Tma16 (translation machinery associated 16 homolog) - Rat Genome Database

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Gene: Tma16 (translation machinery associated 16 homolog) Rattus norvegicus
Analyze
Symbol: Tma16
Name: translation machinery associated 16 homolog
RGD ID: 1305222
Description: Predicted to enable preribosome binding activity. Predicted to be involved in ribosomal large subunit biogenesis. Predicted to be active in nucleus. Orthologous to human TMA16 (translation machinery associated 16 homolog); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC290686; LOC290686; RGD1305222; similar to RIKEN cDNA 1810029B16; translation machinery associated 16 homolog (S. cerevisiae); translation machinery-associated protein 16; uncharacterized protein LOC290686
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81628,003,002 - 28,021,875 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1627,980,900 - 28,021,875 (+)EnsemblGRCr8
mRatBN7.21623,236,686 - 23,252,706 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1623,236,710 - 23,252,701 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1626,600,245 - 26,616,118 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01630,034,957 - 30,050,830 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01625,973,554 - 25,989,442 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01624,978,429 - 24,997,286 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1624,978,527 - 24,997,006 (+)Ensemblrn6Rnor6.0
Rnor_5.01624,862,100 - 24,880,952 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41624,948,510 - 24,964,415 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1623,353,072 - 23,368,380 (+)NCBICelera
RGSC_v3.11624,948,468 - 24,964,413 (+)NCBI
Cytogenetic Map16p14NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
nucleolus  (ISO)
nucleoplasm  (ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:12947022   PMID:21630459  


Genomics

Comparative Map Data
Tma16
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81628,003,002 - 28,021,875 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1627,980,900 - 28,021,875 (+)EnsemblGRCr8
mRatBN7.21623,236,686 - 23,252,706 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1623,236,710 - 23,252,701 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx1626,600,245 - 26,616,118 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01630,034,957 - 30,050,830 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01625,973,554 - 25,989,442 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.01624,978,429 - 24,997,286 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1624,978,527 - 24,997,006 (+)Ensemblrn6Rnor6.0
Rnor_5.01624,862,100 - 24,880,952 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.41624,948,510 - 24,964,415 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1623,353,072 - 23,368,380 (+)NCBICelera
RGSC_v3.11624,948,468 - 24,964,413 (+)NCBI
Cytogenetic Map16p14NCBI
TMA16
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh384163,494,690 - 163,520,539 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl4163,494,442 - 163,520,733 (+)Ensemblhg38GRCh38
GRCh374164,415,842 - 164,441,691 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 364164,635,123 - 164,661,141 (+)NCBIBuild 36Build 36hg18NCBI36
Celera4161,747,938 - 161,773,962 (+)NCBICelera
Cytogenetic Map4q32.2NCBI
HuRef4160,169,554 - 160,195,568 (+)NCBIHuRef
CHM1_14164,392,123 - 164,418,141 (+)NCBICHM1_1
T2T-CHM13v2.04166,842,563 - 166,868,413 (+)NCBIT2T-CHM13v2.0
Tma16
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39866,928,995 - 66,939,182 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl866,925,770 - 66,939,182 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38866,476,343 - 66,486,530 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl866,473,118 - 66,486,530 (-)Ensemblmm10GRCm38
MGSCv37869,000,245 - 69,010,406 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36869,405,335 - 69,415,496 (-)NCBIMGSCv36mm8
Celera869,032,446 - 69,042,622 (-)NCBICelera
Cytogenetic Map8B3.1NCBI
cM Map833.14NCBI
Tma16
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540341,493,413 - 41,510,183 (-)Ensembl
ChiLan1.0NW_00495540341,493,624 - 41,510,162 (-)NCBIChiLan1.0ChiLan1.0
TMA16
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v23161,309,969 - 161,336,250 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan14161,670,138 - 161,698,713 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v04155,760,991 - 155,787,410 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.14167,549,482 - 167,575,665 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl4167,549,943 - 167,575,167 (+)EnsemblpanPan2panpan1.1
TMA16
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11559,720,318 - 59,751,236 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1559,719,633 - 59,750,553 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1560,085,103 - 60,119,190 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01560,479,568 - 60,513,614 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1560,479,635 - 60,509,857 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11559,712,916 - 59,746,653 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01559,804,119 - 59,837,895 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01560,173,264 - 60,207,047 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Tma16
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494316,452,153 - 16,469,248 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365552,102,183 - 2,118,365 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_0049365552,100,958 - 2,118,340 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TMA16
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl852,343,233 - 52,375,044 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1852,343,207 - 52,371,367 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2855,470,791 - 55,498,960 (+)NCBISscrofa10.2Sscrofa10.2susScr3
TMA16
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.17109,944,195 - 109,970,599 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl7109,944,567 - 109,970,593 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603789,768,650 - 89,794,813 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Tma16
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462475813,326,356 - 13,345,246 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Tma16
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11322,767,796 - 22,783,870 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Tma16
127 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:25
Count of miRNA genes:24
Interacting mature miRNAs:25
Transcripts:ENSRNOT00000019363
Prediction methods: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
7411664Foco30Food consumption QTL 30110.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)16435482249354822Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)longest distance run on treadmill (CMO:0001406)1638712345387123Rat
1549842Bp248Blood pressure QTL 2480.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1638712345387123Rat
70183BpQTLcluster13Blood pressure QTL cluster 133.654arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)16423421249757901Rat
2307172Activ4Activity QTL 43.710.00023locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)16133425095Rat
737826Alc11Alcohol consumption QTL 113.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)16423421266955197Rat
1354584Despr6Despair related QTL 63.10.0067locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16139568015Rat
2303566Bw90Body weight QTL 902body mass (VT:0001259)body weight (CMO:0000012)16139568015Rat
737819Hcas4Hepatocarcinoma susceptibility QTL 44.43liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)16423421253708481Rat
2312663Slep9Serum leptin concentration QTL 90.001blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)1683908666195506Rat
2306902Bp339Blood pressure QTL 3390.01arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)16338679049757901Rat
1354625Despr7Despair related QTL 73.160.016locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)16474422249744222Rat
2312660Bw95Body weight QTL 950.05inguinal fat pad mass (VT:0010424)inguinal fat pad weight to body weight ratio (CMO:0001253)1683908666195506Rat
2312666Insul16Insulin level QTL 160.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1683908666195506Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161773081872536785Rat
2293343Glom16Glomerulus QTL 167.4kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1683908652786090Rat
2301406Kidm39Kidney mass QTL 390.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)161590580260905802Rat
2312669Stl23Serum triglyceride level QTL 230.01blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1683908666195506Rat
6903319Bw114Body weight QTL 1142.70.0037body mass (VT:0001259)body weight (CMO:0000012)16330168348301683Rat

Markers in Region
AI137380  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21623,252,408 - 23,252,590 (+)MAPPERmRatBN7.2
Rnor_6.01626,071,675 - 26,071,856NCBIRnor6.0
Rnor_6.01624,994,427 - 24,994,608NCBIRnor6.0
Rnor_5.01625,957,381 - 25,957,562UniSTSRnor5.0
Rnor_5.01624,878,093 - 24,878,274UniSTSRnor5.0
RGSC_v3.41624,964,123 - 24,964,304UniSTSRGSC3.4
Celera1623,368,088 - 23,368,269UniSTS
RH 3.4 Map16278.31UniSTS
Cytogenetic Map16p14UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 165 91 90 59 92 59 6 356 192 11 144 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000019363   ⟹   ENSRNOP00000019363
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1623,236,710 - 23,252,697 (+)Ensembl
Rnor_6.0 Ensembl1624,978,527 - 24,994,718 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000082142   ⟹   ENSRNOP00000069283
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1624,980,723 - 24,997,006 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000111818   ⟹   ENSRNOP00000090655
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1623,236,732 - 23,252,701 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000115829   ⟹   ENSRNOP00000079522
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1623,241,005 - 23,252,701 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000142434   ⟹   ENSRNOP00000101321
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1628,003,365 - 28,021,875 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000152684   ⟹   ENSRNOP00000105532
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1628,005,490 - 28,021,875 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000154342   ⟹   ENSRNOP00000100908
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1627,980,900 - 28,021,875 (+)Ensembl
RefSeq Acc Id: NM_001169102   ⟹   NP_001162573
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81628,003,405 - 28,019,309 (+)NCBI
mRatBN7.21623,236,797 - 23,252,701 (+)NCBI
Rnor_6.01624,978,815 - 24,994,719 (+)NCBI
Rnor_5.01624,862,100 - 24,880,952 (+)NCBI
RGSC_v3.41624,948,510 - 24,964,415 (+)RGD
Celera1623,353,072 - 23,368,380 (+)RGD
Sequence:
RefSeq Acc Id: XM_017600038   ⟹   XP_017455527
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81628,003,002 - 28,021,875 (+)NCBI
mRatBN7.21623,236,894 - 23,252,706 (+)NCBI
Rnor_6.01624,978,870 - 24,997,286 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001162573 (Get FASTA)   NCBI Sequence Viewer  
  XP_017455527 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL75964 (Get FASTA)   NCBI Sequence Viewer  
  EDL75965 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000100908.1
  ENSRNOP00000101321
  ENSRNOP00000101321.1
  ENSRNOP00000105532.1
RefSeq Acc Id: NP_001162573   ⟸   NM_001169102
- UniProtKB: D4AAG0 (UniProtKB/TrEMBL),   A0A8I6AC99 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017455527   ⟸   XM_017600038
- Peptide Label: isoform X1
- UniProtKB: A0A8I6AC99 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000069283   ⟸   ENSRNOT00000082142
Ensembl Acc Id: ENSRNOP00000019363   ⟸   ENSRNOT00000019363
Ensembl Acc Id: ENSRNOP00000079522   ⟸   ENSRNOT00000115829
Ensembl Acc Id: ENSRNOP00000090655   ⟸   ENSRNOT00000111818
Ensembl Acc Id: ENSRNOP00000100908   ⟸   ENSRNOT00000154342
Ensembl Acc Id: ENSRNOP00000101321   ⟸   ENSRNOT00000142434
Ensembl Acc Id: ENSRNOP00000105532   ⟸   ENSRNOT00000152684

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAG0-F1-model_v2 AlphaFold D4AAG0 1-221 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305222 AgrOrtholog
BioCyc Gene G2FUF-11657 BioCyc
Ensembl Genes ENSRNOG00000014188 Ensembl
  ENSRNOG00000089425 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000142434 ENTREZGENE
  ENSRNOT00000142434.1 UniProtKB/TrEMBL
  ENSRNOT00000152684.1 UniProtKB/TrEMBL
  ENSRNOT00000154342.1 UniProtKB/TrEMBL
NCBI Gene 290686 ENTREZGENE
PhenoGen Tma16 PhenoGen
RatGTEx ENSRNOG00000014188 RatGTEx
  ENSRNOG00000089425 RatGTEx
UniProt A0A8I6AC99 ENTREZGENE
  A0ABK0L6K6_RAT UniProtKB/TrEMBL
  A0ABK0L7W5_RAT UniProtKB/TrEMBL
  A0ABK0L9R2_RAT UniProtKB/TrEMBL
  D4AAG0 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-10-01 Tma16  translation machinery associated 16 homolog  Tma16  translation machinery associated 16 homolog (S. cerevisiae)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-10-10 Tma16  translation machinery associated 16 homolog (S. cerevisiae)  RGD1305222  similar to RIKEN cDNA 1810029B16  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 RGD1305222  similar to RIKEN cDNA 1810029B16   RGD1305222_predicted  similar to RIKEN cDNA 1810029B16 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-20 RGD1305222_predicted  similar to RIKEN cDNA 1810029B16 (predicted)  LOC290686_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290686_predicted  similar to RIKEN cDNA 1810029B16 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL