CCDC88B (coiled-coil domain containing 88B) - Rat Genome Database

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Gene: CCDC88B (coiled-coil domain containing 88B) Sus scrofa
Analyze
Symbol: CCDC88B
Name: coiled-coil domain containing 88B
RGD ID: 14035505
Description: ENCODES a protein that exhibits dynein light intermediate chain binding (inferred); microtubule binding (inferred); INVOLVED IN defense response to protozoan (ortholog); positive regulation of cytokine production (ortholog); positive regulation of T cell activation (ortholog); ASSOCIATED WITH genetic disease (ortholog); high grade glioma (ortholog); intellectual disability (ortholog); FOUND IN cytosol (ortholog); membrane (ortholog); nucleoplasm (ortholog); INTERACTS WITH deoxynivalenol
Type: protein-coding
RefSeq Status: MODEL
Previously known as: coiled-coil domain-containing protein 88B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.127,767,924 - 7,784,625 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.226,992,400 - 7,010,214 (+)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
centrosome  (IEA)
cytoplasm  (IEA)
cytosol  (ISO)
membrane  (ISO)
nucleoplasm  (ISO)

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
CCDC88B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.127,767,924 - 7,784,625 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.226,992,400 - 7,010,214 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CCDC88B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381164,340,204 - 64,357,534 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1164,340,204 - 64,357,534 (+)EnsemblGRCh38hg38GRCh38
GRCh371164,107,676 - 64,125,006 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361163,864,271 - 63,881,582 (+)NCBINCBI36Build 36hg18NCBI36
Celera1161,433,773 - 61,451,010 (+)NCBICelera
Cytogenetic Map11q13.1NCBI
HuRef1160,435,387 - 60,452,709 (+)NCBIHuRef
CHM1_11163,990,713 - 64,008,023 (+)NCBICHM1_1
T2T-CHM13v2.01164,330,213 - 64,347,539 (+)NCBIT2T-CHM13v2.0
Ccdc88b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39196,821,991 - 6,835,586 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl196,821,991 - 6,835,579 (-)EnsemblGRCm39 Ensembl
GRCm38196,844,623 - 6,858,222 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl196,844,623 - 6,858,211 (-)EnsemblGRCm38mm10GRCm38
MGSCv37196,919,113 - 6,932,701 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36196,911,667 - 6,925,255 (-)NCBIMGSCv36mm8
Celera196,621,185 - 6,634,250 (-)NCBICelera
Cytogenetic Map19ANCBI
cM Map195.08NCBI
Ccdc88b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81213,466,139 - 213,482,099 (-)NCBIGRCr8
mRatBN7.21204,036,913 - 204,052,878 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1204,036,918 - 204,052,970 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.01222,102,436 - 222,118,485 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1222,102,437 - 222,118,459 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01229,093,019 - 229,108,951 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41209,520,224 - 209,536,201 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11209,678,880 - 209,708,626 (-)NCBI
Celera1201,571,162 - 201,587,460 (-)NCBICelera
Cytogenetic Map1q43NCBI
Ccdc88b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542220,738,645 - 20,750,945 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542220,738,202 - 20,751,016 (-)NCBIChiLan1.0ChiLan1.0
CCDC88B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2965,567,056 - 65,584,707 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11166,612,195 - 66,629,837 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01159,696,276 - 59,714,086 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11163,042,107 - 63,058,480 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1163,042,147 - 63,058,434 (+)Ensemblpanpan1.1panPan2
CCDC88B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11852,722,197 - 52,737,023 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1852,708,838 - 52,736,728 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1851,329,341 - 51,343,974 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01853,767,474 - 53,782,106 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1853,754,109 - 53,782,050 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11852,859,541 - 52,874,172 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01852,446,108 - 52,460,739 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01853,229,912 - 53,244,546 (-)NCBIUU_Cfam_GSD_1.0
Ccdc88b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049478,425,644 - 8,441,539 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365994,867,955 - 4,879,929 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365994,867,993 - 4,881,662 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LOC103233216
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.119,875,909 - 9,892,893 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl19,874,560 - 9,891,481 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023667676110 - 12,390 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ccdc88b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476721,973,147 - 21,987,317 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in CCDC88B
553 total Variants

Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium
Low 7 2 5 3 1 3
Below cutoff 3 1 1 9 1

Sequence


Reference Sequences
RefSeq Acc Id: XM_021082875   ⟹   XP_020938534
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.127,767,924 - 7,784,625 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_020938534 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSSSCP00055002053.1
GenBank Protein JAG69667 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: XP_020938534   ⟸   XM_021082875
- UniProtKB: A0A8D1PEZ8 (UniProtKB/TrEMBL)
- Sequence:
Protein Domains
HOOK N-terminal


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00055001451 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00055002713.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
InterPro CH_dom_sf UniProtKB/TrEMBL
  HOOK_N UniProtKB/TrEMBL
NCBI Gene CCDC88B ENTREZGENE
PANTHER COILED-COIL DOMAIN-CONTAINING PROTEIN 88B UniProtKB/TrEMBL
  HOOK PROTEINS UniProtKB/TrEMBL
Pfam HOOK_N UniProtKB/TrEMBL
Superfamily-SCOP Hook domain UniProtKB/TrEMBL
UniProt A0A8D1PEZ8 ENTREZGENE, UniProtKB/TrEMBL