) and 17 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CDIN1 in Genome Data Viewer
    Location:
    15q14
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 15 NC_000015.10 (36579626..36810244)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 15 NC_060939.1 (34385147..34615722)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 15 NC_000015.9 (36871827..37102445)

    Chromosome 15 - NC_000015.10Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105370770 Neighboring gene VISTA enhancer hs355 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9193 Neighboring gene cytochrome c oxidase subunit 6C pseudogene 4 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:36919333-36919834 Neighboring gene tropomyosin 3 pseudogene Neighboring gene Sharpr-MPRA regulatory region 1254 Neighboring gene LARP4 pseudogene Neighboring gene tyrosylprotein sulfotransferase 2 pseudogene 1 Neighboring gene uncharacterized LOC124903466 Neighboring gene VISTA enhancer hs828 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr15:37045234-37045802 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9194 Neighboring gene casein kinase 1 alpha 1 pseudogene 1 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 9195 Neighboring gene small nucleolar RNA U3 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37169875-37170652 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37170653-37171430 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr15:37172643-37173204 Neighboring gene NANOG hESC enhancer GRCh37_chr15:37173676-37174246 Neighboring gene uncharacterized LOC145845

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. Congenital dyserythropoietic anemia types Ib, II, and III: novel variants in the CDIN1 gene and functional study of a novel variant in the KIF23 gene. Méndez M, et al. Ann Hematol, 2021 Feb. PMID 33159567
    2. Recapitulation of erythropoiesis in congenital dyserythropoietic anaemia type I (CDA-I) identifies defects in differentiation and nucleolar abnormalities. Scott C, et al. Haematologica, 2021 Nov 1. PMID 33121234, Free PMC Article
    3. A complex comprising C15ORF41 and Codanin-1: the products of two genes mutated in congenital dyserythropoietic anaemia type I (CDA-I). Shroff M, et al. Biochem J, 2020 May 29. PMID 32239177, Free PMC Article
    4. Successful management of transfusion-dependent congenital dyserythropoietic anemia type 1b with interferon alfa-2a. Rathe M, et al. Pediatr Blood Cancer, 2018 Mar. PMID 29049846
    5. Congenital Dyserythropoietic Anemia Type I. Adam MP, et al. , 1993. PMID 20301759

    See all (28) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Genetic and functional insights into CDA-I prevalence and pathogenesis.
      Title: Genetic and functional insights into CDA-I prevalence and pathogenesis.
    2. Congenital dyserythropoietic anemia types Ib, II, and III: novel variants in the CDIN1 gene and functional study of a novel variant in the KIF23 gene.
      Title: Congenital dyserythropoietic anemia types Ib, II, and III: novel variants in the CDIN1 gene and functional study of a novel variant in the KIF23 gene.
    3. Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease.
      Title: Characterization of the interactions between Codanin-1 and C15Orf41, two proteins implicated in congenital dyserythropoietic anemia type I disease.
    4. A complex comprising C15ORF41 and Codanin-1: the products of two genes mutated in congenital dyserythropoietic anaemia type I (CDA-I).
      Title: A complex comprising C15ORF41 and Codanin-1: the products of two genes mutated in congenital dyserythropoietic anaemia type I (CDA-I).
    5. Mutation in C!%ORF41 gene is associated with congenital dyserythropoietic anemia.
      Title: Identification of CDAN1, C15ORF41 and SEC23B mutations in Chinese patients affected by congenital dyserythropoietic anemia.
    6. Observational study of gene-disease association, gene-environment interaction, and pharmacogenomic / toxicogenomic. (HuGE Navigator)
      Title: Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study.
    7. Observational study of gene-disease association. (HuGE Navigator)
      Title: Gene-centric association signals for lipids and apolipoproteins identified via the HumanCVD BeadChip.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • FLJ22851, MGC11326

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in erythrocyte differentiation IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in erythrocyte differentiation IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytoplasm IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    CDAN1-interacting nuclease 1
    Names
    protein C15orf41
    uncharacterized protein C15orf41

    NCBI Reference Sequences (RefSeq)

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    NEW Try the new Transcript table

    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.

    Genomic

    1. NG_034055.1 RefSeqGene

      Range
      5024..235642
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001130010.3 → NP_001123482.1  CDAN1-interacting nuclease 1 isoform 1

      See identical proteins and their annotated locations for NP_001123482.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes isoform 1.
      Source sequence(s)
      AA581466, AL526474, BC006254, BX647650, DA467314
      Consensus CDS
      CCDS45215.1
      UniProtKB/Swiss-Prot
      B2RD87, Q9Y2V0
      Related
      ENSP00000401362.2, ENST00000437989.6
      Conserved Domains (1) summary
      pfam14811
      Location:135 → 265
      TPD; Protein of unknown function TPD sequence-motif

    2. NM_001290232.2 → NP_001277161.1  CDAN1-interacting nuclease 1 isoform 2

      See identical proteins and their annotated locations for NP_001277161.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) differs in the 5' and 3' UTRs, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AC013640, AC019016, AC103988, AK315446
      Consensus CDS
      CCDS45216.1
      UniProtKB/Swiss-Prot
      Q9Y2V0
      Related
      ENSP00000457854.1, ENST00000562877.5
      Conserved Domains (1) summary
      pfam14811
      Location:37 → 167
      TPD; Protein of unknown function TPD sequence-motif

    3. NM_001290233.2 → NP_001277162.1  CDAN1-interacting nuclease 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks multiple 3' exons and contains an alternate 3' terminal exon, resulting in a different 3' coding region and 3' UTR, compared to variant 1. The encoded isoform (3) has a distinct C-temrinus and is longer than isoform 1.
      Source sequence(s)
      AC013640, AC103988, AK026504, BC006254
      Consensus CDS
      CCDS86445.1
      UniProtKB/TrEMBL
      A0A2R8YD89
      Related
      ENSP00000493669.1, ENST00000570265.6
      Conserved Domains (1) summary
      pfam14811
      Location:135 → 241
      TPD; Protein of unknown function TPD sequence-motif

    4. NM_001321756.2 → NP_001308685.1  CDAN1-interacting nuclease 1 isoform 2

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Consensus CDS
      CCDS45216.1
      UniProtKB/Swiss-Prot
      Q9Y2V0
      Conserved Domains (1) summary
      pfam14811
      Location:37 → 167
      TPD; Protein of unknown function TPD sequence-motif

    5. NM_001321757.2 → NP_001308686.1  CDAN1-interacting nuclease 1 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Consensus CDS
      CCDS86447.1
      UniProtKB/TrEMBL
      A0A2R8Y7J6
      Related
      ENSP00000496325.1, ENST00000643612.1
      Conserved Domains (1) summary
      pfam14811
      Location:12 → 142
      TPD; Protein of unknown function TPD sequence-motif

    6. NM_001321758.2 → NP_001308687.1  CDAN1-interacting nuclease 1 isoform 5

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Conserved Domains (1) summary
      pfam14811
      Location:98 → 228
      TPD; Protein of unknown function TPD sequence-motif

    7. NM_001321759.2 → NP_001308688.1  CDAN1-interacting nuclease 1 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Consensus CDS
      CCDS45215.1
      UniProtKB/Swiss-Prot
      B2RD87, Q9Y2V0
      Related
      ENSP00000455397.1, ENST00000566621.6
      Conserved Domains (1) summary
      pfam14811
      Location:135 → 265
      TPD; Protein of unknown function TPD sequence-motif

    8. NM_001321760.2 → NP_001308689.1  CDAN1-interacting nuclease 1 isoform 6

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Consensus CDS
      CCDS86446.1
      UniProtKB/TrEMBL
      A0A2R8YEZ2
      Related
      ENSP00000494718.1, ENST00000646533.1
      Conserved Domains (1) summary
      pfam14811
      Location:135 → 203
      TPD; Protein of unknown function TPD sequence-motif

    9. NM_001321761.2 → NP_001308690.1  CDAN1-interacting nuclease 1 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AC013640, AC019016, AC103988
      Consensus CDS
      CCDS81861.1
      UniProtKB/TrEMBL
      H3BS01
      Related
      ENSP00000456477.1, ENST00000569302.6
      Conserved Domains (1) summary
      pfam14811
      Location:135 → 271
      TPD; Protein of unknown function TPD sequence-motif

    10. NM_032499.6 → NP_115888.1  CDAN1-interacting nuclease 1 isoform 2

      See identical proteins and their annotated locations for NP_115888.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) differs in the 5' and 3' UTRs, lacks a portion of the 5' coding region, and initiates translation at a downstream in-frame start codon, compared to variant 1. The encoded isoform (2) has a shorter N-terminus than isoform 1. Variants 2 and 3 encode the same isoform (2).
      Source sequence(s)
      AA581466, AC013640, AC103988, AF114263, AL526474, BX647650, DA534917
      Consensus CDS
      CCDS45216.1
      UniProtKB/Swiss-Prot
      Q9Y2V0
      Related
      ENSP00000456736.1, ENST00000567389.5
      Conserved Domains (1) summary
      pfam14811
      Location:37 → 167
      TPD; Protein of unknown function TPD sequence-motif

    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_000015.10 Reference GRCh38.p14 Primary Assembly

      Range
      36579626..36810244
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047433174.1 → XP_047289130.1  CDAN1-interacting nuclease 1 isoform X4

    2. XM_017022676.2 → XP_016878165.1  CDAN1-interacting nuclease 1 isoform X1

      Conserved Domains (1) summary
      pfam14811
      Location:103 → 199
      TPD; Protein of unknown function TPD sequence-motif

    3. XM_017022677.2 → XP_016878166.1  CDAN1-interacting nuclease 1 isoform X1

      Conserved Domains (1) summary
      pfam14811
      Location:103 → 199
      TPD; Protein of unknown function TPD sequence-motif

    4. XM_047433171.1 → XP_047289127.1  CDAN1-interacting nuclease 1 isoform X2

    5. XM_047433172.1 → XP_047289128.1  CDAN1-interacting nuclease 1 isoform X3

    6. XM_047433173.1 → XP_047289129.1  CDAN1-interacting nuclease 1 isoform X3

    7. XM_047433175.1 → XP_047289131.1  CDAN1-interacting nuclease 1 isoform X5

    8. XM_047433176.1 → XP_047289132.1  CDAN1-interacting nuclease 1 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y7J6

    RNA

    1. XR_007064491.1 RNA Sequence

    2. XR_007064492.1 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060939.1 Alternate T2T-CHM13v2.0

      Range
      34385147..34615722
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054378997.1 → XP_054234972.1  CDAN1-interacting nuclease 1 isoform X4

    2. XM_054378995.1 → XP_054234970.1  CDAN1-interacting nuclease 1 isoform X1

    3. XM_054378996.1 → XP_054234971.1  CDAN1-interacting nuclease 1 isoform X1

    4. XM_054378998.1 → XP_054234973.1  CDAN1-interacting nuclease 1 isoform X6

      UniProtKB/TrEMBL
      A0A2R8Y7J6

    RNA

    1. XR_008489019.1 RNA Sequence

    2. XR_008489020.1 RNA Sequence

    3. XR_008489021.1 RNA Sequence

    4. XR_008489022.1 RNA Sequence

    5. XR_008489023.1 RNA Sequence

    6. XR_008489024.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9Y2V0.2 GenPept UniProtKB/Swiss-Prot:Q9Y2V0

    Gene LinkOut

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