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    CNBD2 cyclic nucleotide binding domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 140894, updated on 9-Dec-2024

    Summary

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    Official Symbol
    CNBD2provided by HGNC
    Official Full Name
    cyclic nucleotide binding domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:16145
    See related
    Ensembl:ENSG00000149646 AllianceGenome:HGNC:16145
    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
    CNMPD1; C20orf152
    Summary
    Predicted to enable cAMP binding activity. Predicted to be involved in spermatogenesis. Predicted to be located in cytosol. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Biased expression in testis (RPKM 3.5) and kidney (RPKM 0.1) See more
    Orthologs
    mouse all
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    Genomic context

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    See CNBD2 in Genome Data Viewer
    Location:
    20q11.23
    Exon count:
    20
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 20 NC_000020.11 (35954386..36030700)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 20 NC_060944.1 (37675577..37751679)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 20 NC_000020.10 (34556512..34618622)

    Chromosome 20 - NC_000020.11Genomic Context describing neighboring genes Neighboring gene PHD finger protein 20 Neighboring gene RNA, U4 small nuclear 40, pseudogene Neighboring gene H3K27ac hESC enhancer GRCh37_chr20:34494545-34495045 Neighboring gene RNA, U6 small nuclear 937, pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17799 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17800 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17801 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17802 Neighboring gene uncharacterized LOC124904982 Neighboring gene SCAN domain containing 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr20:34637879-34639078 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 17803 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 12866 Neighboring gene non-coding RNA activated by DNA damage Neighboring gene high mobility group box 3 pseudogene 2

    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 DNA sequence and comparative analysis of human chromosome 20. Deloukas P, et al. Nature, 2001 Dec 20-27. PMID 11780052
    2. Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Kimura K, et al. Genome Res, 2006 Jan. PMID 16344560, Free PMC Article
    3. Complete sequencing and characterization of 21,243 full-length human cDNAs. Ota T, et al. Nat Genet, 2004 Jan. PMID 14702039
    4. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, et al. Proc Natl Acad Sci U S A, 2002 Dec 24. PMID 12477932, Free PMC Article
    5. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, et al. Brief Bioinform, 2011 Sep. PMID 21873635, Free PMC Article

    GeneRIFs: Gene References Into Functions

    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)

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC138880

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables cAMP binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in spermatogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    located_in cytosol IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    cyclic nucleotide-binding domain-containing protein 2
    Names
    cyclic nucleotide (cNMP) binding domain containing 1

    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_001207076.3 → NP_001194005.1  cyclic nucleotide-binding domain-containing protein 2 isoform 2

      See identical proteins and their annotated locations for NP_001194005.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (2) lacks a coding exon in the 3' region, which results in a frameshift, compared to variant 1. The resulting isoform (2) has a shorter C-terminus than isoform 1.
      Source sequence(s)
      AI191598, BC114945, HY023889
      Consensus CDS
      CCDS56189.1
      UniProtKB/Swiss-Prot
      Q96M20
      Related
      ENSP00000442729.1, ENST00000538900.1
      Conserved Domains (2) summary
      COG0664
      Location:110 → 241
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:122 → 218
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    2. NM_001304367.2 → NP_001291296.1  cyclic nucleotide-binding domain-containing protein 2 isoform 3

      See identical proteins and their annotated locations for NP_001291296.1

      Status: VALIDATED

      Description
      Transcript Variant: This variant (3) lacks multiple 3' exons and its transcription extends past a splice site used in variant 1, resulting in a different 3' coding region and 3' UTR. The resulting isoform (3) has a distinct C-terminus and is shorter than isoform 1.
      Source sequence(s)
      AL109965, BC030782, HY023889
      Consensus CDS
      CCDS77575.1
      UniProtKB/TrEMBL
      Q4G141
      Related
      ENSP00000480804.1, ENST00000489667.1

    3. NM_001365709.1 → NP_001352638.1  cyclic nucleotide-binding domain-containing protein 2 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL109965, AL359828
      Consensus CDS
      CCDS93033.1
      UniProtKB/Swiss-Prot
      Q14C79, Q5JWY7, Q5T3S1, Q96M20, Q9BR36, Q9BWY5
      Related
      ENSP00000363084.3, ENST00000373973.7
      Conserved Domains (1) summary
      cd00038
      Location:122 → 218
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    4. NM_080834.4 → NP_543024.2  cyclic nucleotide-binding domain-containing protein 2 isoform 1

      See identical proteins and their annotated locations for NP_543024.2

      Status: VALIDATED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AI191598, AK057454, BC114945, HY023889
      Consensus CDS
      CCDS13270.1
      UniProtKB/Swiss-Prot
      Q96M20
      Related
      ENSP00000340954.1, ENST00000349339.5
      Conserved Domains (2) summary
      COG0664
      Location:110 → 241
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:122 → 218
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    RNA

    1. NR_130714.2 RNA Sequence

      Status: VALIDATED

      Description
      Transcript Variant: This variant (4) lacks three internal exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).
      Source sequence(s)
      AI191598, BC114634, HY023889
      Related
      ENST00000463258.6

    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_000020.11 Reference GRCh38.p14 Primary Assembly

      Range
      35954386..36030700
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047439921.1 → XP_047295877.1  cyclic nucleotide-binding domain-containing protein 2 isoform X1

    2. XM_047439922.1 → XP_047295878.1  cyclic nucleotide-binding domain-containing protein 2 isoform X2

    3. XM_047439927.1 → XP_047295883.1  cyclic nucleotide-binding domain-containing protein 2 isoform X11

    4. XM_011528593.3 → XP_011526895.1  cyclic nucleotide-binding domain-containing protein 2 isoform X8

    5. XM_011528590.3 → XP_011526892.1  cyclic nucleotide-binding domain-containing protein 2 isoform X3

      Conserved Domains (2) summary
      COG0664
      Location:151 → 282
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:163 → 259
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    6. XM_047439924.1 → XP_047295880.1  cyclic nucleotide-binding domain-containing protein 2 isoform X6

    7. XM_047439926.1 → XP_047295882.1  cyclic nucleotide-binding domain-containing protein 2 isoform X10

    8. XM_047439925.1 → XP_047295881.1  cyclic nucleotide-binding domain-containing protein 2 isoform X9

    9. XM_047439928.1 → XP_047295884.1  cyclic nucleotide-binding domain-containing protein 2 isoform X13

    10. XM_047439929.1 → XP_047295885.1  cyclic nucleotide-binding domain-containing protein 2 isoform X14

    11. XM_047439923.1 → XP_047295879.1  cyclic nucleotide-binding domain-containing protein 2 isoform X4

    12. XM_017027683.3 → XP_016883172.1  cyclic nucleotide-binding domain-containing protein 2 isoform X5

    13. XM_011528592.1 → XP_011526894.1  cyclic nucleotide-binding domain-containing protein 2 isoform X7

      Conserved Domains (2) summary
      COG0664
      Location:63 → 194
      Crp; cAMP-binding domain of CRP or a regulatory subunit of cAMP-dependent protein kinases [Signal transduction mechanisms]
      cd00038
      Location:75 → 171
      CAP_ED; effector domain of the CAP family of transcription factors; members include CAP (or cAMP receptor protein (CRP)), which binds cAMP, FNR (fumarate and nitrate reduction), which uses an iron-sulfur cluster to sense oxygen) and CooA, a heme containing CO ...

    14. XM_011528598.1 → XP_011526900.1  cyclic nucleotide-binding domain-containing protein 2 isoform X12

    RNA

    1. XR_001754187.2 RNA Sequence

    2. XR_001754188.2 RNA Sequence

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060944.1 Alternate T2T-CHM13v2.0

      Range
      37675577..37751679
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054323055.1 → XP_054179030.1  cyclic nucleotide-binding domain-containing protein 2 isoform X1

    2. XM_054323056.1 → XP_054179031.1  cyclic nucleotide-binding domain-containing protein 2 isoform X2

    3. XM_054323065.1 → XP_054179040.1  cyclic nucleotide-binding domain-containing protein 2 isoform X11

    4. XM_054323062.1 → XP_054179037.1  cyclic nucleotide-binding domain-containing protein 2 isoform X8

    5. XM_054323057.1 → XP_054179032.1  cyclic nucleotide-binding domain-containing protein 2 isoform X3

    6. XM_054323060.1 → XP_054179035.1  cyclic nucleotide-binding domain-containing protein 2 isoform X6

    7. XM_054323064.1 → XP_054179039.1  cyclic nucleotide-binding domain-containing protein 2 isoform X10

    8. XM_054323063.1 → XP_054179038.1  cyclic nucleotide-binding domain-containing protein 2 isoform X9

    9. XM_054323067.1 → XP_054179042.1  cyclic nucleotide-binding domain-containing protein 2 isoform X13

    10. XM_054323068.1 → XP_054179043.1  cyclic nucleotide-binding domain-containing protein 2 isoform X14

    11. XM_054323058.1 → XP_054179033.1  cyclic nucleotide-binding domain-containing protein 2 isoform X4

    12. XM_054323059.1 → XP_054179034.1  cyclic nucleotide-binding domain-containing protein 2 isoform X5

    13. XM_054323061.1 → XP_054179036.1  cyclic nucleotide-binding domain-containing protein 2 isoform X7

    14. XM_054323066.1 → XP_054179041.1  cyclic nucleotide-binding domain-containing protein 2 isoform X12

    RNA

    1. XR_008485237.1 RNA Sequence

    2. XR_008485238.1 RNA Sequence

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96M20.2 GenPept UniProtKB/Swiss-Prot:Q96M20

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