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

Gene ID: 140894, updated on 2-Nov-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, Nov 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 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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