Ttc39b (tetratricopeptide repeat domain 39B) - Rat Genome Database

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Gene: Ttc39b (tetratricopeptide repeat domain 39B) Heterocephalus glaber
Analyze
Symbol: Ttc39b
Name: tetratricopeptide repeat domain 39B
RGD ID: 18932614
Description: INVOLVED IN cholesterol homeostasis (inferred); lipid metabolic process (inferred); negative regulation of cholesterol storage (inferred); ASSOCIATED WITH atherosclerosis (ortholog); genetic disease (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Previously known as: tetratricopeptide repeat protein 39B
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Latest Assembly: HetGla 1.0 - Naked Mole-Rat female 1.0 Assembly
Position:
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473619,349,599 - 19,480,039 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473619,304,586 - 19,480,182 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
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

Molecular Function

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
Ttc39b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473619,349,599 - 19,480,039 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473619,304,586 - 19,480,182 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2
TTC39B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38915,163,622 - 15,307,216 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl915,163,622 - 15,307,360 (-)EnsemblGRCh38hg38GRCh38
GRCh37915,163,620 - 15,307,214 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36915,161,561 - 15,297,244 (-)NCBINCBI36Build 36hg18NCBI36
Build 34915,161,560 - 15,297,244NCBI
Celera915,104,514 - 15,241,039 (-)NCBICelera
Cytogenetic Map9p22.3NCBI
HuRef915,134,002 - 15,270,023 (-)NCBIHuRef
CHM1_1915,171,189 - 15,307,662 (-)NCBICHM1_1
T2T-CHM13v2.0915,175,161 - 15,318,914 (-)NCBIT2T-CHM13v2.0
Ttc39b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39483,138,537 - 83,242,488 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl483,138,537 - 83,242,492 (-)EnsemblGRCm39 Ensembl
GRCm38483,220,300 - 83,324,309 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl483,220,300 - 83,324,255 (-)EnsemblGRCm38mm10GRCm38
MGSCv37482,866,205 - 82,970,093 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36482,698,073 - 82,795,420 (-)NCBIMGSCv36mm8
Celera481,749,116 - 81,852,836 (-)NCBICelera
Cytogenetic Map4C3NCBI
cM Map439.41NCBI
Ttc39b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr85102,649,259 - 102,754,092 (-)NCBIGRCr8
mRatBN7.2597,603,329 - 97,708,103 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl597,609,392 - 97,736,270 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx599,994,732 - 100,093,451 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.05101,787,468 - 101,886,060 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.05101,805,603 - 101,904,315 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.05101,304,982 - 101,405,689 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl5101,304,982 - 101,405,656 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.05105,325,543 - 105,422,721 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.45102,064,300 - 102,162,978 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.15102,082,312 - 102,168,201 (-)NCBI
Celera596,161,736 - 96,260,502 (-)NCBICelera
Cytogenetic Map5q31NCBI
Ttc39b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543418,070,536 - 18,150,858 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543418,063,520 - 18,150,858 (-)NCBIChiLan1.0ChiLan1.0
TTC39B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v211109,186,588 - 109,381,289 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan19109,192,529 - 109,387,237 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0914,994,729 - 15,127,877 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1915,502,811 - 15,633,374 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl915,502,811 - 15,633,374 (-)Ensemblpanpan1.1panPan2
TTC39B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11135,465,198 - 35,557,800 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1135,472,016 - 35,589,835 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1134,114,261 - 34,244,798 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01136,369,628 - 36,498,809 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1136,374,223 - 36,498,902 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11135,073,616 - 35,204,176 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01134,863,606 - 34,994,353 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01135,522,676 - 35,653,287 (-)NCBIUU_Cfam_GSD_1.0
Ttc39b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947150,190,771 - 150,314,021 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365398,646,074 - 8,695,765 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365398,644,456 - 8,766,696 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TTC39B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1207,347,360 - 207,495,965 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11207,347,345 - 207,490,753 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21231,160,107 - 231,280,020 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TTC39B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11264,315,240 - 64,452,161 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1264,372,763 - 64,450,973 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366603852,515,449 - 52,659,743 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0


Expression


Sequence

Nucleotide Sequences
RefSeq Transcripts XM_004838305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_004838307 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_004838308 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_021252866 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392484 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392485 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392486 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392487 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392488 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_002392489 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_204912 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AHKG01012838 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01012839 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01012840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01012841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01012842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AHKG01012843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSHGLT00000026274   ⟹   ENSHGLP00000026044
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462473619,349,599 - 19,480,039 (-)Ensembl
RefSeq Acc Id: ENSHGLT00000026275   ⟹   ENSHGLP00000026045
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla_female_1.0 EnsemblNW_00462473619,362,314 - 19,403,382 (-)Ensembl
RefSeq Acc Id: XM_004838305   ⟹   XP_004838362
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,342,394 - 19,480,179 (-)NCBI
RefSeq Acc Id: XM_004838307   ⟹   XP_004838364
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,304,586 - 19,480,182 (-)NCBI
RefSeq Acc Id: XM_004838308   ⟹   XP_004838365
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,643 - 19,480,181 (-)NCBI
RefSeq Acc Id: XM_021252866   ⟹   XP_021108525
Type: CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,643 - 19,480,181 (-)NCBI
RefSeq Acc Id: XR_002392484
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,649 - 19,480,179 (-)NCBI
RefSeq Acc Id: XR_002392485
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,649 - 19,480,179 (-)NCBI
RefSeq Acc Id: XR_002392486
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,649 - 19,480,179 (-)NCBI
RefSeq Acc Id: XR_002392487
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,649 - 19,480,110 (-)NCBI
RefSeq Acc Id: XR_002392488
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,646 - 19,424,815 (-)NCBI
RefSeq Acc Id: XR_002392489
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,646 - 19,480,092 (-)NCBI
RefSeq Acc Id: XR_204912
Type: NON-CODING
Position:
Naked Mole-Rat AssemblyChrPosition (strand)Source
HetGla 1.0NW_00462473619,323,643 - 19,480,182 (-)NCBI
Protein Sequences
Protein RefSeqs XP_004838362 (Get FASTA)   NCBI Sequence Viewer  
  XP_004838364 (Get FASTA)   NCBI Sequence Viewer  
  XP_004838365 (Get FASTA)   NCBI Sequence Viewer  
  XP_021108525 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSHGLP00000026044
Reference Protein Sequences
RefSeq Acc Id: XP_004838364   ⟸   XM_004838307
- Peptide Label: isoform X2
- UniProtKB: G5AP59 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_021108525   ⟸   XM_021252866
- Peptide Label: isoform X4
- UniProtKB: G5AP59 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004838365   ⟸   XM_004838308
- Peptide Label: isoform X3
- UniProtKB: G5AP59 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_004838362   ⟸   XM_004838305
- Peptide Label: isoform X1
- UniProtKB: G5AP59 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSHGLP00000026044   ⟸   ENSHGLT00000026274
RefSeq Acc Id: ENSHGLP00000026045   ⟸   ENSHGLT00000026275


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSHGLG00000018545 Ensembl, ENTREZGENE
Ensembl Transcript ENSHGLT00000026274 ENTREZGENE
Gene3D-CATH Tetratricopeptide repeat domain UniProtKB/TrEMBL
InterPro Iml2/TPR_39 UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/TrEMBL
  TPR_repeat UniProtKB/TrEMBL
NCBI Gene Ttc39b ENTREZGENE
PANTHER TETRATRICOPEPTIDE REPEAT PROTEIN 39 FAMILY MEMBER UniProtKB/TrEMBL
  TETRATRICOPEPTIDE REPEAT PROTEIN 39B UniProtKB/TrEMBL
Pfam Iml2-TPR_39 UniProtKB/TrEMBL
  TPR_6 UniProtKB/TrEMBL
Superfamily-SCOP TPR-like UniProtKB/TrEMBL
UniProt G5AP59 ENTREZGENE, UniProtKB/TrEMBL