Ccdc28a (coiled-coil domain containing 28A) - Rat Genome Database

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Gene: Ccdc28a (coiled-coil domain containing 28A) Mus musculus
Analyze
Symbol: Ccdc28a
Name: coiled-coil domain containing 28A
RGD ID: 1321165
MGI Page MGI
Description: Is expressed in several structures, including alimentary system; brain; cardiovascular system; genitourinary system; and respiratory system. Orthologous to human CCDC28A (coiled-coil domain containing 28A).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 1700009P13Rik; AI480677; coiled-coil domain-containing protein 28A; MGC19351
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391018,089,424 - 18,110,940 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1018,089,424 - 18,110,746 (-)EnsemblGRCm39 Ensembl
GRCm381018,213,676 - 18,235,805 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1018,213,676 - 18,234,998 (-)EnsemblGRCm38mm10GRCm38
MGSCv371017,933,491 - 17,954,787 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361017,906,343 - 17,924,394 (-)NCBIMGSCv36mm8
MGSCv361018,092,971 - 18,111,028 (-)NCBIMGSCv36mm8
Celera1018,112,973 - 18,144,756 (-)NCBICelera
Cytogenetic Map10A3NCBI
cM Map107.53NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:12466851   PMID:12477932   PMID:16141072   PMID:16141073   PMID:18973680   PMID:21267068   PMID:21677750  
PMID:24194600  


Genomics

Comparative Map Data
Ccdc28a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391018,089,424 - 18,110,940 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1018,089,424 - 18,110,746 (-)EnsemblGRCm39 Ensembl
GRCm381018,213,676 - 18,235,805 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1018,213,676 - 18,234,998 (-)EnsemblGRCm38mm10GRCm38
MGSCv371017,933,491 - 17,954,787 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361017,906,343 - 17,924,394 (-)NCBIMGSCv36mm8
MGSCv361018,092,971 - 18,111,028 (-)NCBIMGSCv36mm8
Celera1018,112,973 - 18,144,756 (-)NCBICelera
Cytogenetic Map10A3NCBI
cM Map107.53NCBI
CCDC28A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386138,773,769 - 138,793,319 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6138,773,769 - 138,793,319 (+)EnsemblGRCh38hg38GRCh38
GRCh376139,094,906 - 139,114,456 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366139,136,350 - 139,156,149 (+)NCBINCBI36Build 36hg18NCBI36
Build 346139,136,349 - 139,156,147NCBI
Celera6139,834,761 - 139,854,557 (+)NCBICelera
Cytogenetic Map6q24.1NCBI
HuRef6136,656,063 - 136,675,758 (+)NCBIHuRef
CHM1_16139,357,677 - 139,377,457 (+)NCBICHM1_1
T2T-CHM13v2.06139,962,307 - 139,981,863 (+)NCBIT2T-CHM13v2.0
Ccdc28a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8114,677,451 - 14,692,729 (-)NCBIGRCr8
mRatBN7.2112,857,668 - 12,872,944 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl112,857,666 - 12,873,003 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx112,629,455 - 12,644,028 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0118,631,379 - 18,645,952 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0112,837,959 - 12,852,996 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0113,384,153 - 13,395,643 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl113,384,156 - 13,395,370 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0115,072,108 - 15,083,495 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4113,269,164 - 13,284,200 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1113,269,225 - 13,284,298 (-)NCBI
Celera111,314,407 - 11,329,332 (-)NCBICelera
Cytogenetic Map1p12NCBI
Ccdc28a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543620,846,227 - 20,873,552 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543620,849,493 - 20,875,284 (-)NCBIChiLan1.0ChiLan1.0
CCDC28A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25158,740,208 - 158,759,522 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16156,637,791 - 156,657,108 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06136,533,841 - 136,553,303 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16140,619,716 - 140,638,830 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6140,619,716 - 140,638,830 (+)Ensemblpanpan1.1panPan2
CCDC28A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1131,044,102 - 31,058,173 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl131,044,126 - 31,057,800 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha131,920,945 - 31,935,141 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0131,207,239 - 31,221,442 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl131,207,395 - 31,221,439 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1131,084,696 - 31,098,895 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0130,966,784 - 30,981,007 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0131,276,492 - 31,290,694 (+)NCBIUU_Cfam_GSD_1.0
CCDC28A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl125,647,000 - 25,663,273 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1125,646,997 - 25,663,277 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2128,782,282 - 28,798,563 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC28A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11334,596,584 - 34,615,633 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660406,769,559 - 6,788,468 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc28a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475315,157,391 - 15,185,029 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475315,157,509 - 15,185,253 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ccdc28a
662 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1544
Count of miRNA genes:658
Interacting mature miRNAs:812
Transcripts:ENSMUST00000052648, ENSMUST00000080860, ENSMUST00000173243, ENSMUST00000173962, ENSMUST00000174592, ENSMUST00000174631
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
11532725Sluc44b_msusceptibility to lung cancer 44b (mouse)10126289265Mouse
11532724Sluc44c_msusceptibility to lung cancer 44c (mouse)10126289265Mouse
11532723Sluc44d_msusceptibility to lung cancer 44d (mouse)10126289265Mouse
11532722Sluc44e_msusceptibility to lung cancer 44e (mouse)10126289265Mouse
11532721Sluc44_msusceptibility to lung cancer 44 (mouse)10126289265Mouse
11532720Sluc44a_msusceptibility to lung cancer 44a (mouse)10126289265Mouse
11532718Sluc44f_msusceptibility to lung cancer 44f (mouse)10126289265Mouse
11532717Sluc44g_msusceptibility to lung cancer 44g (mouse)10126289265Mouse
11533917Mts2_mmammary tumor susceptibility 2 (mouse)10126289265Mouse
1300759Geot_mgeotaxia (mouse)Not determined10126289265Mouse
1300881Sluc29_msusceptibility to lung cancer 29 (mouse)Not determined10126289265Mouse
12879494Facq1_mfear acquisition QTL 1 (mouse)10131279130Mouse
15039341Nmrs28_mNAFLD-associated magnetic resonance shift 28 (mouse)1035100134351001Mouse
1357813Ath20_matherosclerosis 20 (mouse)Not determined10328318537283334Mouse
1300790Pgia6_mproteoglycan induced arthritis 6 (mouse)Not determined10381017137810295Mouse
1300997Eae15_msusceptibility to experimental allergic encephalomyelitis 15 (mouse)Not determined10440815438408276Mouse
13208561Wght8_mweight 8 (mouse)10495000043875996Mouse
1302092Ath11_matherosclerosis 11 (mouse)Not determined10615194558693521Mouse
1357740Obsty3_mobesity 3 (mouse)Not determined108235478116190980Mouse
1558865Lith21_mlithogenic gene 21 (mouse)Not determined10852500342525126Mouse
1301796Mop2_mmorphine preference 2 (mouse)Not determined10928911929028424Mouse
1301448Pas11_mpulmonary adenoma susceptibility 11 (mouse)Not determined10989026443890391Mouse
1301129Alcp15_malcohol preference locus 15 (mouse)Not determined10989026443890391Mouse
1302133Alcp16_malcohol preference locus 16 (mouse)Not determined10989026443890391Mouse
1301386Sysbp1_msystolic blood pressure 1 (mouse)Not determined101010826587401095Mouse
1357825Kidpq2_mkidney weight percentage QTL 2 (mouse)Not determined101270405184079784Mouse
1357656Hrtq3_mheart weight QTL 3 (mouse)Not determined101270405184079784Mouse
1357864Scfpq1_msubcutaneous fat pad percentage QTL 1 (mouse)Not determined101270405184079784Mouse
39128215Lwq17_mliver weight QTL 17 (mouse)101270405184079784Mouse
4141956Egq7_mearly growth QTL 7 (mouse)Not determined1270405184079784Mouse
4141943W6q6_mweight 6 weeks QTL 6 (mouse)Not determined1270405184079784Mouse
4142272W10q5_mweight 10 weeks QTL 5 (mouse)Not determined1270405184079784Mouse
4142380W3q11_mweight 3 weeks QTL 11 (mouse)Not determined1270405184079784Mouse
13208570Bmiq9_mbody mass index QTL 9 (mouse)101287574424875898Mouse
1558857Igan1_mIgA nephropathy 1 (mouse)Not determined101771831329704155Mouse

Markers in Region
AI480677  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381018,213,783 - 18,213,968UniSTSGRCm38
MGSCv371017,933,589 - 17,933,774UniSTSGRCm37
Celera1018,113,071 - 18,113,256UniSTS
Cytogenetic Map10A3UniSTS
Whitehead/MRC_RH10195.75UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000052648   ⟹   ENSMUSP00000050107
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,092,532 - 18,110,726 (-)Ensembl
GRCm38.p6 Ensembl1018,216,784 - 18,234,978 (-)Ensembl
RefSeq Acc Id: ENSMUST00000080860   ⟹   ENSMUSP00000079671
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,089,424 - 18,110,744 (-)Ensembl
GRCm38.p6 Ensembl1018,213,676 - 18,234,996 (-)Ensembl
RefSeq Acc Id: ENSMUST00000173243   ⟹   ENSMUSP00000133585
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,089,826 - 18,110,746 (-)Ensembl
GRCm38.p6 Ensembl1018,214,078 - 18,234,998 (-)Ensembl
RefSeq Acc Id: ENSMUST00000173962   ⟹   ENSMUSP00000133848
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,089,806 - 18,095,362 (-)Ensembl
GRCm38.p6 Ensembl1018,214,058 - 18,219,614 (-)Ensembl
RefSeq Acc Id: ENSMUST00000174592   ⟹   ENSMUSP00000134307
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,089,430 - 18,103,221 (-)Ensembl
GRCm38.p6 Ensembl1018,213,682 - 18,227,473 (-)Ensembl
RefSeq Acc Id: ENSMUST00000174631
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1018,089,523 - 18,092,083 (-)Ensembl
GRCm38.p6 Ensembl1018,213,775 - 18,216,335 (-)Ensembl
RefSeq Acc Id: NM_001346751   ⟹   NP_001333680
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391018,092,675 - 18,110,729 (-)NCBI
GRCm381018,216,927 - 18,234,981 (-)NCBI
Sequence:
RefSeq Acc Id: NM_144820   ⟹   NP_659069
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391018,089,424 - 18,110,729 (-)NCBI
GRCm381018,213,676 - 18,234,981 (-)NCBI
MGSCv371017,933,491 - 17,954,787 (-)RGD
Celera1018,112,973 - 18,144,756 (-)RGD
cM Map10 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_030245002   ⟹   XP_030100862
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391018,089,424 - 18,110,733 (-)NCBI
GRCm381018,213,678 - 18,235,805 (-)NCBI
Sequence:
RefSeq Acc Id: XR_003948656
Type: NON-CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391018,089,426 - 18,110,940 (-)NCBI
GRCm381018,213,678 - 18,235,805 (-)NCBI
Sequence:
RefSeq Acc Id: NP_659069   ⟸   NM_144820
- Peptide Label: isoform 1
- UniProtKB: Q3UFK1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_030100862   ⟸   XM_030245002
- Peptide Label: isoform X1
- UniProtKB: G3UX80 (UniProtKB/TrEMBL),   G3UZ16 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001333680   ⟸   NM_001346751
- Peptide Label: isoform 2
- UniProtKB: Q8CEI3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSMUSP00000050107   ⟸   ENSMUST00000052648
RefSeq Acc Id: ENSMUSP00000134307   ⟸   ENSMUST00000174592
RefSeq Acc Id: ENSMUSP00000133585   ⟸   ENSMUST00000173243
RefSeq Acc Id: ENSMUSP00000079671   ⟸   ENSMUST00000080860
RefSeq Acc Id: ENSMUSP00000133848   ⟸   ENSMUST00000173962

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8CEI3-F1-model_v2 AlphaFold Q8CEI3 1-192 view protein structure

Promoters
RGD ID:6819352
Promoter ID:MM_KWN:3617
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:AK133237_GM10827,   NM_144820,   UC007EMF.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361017,954,579 - 17,955,079 (+)MPROMDB
RGD ID:8671548
Promoter ID:EPDNEW_M13805
Type:initiation region
Name:Ccdc28a_1
Description:Mus musculus coiled-coil domain containing 28A , transcript variant2, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381018,234,949 - 18,235,009EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2443508 AgrOrtholog
Ensembl Genes ENSMUSG00000059554 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000052648 ENTREZGENE
  ENSMUST00000052648.9 UniProtKB/TrEMBL
  ENSMUST00000080860 ENTREZGENE
  ENSMUST00000080860.13 UniProtKB/TrEMBL
  ENSMUST00000173243 ENTREZGENE
  ENSMUST00000173243.8 UniProtKB/TrEMBL
  ENSMUST00000173962.2 UniProtKB/TrEMBL
  ENSMUST00000174592.8 UniProtKB/TrEMBL
InterPro DUF4061 UniProtKB/TrEMBL
KEGG Report mmu:215814 UniProtKB/TrEMBL
MGD MGI:2443508 ENTREZGENE
NCBI Gene 215814 ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 28A UniProtKB/TrEMBL
  PTHR13400 UniProtKB/TrEMBL
Pfam DUF4061 UniProtKB/TrEMBL
PhenoGen Ccdc28a PhenoGen
UniProt G3UX80 ENTREZGENE, UniProtKB/TrEMBL
  G3UXW3_MOUSE UniProtKB/TrEMBL
  G3UZ16 ENTREZGENE, UniProtKB/TrEMBL
  Q3UFK1 ENTREZGENE, UniProtKB/TrEMBL
  Q8C8I4_MOUSE UniProtKB/TrEMBL
  Q8CEI3 ENTREZGENE, UniProtKB/TrEMBL