Tmco5b (transmembrane and coiled-coil domains 5B) - Rat Genome Database

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Gene: Tmco5b (transmembrane and coiled-coil domains 5B) Rattus norvegicus
Analyze
Symbol: Tmco5b
Name: transmembrane and coiled-coil domains 5B
RGD ID: 1561237
Description: Predicted to be located in membrane. Orthologous to human TMCO5B (transmembrane and coiled-coil domains 5B (pseudogene)); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; endosulfan; gentamycin.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC366158; RGD1561237; similar to RIKEN cDNA 1700095F04; transmembrane and coiled-coil domain-containing protein 5B
RGD Orthologs
Human
Mouse
Dog
Pig
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83120,510,255 - 120,537,504 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3120,519,323 - 120,537,501 (+)EnsemblGRCr8
mRatBN7.23100,055,744 - 100,083,303 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3100,064,979 - 100,083,289 (+)EnsemblmRatBN7.2
Rnor_6.03104,721,643 - 104,765,179 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3104,749,051 - 104,765,436 (+)Ensemblrn6Rnor6.0
Rnor_5.03111,325,104 - 111,350,522 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4399,125,476 - 99,145,772 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera399,018,885 - 99,063,113 (+)NCBICelera
Cytogenetic Map3q35NCBI
JBrowse:




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

Cellular Component
membrane  (IEA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Tmco5b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83120,510,255 - 120,537,504 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3120,519,323 - 120,537,501 (+)EnsemblGRCr8
mRatBN7.23100,055,744 - 100,083,303 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3100,064,979 - 100,083,289 (+)EnsemblmRatBN7.2
Rnor_6.03104,721,643 - 104,765,179 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3104,749,051 - 104,765,436 (+)Ensemblrn6Rnor6.0
Rnor_5.03111,325,104 - 111,350,522 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4399,125,476 - 99,145,772 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera399,018,885 - 99,063,113 (+)NCBICelera
Cytogenetic Map3q35NCBI
TMCO5B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381533,236,476 - 33,247,555 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1533,235,750 - 33,246,603 (-)Ensemblhg38GRCh38
GRCh371533,528,677 - 33,539,756 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361531,321,027 - 31,373,562 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1510,335,413 - 10,340,485 (-)NCBICelera
Cytogenetic Map15q13.3NCBI
HuRef1510,390,188 - 10,401,310 (-)NCBIHuRef
CHM1_11533,646,700 - 33,657,780 (-)NCBICHM1_1
T2T-CHM13v2.01531,032,972 - 31,044,045 (-)NCBIT2T-CHM13v2.0
Tmco5b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392113,115,440 - 113,127,535 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2113,116,077 - 113,127,535 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm382113,285,095 - 113,297,190 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2113,285,732 - 113,297,190 (+)Ensemblmm10GRCm38
MGSCv372113,125,889 - 113,137,347 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv362113,086,571 - 113,098,027 (+)NCBIMGSCv36mm8
Celera2114,433,765 - 114,445,240 (+)NCBICelera
Cytogenetic Map2E4NCBI
cM Map257.3NCBI
TMCO5B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1301,741,460 - 1,775,114 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha301,790,473 - 1,823,909 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0301,846,484 - 1,879,980 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl301,846,382 - 1,855,264 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1301,789,691 - 1,823,194 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0301,888,974 - 1,922,463 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0302,017,202 - 2,050,704 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
TMCO5B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1781,258,530 - 81,270,437 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2787,100,075 - 87,112,885 (+)NCBISscrofa10.2Sscrofa10.2susScr3

Variants

.
Variants in Tmco5b
246 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:140
Count of miRNA genes:108
Interacting mature miRNAs:117
Transcripts:ENSRNOT00000000010
Prediction methods:Microtar, Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301414Kidm37Kidney mass QTL 370.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)396509147141509147Rat
1582238Bw68Body weight QTL 683.20.0064body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582239Epfw1Epididymal fat weight QTL 14.50.0006epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)373592512136118980Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
1358362Srcrt2Stress Responsive Cort QTL 22.78blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)358601291153936591Rat
737818Hcar12Hepatocarcinoma resistance QTL 122.6liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)349872657138829559Rat
1582218Bw74Body weight QTL 743.90.0021body mass (VT:0001259)body weight (CMO:0000012)373592512136118980Rat
1582219Bw63Body weight QTL 633.80.001body mass (VT:0001259)body weight (CMO:0000012)3116582412136118980Rat
1582221Kidm30Kidney mass QTL 303.50.0008kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)385062224136118980Rat
1582210Bw71Body weight QTL 713.30.0012body mass (VT:0001259)body weight (CMO:0000012)385062224136118980Rat
7387306Bw124Body weight QTL 1243.20.0003body mass (VT:0001259)body weight (CMO:0000012)3104545086149545086Rat
1300111Rf12Renal function QTL 123.78renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)381425008141509147Rat
724523Tsu1Thymus enlargement suppressive QTL 13.84thymus mass (VT:0004954)thymus weight to body weight ratio (CMO:0000612)370845569136091483Rat
1600376Arunc5Aerobic running capacity QTL 50.21exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)393829559138829559Rat
8694437Bw167Body weight QTL 16722.460.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)3112250810157250810Rat
2302273Gluco35Glucose level QTL 355.30.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3101255536134750886Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1581503Cm58Cardiac mass QTL 582.70.05heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)396509147141509147Rat
1354611Despr2Despair related QTL 23.030.0028locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)3117537367162537367Rat
2292613Ept16Estrogen-induced pituitary tumorigenesis QTL 168.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
631649Bp123Blood pressure QTL 1233.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3110225882155225882Rat
631200Cm25Cardiac mass QTL 254.80.0001heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)381541464126563126Rat
12879848Bw181Body weght QTL 1810.015body mass (VT:0001259)body weight (CMO:0000012)390755164141509147Rat
1354597Kidm13Kidney mass QTL 132.9kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)342158111124558371Rat
1358885Bp251Blood pressure QTL 2513.8arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)31141509147Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
1582252Sual1Serum uric acid level QTL 13.40.0123blood uric acid amount (VT:0010302)blood uric acid level (CMO:0000501)3116582412122654872Rat
1354604Bw36Body weight QTL 362.9body mass (VT:0001259)body weight (CMO:0000012)342158111124558371Rat
1331758Bp207Blood pressure QTL 2072.848arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3110634702155634702Rat
1358888Bp264Blood pressure QTL 2644.43arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)35675975141509147Rat
1358186Ept2Estrogen-induced pituitary tumorigenesis QTL 28.3pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)367641995130815812Rat
724532Cm17Cardiac mass QTL 172heart mass (VT:0007028)calculated heart weight (CMO:0000073)3116188400161188400Rat

Markers in Region
D3Rat284  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.23100,068,197 - 100,068,403 (+)MAPPERmRatBN7.2
Rnor_6.03104,752,267 - 104,752,472NCBIRnor6.0
Rnor_5.03111,337,370 - 111,337,575UniSTSRnor5.0
RGSC_v3.4399,127,729 - 99,127,931RGDRGSC3.4
RGSC_v3.4399,127,730 - 99,127,935UniSTSRGSC3.4
Celera399,049,387 - 99,049,592UniSTS
RGSC_v3.1399,024,157 - 99,024,359RGD
FHH x ACI Map357.2899RGD
FHH x ACI Map357.2899UniSTS
Cytogenetic Map3q34UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
hemolymphoid system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
3 1 21 49 8 14 2 6 42 37 7 32 1 50 14 3 3

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001430665 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_001430666 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_190984 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_001080546 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008762110 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008775471 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592190 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017592192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602573 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602574 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017602575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106464 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039106465 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_575205 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CH473949 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000000010   ⟹   ENSRNOP00000000010
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3120,519,323 - 120,537,501 (+)Ensembl
mRatBN7.2 Ensembl3100,064,979 - 100,083,289 (+)Ensembl
Rnor_6.0 Ensembl3104,749,051 - 104,765,436 (+)Ensembl
RefSeq Acc Id: XM_017592191   ⟹   XP_017447680
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83120,510,255 - 120,537,504 (+)NCBI
mRatBN7.23100,055,744 - 100,083,303 (+)NCBI
Rnor_6.03104,739,961 - 104,765,179 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017592192   ⟹   XP_017447681
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83120,520,272 - 120,537,504 (+)NCBI
mRatBN7.23100,065,928 - 100,083,303 (+)NCBI
Rnor_6.03104,750,701 - 104,765,179 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039106464   ⟹   XP_038962392
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83120,519,298 - 120,536,014 (+)NCBI
mRatBN7.23100,064,881 - 100,081,675 (+)NCBI
RefSeq Acc Id: XM_039106465   ⟹   XP_038962393
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83120,519,297 - 120,523,982 (+)NCBI
mRatBN7.23100,064,438 - 100,069,642 (+)NCBI
RefSeq Acc Id: XM_575205   ⟹   XP_575205
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83120,519,298 - 120,537,504 (+)NCBI
mRatBN7.23100,064,957 - 100,083,303 (+)NCBI
Rnor_6.03104,749,048 - 104,765,179 (+)NCBI
Rnor_5.03111,325,104 - 111,350,522 (+)NCBI
RGSC_v3.4399,125,476 - 99,145,772 (+)RGD
Sequence:
RefSeq Acc Id: XP_575205   ⟸   XM_575205
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017447680   ⟸   XM_017592191
- Peptide Label: isoform X1
- UniProtKB: D3ZEL3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017447681   ⟸   XM_017592192
- Peptide Label: isoform X2
- Sequence:
Ensembl Acc Id: ENSRNOP00000000010   ⟸   ENSRNOT00000000010
RefSeq Acc Id: XP_038962393   ⟸   XM_039106465
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038962392   ⟸   XM_039106464
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEL3-F1-model_v2 AlphaFold D3ZEL3 1-307 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13692294
Promoter ID:EPDNEW_R2819
Type:single initiation site
Name:Tmco5b_1
Description:transmembrane and coiled-coil domains 5B
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.03104,749,070 - 104,749,130EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561237 AgrOrtholog
BioCyc Gene G2FUF-48369 BioCyc
Ensembl Genes ENSRNOG00000000009 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000000010 ENTREZGENE
  ENSRNOT00000000010.7 UniProtKB/TrEMBL
InterPro Tmco5 UniProtKB/TrEMBL
KEGG Report rno:366158 UniProtKB/TrEMBL
NCBI Gene 366158 ENTREZGENE
PANTHER PTHR22422 UniProtKB/TrEMBL
  TRANSMEMBRANE AND COILED-COIL DOMAIN-CONTAINING PROTEIN 5B UniProtKB/TrEMBL
Pfam TMCO5 UniProtKB/TrEMBL
PhenoGen Tmco5b PhenoGen
RatGTEx ENSRNOG00000000009 RatGTEx
UniProt D3ZEL3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2010-03-09 Tmco5b  transmembrane and coiled-coil domains 5B  RGD1561237  similar to RIKEN cDNA 1700095F04   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1561237  similar to RIKEN cDNA 1700095F04   RGD1561237_predicted  similar to RIKEN cDNA 1700095F04 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1561237_predicted  similar to RIKEN cDNA 1700095F04 (predicted)  LOC366158  similar to RIKEN cDNA 1700095F04  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC366158  similar to RIKEN cDNA 1700095F04      Symbol and Name status set to provisional 70820 PROVISIONAL