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CCND3 cyclin D3 [ Homo sapiens (human) ]

Gene ID: 896, updated on 1-Mar-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
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Genomic context

See CCND3 in Genome Data Viewer
Location:
6p21.1
Exon count:
10
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 6 NC_000006.12 (41934933..42050035, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 6 NC_060930.1 (41763493..41878294, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 6 NC_000006.11 (41902671..42016632, 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
is_active_in centrosome IBA
Inferred from Biological aspect of Ancestor
more info
 
part_of cyclin D3-CDK4 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
 
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)

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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.

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_2023_10

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