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    CCND3 cyclin D3 [ Homo sapiens (human) ]

    Gene ID: 896, updated on 3-Dec-2024

    Summary

    Official Symbol
    CCND3provided by HGNC
    Official Full Name
    cyclin D3provided by HGNC
    Primary source
    HGNC:HGNC:1585
    See related
    Ensembl:ENSG00000112576 MIM:123834; AllianceGenome:HGNC:1585
    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
    Summary
    The protein encoded by this gene belongs to the highly conserved cyclin family, whose members are characterized by a dramatic periodicity in protein abundance through the cell cycle. Cyclins function as regulators of CDK kinases. Different cyclins exhibit distinct expression and degradation patterns which contribute to the temporal coordination of each mitotic event. This cyclin forms a complex with and functions as a regulatory subunit of CDK4 or CDK6, whose activtiy is required for cell cycle G1/S transition. This protein has been shown to interact with and be involved in the phosphorylation of tumor suppressor protein Rb. The CDK4 activity associated with this cyclin was reported to be necessary for cell cycle progression through G2 phase into mitosis after UV radiation. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
    Expression
    Broad expression in bone marrow (RPKM 45.2), lymph node (RPKM 40.1) and 24 other tissues See more
    Orthologs
    NEW
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    Try the new Transcript table

    Genomic context

    See CCND3 in Genome Data Viewer
    Location:
    6p21.1
    Exon count:
    10
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41934933..42050035, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41763493..41878294, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41902671..42017773, complement)

    Chromosome 6 - NC_000006.12Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 49 Neighboring gene small nucleolar RNA SNORA8 Neighboring gene MPRA-validated peak5805 silencer Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41861872-41862386 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41862979-41863271 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24529 Neighboring gene MED14-independent group 3 enhancer GRCh37_chr6:41884515-41885714 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24530 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41892998-41893498 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41906017-41906832 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41906833-41907648 Neighboring gene mediator complex subunit 20 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24531 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41908777-41909728 Neighboring gene bystin like Neighboring gene ReSE screen-validated silencer GRCh37_chr6:41928638-41928835 Neighboring gene H3K27ac hESC enhancer GRCh37_chr6:41932711-41933221 Neighboring gene uncharacterized LOC105375059 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24532 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41976875-41977831 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:41977832-41978787 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:41984389-41984890 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24534 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24535 Neighboring gene Sharpr-MPRA regulatory regions 12575 and 14060 Neighboring gene skeletal muscle cis-regulatory module in CCND3 intron Neighboring gene RNA, U6 small nuclear 761, pseudogene Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42007359-42007580 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr6:42011196-42011696 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24537 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:42013050-42013640 Neighboring gene OCT4-NANOG-H3K4me1 hESC enhancer GRCh37_chr6:42013641-42014230 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17197 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 24540 Neighboring gene H3K27ac hESC enhancers GRCh37_chr6:42017885-42018436 and GRCh37_chr6:42018437-42018988 Neighboring gene Sharpr-MPRA regulatory region 7068 Neighboring gene TATA-box binding protein associated factor 8 Neighboring gene ReSE screen-validated silencer GRCh37_chr6:42067953-42068174 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17198 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17199 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 17200 Neighboring gene chromosome 6 open reading frame 132 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42104000-42104697 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr6:42108933-42109612

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    EBI GWAS Catalog

    Description
    A genome-wide meta-analysis identifies 22 loci associated with eight hematological parameters in the HaemGen consortium.
    EBI GWAS Catalog
    Duffy-null-associated low neutrophil counts influence HIV-1 susceptibility in high-risk South African black women.
    EBI GWAS Catalog
    Genome-wide association study of hematological and biochemical traits in a Japanese population.
    EBI GWAS Catalog
    Genome-wide association study of monoamine metabolite levels in human cerebrospinal fluid.
    EBI GWAS Catalog
    GWAS of blood cell traits identifies novel associated loci and epistatic interactions in Caucasian and African-American children.
    EBI GWAS Catalog
    Multiple loci influence erythrocyte phenotypes in the CHARGE Consortium.
    EBI GWAS Catalog
    Seventy-five genetic loci influencing the human red blood cell.
    EBI GWAS Catalog

    HIV-1 interactions

    Protein interactions

    Protein Gene Interaction Pubs
    Tat tat When expressed in astrocytes, neurons, and non-glial 293T cells, HIV-1 Tat interacts with a number of cell cycle-related proteins including cyclin A, cyclin B, cyclin D3, Cdk2, Cdk4, Cdk1/Cdc2, cdc6, p27, p53, p63, hdlg, and PCNA PubMed
    matrix gag HIV-1 MA natural variant S75X upregulates the expression of two cyclins D2 and D3, and induces significant release of cytokine IL-6, which leads to enhance proliferation of both Epstein-Barr virus (EBV)-infected primary and fully transformed B-lymphocytes PubMed

    Go to the HIV-1, Human Interaction Database

    Pathways from PubChem

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    Markers

    Gene Ontology Provided by GOA

    Component Evidence Code Pubs
    part_of cyclin D3-CDK4 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of cyclin D3-CDK6 complex IPI
    Inferred from Physical Interaction
    more info
    PubMed 
    part_of cyclin-dependent protein kinase holoenzyme complex IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    part_of cyclin-dependent protein kinase holoenzyme complex IDA
    Inferred from Direct Assay
    more info
    PubMed 
    is_active_in cytoplasm IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in cytosol TAS
    Traceable Author Statement
    more info
     
    is_active_in microtubule organizing center IBA
    Inferred from Biological aspect of Ancestor
    more info
     
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
     
    located_in nucleoplasm TAS
    Traceable Author Statement
    more info
     
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
     

    General protein information

    Preferred Names
    G1/S-specific cyclin-D3
    Names
    D3-type cyclin

    NCBI Reference Sequences (RefSeq)

    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_041939.1 RefSeqGene

      Range
      5001..118962
      Download
      GenBank, FASTA, Sequence Viewer (Graphics), LRG_998

    mRNA and Protein(s)

    1. NM_001136017.3NP_001129489.1  G1/S-specific cyclin-D3 isoform 1

      See identical proteins and their annotated locations for NP_001129489.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) differs in the 5' UTR and coding sequence, and represents use of an alternate promoter, compared to variant 2. The resulting isoform (1) is shorter at the N-terminus compared to isoform 2. Variants 1, 8, and 9 all encode the same isoform (1).
      Source sequence(s)
      AK057206, AL160163, BC011616, DA999482, DB001987
      Consensus CDS
      CCDS47426.1
      UniProtKB/TrEMBL
      B3KTY3
      Related
      ENSP00000362079.4, ENST00000372988.8
      Conserved Domains (2) summary
      pfam00134
      Location:172
      Cyclin_N; Cyclin, N-terminal domain
      pfam02984
      Location:74170
      Cyclin_C; Cyclin, C-terminal domain
    2. NM_001136125.3NP_001129597.1  G1/S-specific cyclin-D3 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) lacks an alternate in-frame exon compared to variant 2. The resulting isoform (3) has the same N- and C-termini but is shorter compared to isoform 2.
      Source sequence(s)
      AK057206, AL160163, BC011616, DC360231, M92287
      Consensus CDS
      CCDS47425.1
      UniProtKB/Swiss-Prot
      P30281
      Related
      ENSP00000397545.2, ENST00000414200.6
      Conserved Domains (2) summary
      pfam02984
      Location:83179
      Cyclin_C; Cyclin, C-terminal domain
      cl00050
      Location:2766
      CYCLIN; Cyclin box fold. Protein binding domain functioning in cell-cycle and transcription control. Present in cyclins, TFIIB and Retinoblastoma (RB).The cyclins consist of 8 classes of cell cycle regulators that regulate cyclin dependent kinases (CDKs). TFIIB ...
    3. NM_001136126.3NP_001129598.1  G1/S-specific cyclin-D3 isoform 4

      See identical proteins and their annotated locations for NP_001129598.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) differs in the 5' UTR and coding sequence compared to variant 2. The resulting isoform (4) is shorter at the N-terminus compared to isoform 2. Variants 4, 5, 10, and 11 all encode the same protein.
      Source sequence(s)
      AK057206, AL160163, BC011616, DA069566, DB001987
      Consensus CDS
      CCDS47427.1
      UniProtKB/Swiss-Prot
      P30281
      Related
      ENSP00000401595.2, ENST00000415497.6
      Conserved Domains (1) summary
      pfam02984
      Location:155
      Cyclin_C; Cyclin, C-terminal domain
    4. NM_001287427.2NP_001274356.1  G1/S-specific cyclin-D3 isoform 5

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate in-frame splice site in the 5' coding region and uses a downstream start codon compared to variant 2. It encodes isoform 5 which has a shorter N-terminus compared to isoform 2.
      Source sequence(s)
      AK055519, AL160163, BC011616, BE247367, DA411470, M92287
      Consensus CDS
      CCDS75452.1
      UniProtKB/TrEMBL
      B3KP19, Q5T8J1
      Related
      ENSP00000362078.4, ENST00000372987.8
      Conserved Domains (2) summary
      pfam00134
      Location:16103
      Cyclin_N; Cyclin, N-terminal domain
      pfam02984
      Location:105201
      Cyclin_C; Cyclin, C-terminal domain
    5. NM_001287434.2NP_001274363.1  G1/S-specific cyclin-D3 isoform 4

      See identical proteins and their annotated locations for NP_001274363.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) differs in the 5' UTR and coding sequence, and represents use of an alternate promoter, compared to variant 2. The resulting isoform (4) is shorter at the N-terminus compared to isoform 2. Variants 4, 5, 10, and 11 all encode the same protein.
      Source sequence(s)
      AL513008, BX117734, CA424172, DB104254, DB110132, DB544217, DR761231
      Consensus CDS
      CCDS47427.1
      UniProtKB/Swiss-Prot
      P30281
      Related
      ENSP00000484424.1, ENST00000616010.4
      Conserved Domains (1) summary
      pfam02984
      Location:155
      Cyclin_C; Cyclin, C-terminal domain
    6. NM_001424052.1NP_001410981.1  G1/S-specific cyclin-D3 isoform 6

      Status: REVIEWED

      Description
      Transcript Variant: This variant (7) encodes the longest isoform (6).
      Source sequence(s)
      AL160163
    7. NM_001424053.1NP_001410982.1  G1/S-specific cyclin-D3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL160163, AL513008
      UniProtKB/TrEMBL
      B3KTY3
      Related
      ENSP00000426212.1, ENST00000511642.5
    8. NM_001424055.1NP_001410984.1  G1/S-specific cyclin-D3 isoform 1

      Status: REVIEWED

      Source sequence(s)
      AL160163, AL513008
      UniProtKB/TrEMBL
      B3KTY3
    9. NM_001424056.1NP_001410985.1  G1/S-specific cyclin-D3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL160163
    10. NM_001424057.1NP_001410986.1  G1/S-specific cyclin-D3 isoform 4

      Status: REVIEWED

      Source sequence(s)
      AL160163, AL513008
    11. NM_001424058.1NP_001410987.1  G1/S-specific cyclin-D3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL160163, AL513008
    12. NM_001424059.1NP_001410988.1  G1/S-specific cyclin-D3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL160163
    13. NM_001424060.1NP_001410989.1  G1/S-specific cyclin-D3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL160163
    14. NM_001424061.1NP_001410990.1  G1/S-specific cyclin-D3 isoform 7

      Status: REVIEWED

      Source sequence(s)
      AL160163, AL513008
    15. NM_001760.5NP_001751.1  G1/S-specific cyclin-D3 isoform 2

      See identical proteins and their annotated locations for NP_001751.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) encodes isoform 2.
      Source sequence(s)
      AK057206, AL160163, BC011616, M92287
      Consensus CDS
      CCDS4863.1
      UniProtKB/Swiss-Prot
      B2RD63, B3KQ22, E9PAS4, E9PB36, P30281, Q5T8J0, Q6FG62, Q96F49
      Related
      ENSP00000362082.5, ENST00000372991.9
      Conserved Domains (2) summary
      pfam00134
      Location:27153
      Cyclin_N; Cyclin, N-terminal domain
      pfam02984
      Location:155251
      Cyclin_C; Cyclin, C-terminal domain

    RNA

    1. NR_187571.1 RNA Sequence

      Status: REVIEWED

      Source sequence(s)
      AL513008

    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_000006.12 Reference GRCh38.p14 Primary Assembly

      Range
      41934933..42050035 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047419491.1XP_047275447.1  G1/S-specific cyclin-D3 isoform X2

    2. XM_011514971.3XP_011513273.1  G1/S-specific cyclin-D3 isoform X1

      Conserved Domains (1) summary
      pfam00134
      Location:27153
      Cyclin_N; Cyclin, N-terminal domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060930.1 Alternate T2T-CHM13v2.0

      Range
      41763493..41878294 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054356699.1XP_054212674.1  G1/S-specific cyclin-D3 isoform X2

    2. XM_054356698.1XP_054212673.1  G1/S-specific cyclin-D3 isoform X1