Trim28 (tripartite motif-containing 28) - Rat Genome Database

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Gene: Trim28 (tripartite motif-containing 28) Rattus norvegicus
Analyze
Symbol: Trim28
Name: tripartite motif-containing 28
RGD ID: 620289
Description: Predicted to enable several functions, including promoter-specific chromatin binding activity; protein domain specific binding activity; and ubiquitin-like protein transferase activity. Predicted to be involved in several processes, including defense response to other organism; positive regulation of DNA methylation-dependent heterochromatin assembly; and regulation of nucleobase-containing compound metabolic process. Predicted to act upstream of or within several processes, including negative regulation of nucleobase-containing compound metabolic process; negative regulation of single stranded viral RNA replication via double stranded DNA intermediate; and regulation of genetic imprinting. Predicted to be located in euchromatin; heterochromatin; and nucleus. Predicted to be part of RNA polymerase II transcription regulator complex. Predicted to be active in chromatin and nucleoplasm. Orthologous to human TRIM28 (tripartite motif containing 28); PARTICIPATES IN p53 signaling pathway; INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: E3 SUMO-protein ligase TRIM28; Kap1; KRAB-associated protein 1; Krip1; nuclear corepressor KAP-1; RING-type E3 ubiquitin transferase TIF1-beta; TIF1-beta; Tif1b; transcription intermediary factor 1-beta; tripartite motif protein 28; tripartite motif-containing protein 28
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2173,652,441 - 73,659,388 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl173,652,709 - 73,659,380 (+)Ensembl
Rnor_6.0165,544,369 - 65,551,043 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl165,544,373 - 65,551,043 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0166,355,602 - 66,362,276 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4172,892,399 - 72,899,070 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1172,973,571 - 72,973,906 (-)NCBI
Celera160,180,424 - 60,187,048 (-)NCBICelera
Cytogenetic Map1q12NCBI
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
(-)-epigallocatechin 3-gallate  (ISO)
(S)-nicotine  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-dichlorobenzene  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17alpha-ethynylestradiol  (EXP)
17beta-hydroxy-17-methylestra-4,9,11-trien-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-amino-14,16-dimethyloctadecan-3-ol  (ISO)
4-amino-2,6-dinitrotoluene  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
ammonium chloride  (EXP)
aphidicolin  (ISO)
aristolochic acid  (ISO)
arsenite(3-)  (ISO)
benzatropine  (ISO)
bisphenol A  (EXP,ISO)
bleomycin A2  (ISO)
C60 fullerene  (EXP)
caffeine  (ISO)
camptothecin  (ISO)
cannabidiol  (ISO)
captan  (ISO)
chromium(6+)  (ISO)
cisplatin  (ISO)
clofibrate  (ISO)
clozapine  (ISO)
cocaine  (EXP)
Cuprizon  (ISO)
deoxynivalenol  (ISO)
diazinon  (ISO)
dibutyl phthalate  (ISO)
dicrotophos  (ISO)
diethylstilbestrol  (EXP)
doxorubicin  (ISO)
elemental selenium  (ISO)
enzyme inhibitor  (ISO)
ethanol  (ISO)
folic acid  (ISO)
folpet  (ISO)
gentamycin  (EXP)
haloperidol  (ISO)
hydrogen peroxide  (ISO)
ivermectin  (ISO)
L-ascorbic acid  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
methotrexate  (ISO)
methyl methanesulfonate  (ISO)
miconazole  (ISO)
N-acetyl-L-cysteine  (ISO)
nicotine  (ISO)
paracetamol  (ISO)
pentachlorophenol  (ISO)
perfluorooctane-1-sulfonic acid  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
resveratrol  (ISO)
selenium atom  (ISO)
sodium dichromate  (ISO)
tetrachloromethane  (ISO)
thimerosal  (ISO)
thioacetamide  (EXP)
trichloroethene  (ISO)
uranium atom  (ISO)
valproic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:8769649   PMID:8986806   PMID:9016654   PMID:10562550   PMID:10653693   PMID:11226167   PMID:11331580   PMID:11331592   PMID:12477932   PMID:15469996   PMID:15882967   PMID:17178852  
PMID:17273560   PMID:17298944   PMID:17512541   PMID:18082607   PMID:18248090   PMID:19270682   PMID:19321449   PMID:20164836   PMID:21518874   PMID:22082260   PMID:22110054   PMID:22495301  
PMID:22681889   PMID:22801370   PMID:22871113   PMID:23665872   PMID:24623306   PMID:24625528   PMID:25002582   PMID:27029610   PMID:30053369  


Genomics

Comparative Map Data
Trim28
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2173,652,441 - 73,659,388 (+)NCBImRatBN7.2
mRatBN7.2 Ensembl173,652,709 - 73,659,380 (+)Ensembl
Rnor_6.0165,544,369 - 65,551,043 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl165,544,373 - 65,551,043 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0166,355,602 - 66,362,276 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4172,892,399 - 72,899,070 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1172,973,571 - 72,973,906 (-)NCBI
Celera160,180,424 - 60,187,048 (-)NCBICelera
Cytogenetic Map1q12NCBI
TRIM28
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381958,544,064 - 58,550,715 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1958,544,064 - 58,550,722 (+)EnsemblGRCh38hg38GRCh38
GRCh371959,055,431 - 59,062,082 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361963,747,648 - 63,753,894 (+)NCBINCBI36hg18NCBI36
Build 341963,747,647 - 63,753,894NCBI
Celera1956,099,015 - 56,105,261 (+)NCBI
Cytogenetic Map19q13.43NCBI
HuRef1955,366,200 - 55,372,319 (+)NCBIHuRef
CHM1_11959,049,665 - 59,055,911 (+)NCBICHM1_1
Trim28
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39712,758,079 - 12,764,959 (+)NCBIGRCm39mm39
GRCm39 Ensembl712,733,041 - 12,764,962 (+)Ensembl
GRCm38713,024,152 - 13,031,032 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl712,999,114 - 13,031,035 (+)EnsemblGRCm38mm10GRCm38
MGSCv37713,609,501 - 13,616,381 (+)NCBIGRCm37mm9NCBIm37
MGSCv36711,924,340 - 11,931,208 (+)NCBImm8
Celera710,651,338 - 10,658,223 (+)NCBICelera
Cytogenetic Map7A1NCBI
Trim28
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049555841,148,903 - 1,156,001 (+)NCBIChiLan1.0ChiLan1.0
TRIM28
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11964,369,979 - 64,377,144 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1964,371,477 - 64,377,144 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01955,557,130 - 55,563,802 (+)NCBIMhudiblu_PPA_v0panPan3
TRIM28
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1199,408,920 - 99,415,432 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl199,408,925 - 99,415,146 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha199,786,699 - 99,813,478 (-)NCBI
ROS_Cfam_1.01100,001,554 - 100,028,322 (-)NCBI
ROS_Cfam_1.0 Ensembl1100,022,040 - 100,028,984 (-)Ensembl
UMICH_Zoey_3.1199,646,919 - 99,673,683 (-)NCBI
UNSW_CanFamBas_1.0199,359,536 - 99,386,515 (-)NCBI
UU_Cfam_GSD_1.01100,114,388 - 100,141,157 (-)NCBI
Trim28
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118217,986,447 - 217,992,258 (-)NCBI
SpeTri2.0NW_004937062126,832 - 132,938 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TRIM28
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl663,094,648 - 63,101,532 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1663,094,382 - 63,101,532 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
TRIM28
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1650,820,188 - 50,826,376 (+)NCBIChlSab1.1chlSab2
ChlSab1.1 Ensembl650,819,833 - 50,827,010 (+)EnsemblChlSab1.1chlSab2
Vero_WHO_p1.0NW_0236660454,125,654 - 4,132,206 (+)NCBIVero_WHO_p1.0
Trim28
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462483249,324 - 56,113 (-)NCBIHetGla_female_1.0hetGla2

Position Markers
RH137168  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2173,659,062 - 73,659,270 (-)MAPPERmRatBN7.2
Rnor_6.0165,544,483 - 65,544,690NCBIRnor6.0
Rnor_5.0166,355,716 - 66,355,923UniSTSRnor5.0
RGSC_v3.4172,892,510 - 72,892,717UniSTSRGSC3.4
Celera160,180,535 - 60,180,742UniSTS
Cytogenetic Map1q21UniSTS
RH143061  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2173,648,021 - 73,648,135 (-)MAPPERmRatBN7.2
Rnor_6.0165,555,613 - 65,555,726NCBIRnor6.0
Rnor_5.0166,366,846 - 66,366,959UniSTSRnor5.0
RGSC_v3.4172,903,644 - 72,903,757UniSTSRGSC3.4
Celera160,191,344 - 60,191,457UniSTS
RH 3.4 Map4624.54UniSTS
Cytogenetic Map1q21UniSTS
RH126533  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2173,659,159 - 73,659,362 (-)MAPPERmRatBN7.2
Rnor_6.0165,544,391 - 65,544,593NCBIRnor6.0
Rnor_5.0166,355,624 - 66,355,826UniSTSRnor5.0
RGSC_v3.4172,892,418 - 72,892,620UniSTSRGSC3.4
Celera160,180,443 - 60,180,645UniSTS
Cytogenetic Map1q21UniSTS
Trim28  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21842,845,774 - 42,846,639 (+)MAPPERmRatBN7.2
Rnor_6.01843,889,372 - 43,890,236NCBIRnor6.0
Rnor_5.01446,101,219 - 46,102,083UniSTSRnor5.0
RGSC_v3.41844,661,266 - 44,662,130UniSTSRGSC3.4
Celera1841,074,256 - 41,075,120UniSTS
Cytogenetic Map18q11UniSTS
Cytogenetic Map1q21UniSTS
Cytogenetic Map14p11UniSTS


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554320Bmd1Bone mineral density QTL 112.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)150910886060548Rat
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15925874115540829Rat
1300167Hrtrt2Heart rate QTL 24.35heart pumping trait (VT:2000009)heart rate (CMO:0000002)11148131275088344Rat
2313062Bmd73Bone mineral density QTL 733.90.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)11148131282174945Rat
2313065Bss67Bone structure and strength QTL 673.10.0001tibia area (VT:1000281)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313069Bss68Bone structure and strength QTL 682.90.0001tibia size trait (VT:0100001)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
2313075Bss66Bone structure and strength QTL 663.40.0001tibia length (VT:0004357)tibia length (CMO:0000450)11148131282174945Rat
2313077Bss69Bone structure and strength QTL 693.50.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)11148131282174945Rat
2313092Bmd72Bone mineral density QTL 722.50.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)11148131282174945Rat
2313097Bss70Bone structure and strength QTL 703.50.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)11148131282174945Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)122340647102268831Rat
1331785Rf27Renal function QTL 274.643urine sodium amount (VT:0006274)urine sodium level (CMO:0000129)12887978078430678Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)130882023123479925Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132356093162846471Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13273727390665040Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)132737458199368955Rat
1354599Bw29Body weight QTL 293.460.001body mass (VT:0001259)body weight (CMO:0000012)13344984878449848Rat
1354643Foco2Food consumption QTL 27.170.0001eating behavior trait (VT:0001431)food intake rate (CMO:0000427)13344984878449848Rat
8552900Pigfal1Plasma insulin-like growth factor 1 level QTL 17.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
8552948Pigfal11Plasma insulin-like growth factor 1 level QTL 114.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)13483685879836858Rat
9589820Insglur3Insulin/glucose ratio QTL 310.750.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)13483685879836858Rat
1331732Srn4Serum renin concentration QTL 44.467renin activity (VT:0005581)plasma renin activity level (CMO:0000116)13523959878430678Rat
1331792Rf29Renal function QTL 294.589urine potassium amount (VT:0010539)urine potassium level (CMO:0000128)13523959878430678Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143284731118944897Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143284731118944897Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143284731118944897Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143284731118944897Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143284731118944897Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143284731118944897Rat
2302059Pia36Pristane induced arthritis QTL 363.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)14333300288333002Rat
1331778Rf28Renal function QTL 284.66urine potassium amount (VT:0010539)urine potassium excretion rate (CMO:0000761)14580314078430678Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)148963584144267916Rat
4889962Bss94Bone structure and strength QTL 943.8tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)14936146582174945Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14939317294393172Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149393172159356837Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149393289199050459Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15386304190532583Rat
4889919Bss86Bone structure and strength QTL 864.1tibia area (VT:1000281)tibia midshaft total cross-sectional area (CMO:0001715)15389511782174945Rat
4889929Bss87Bone structure and strength QTL 876.7tibia area (VT:1000281)tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)15389511782174945Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)15673266898773277Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)156949932101949932Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)157336763151090257Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)165789093115540829Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)166023617118608521Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)17219768090508767Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:130
Count of miRNA genes:98
Interacting mature miRNAs:107
Transcripts:ENSRNOT00000029996
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.


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 endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 43 57 41 19 41 8 11 74 35 41 11 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000029996   ⟹   ENSRNOP00000031061
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl173,652,709 - 73,659,380 (+)Ensembl
Rnor_6.0 Ensembl165,544,373 - 65,551,043 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000100960   ⟹   ENSRNOP00000090373
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl173,652,709 - 73,659,380 (+)Ensembl
RefSeq Acc Id: NM_053916   ⟹   NP_446368
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2173,652,709 - 73,659,381 (+)NCBI
Rnor_6.0165,544,372 - 65,551,043 (-)NCBI
Rnor_5.0166,355,602 - 66,362,276 (-)NCBI
RGSC_v3.4172,892,399 - 72,899,070 (-)RGD
Celera160,180,424 - 60,187,048 (-)RGD
Sequence:
RefSeq Acc Id: XM_006228108   ⟹   XP_006228170
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2173,652,441 - 73,659,388 (+)NCBI
Rnor_6.0165,544,369 - 65,551,039 (-)NCBI
Rnor_5.0166,355,602 - 66,362,276 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446368 (Get FASTA)   NCBI Sequence Viewer  
  XP_006228170 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAB51518 (Get FASTA)   NCBI Sequence Viewer  
  AAI66843 (Get FASTA)   NCBI Sequence Viewer  
  O08629 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446368   ⟸   NM_053916
- UniProtKB: O08629 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006228170   ⟸   XM_006228108
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000031061   ⟸   ENSRNOT00000029996
RefSeq Acc Id: ENSRNOP00000090373   ⟸   ENSRNOT00000100960
Protein Domains
Bromo

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08629-F1-model_v2 AlphaFold O08629 1-835 view protein structure

Transcriptome

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

Promoters
RGD ID:13689671
Promoter ID:EPDNEW_R196
Type:initiation region
Name:Trim28_2
Description:tripartite motif-containing 28
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R197  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0165,550,772 - 65,550,832EPDNEW
RGD ID:13689672
Promoter ID:EPDNEW_R197
Type:initiation region
Name:Trim28_1
Description:tripartite motif-containing 28
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R196  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0165,551,068 - 65,551,128EPDNEW

Strain Variation

Strain Sequence Variants (MRatBN7.2)
ACI/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
ACI/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN-Lx/CubMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/NHsdMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BN/SsN (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BUF/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH2/CubMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
BXH3/CubMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
DA/OlaHsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/DuCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
F344/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FHH/EurMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE16/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
FXLE18/Stm (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
GK/FarMcwi (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB10/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB2/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB20/IpcvMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB31/IpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
HXB4/IpcvMcwi (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LE/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEW/Crl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF10A/StmMcwi (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF11/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1A/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF1C/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF2B/Stm (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF3/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LEXF4/Stm (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LH/MavRrrcAek (2020)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LL/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
LN/MavRrrcAek (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Kwitek
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
M520/NRrrcMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MR/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
MWF/Hsd (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
PVG/Seac (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Japan
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHR/OlalpcvMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SHRSP/A3NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SR/JrHsd (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Envigo
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
SS/JrHsdMcwi (2019)
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Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: MCW
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WAG/RijCrl (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WKY/NCrl (2019)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: Charles River
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
WN/N (2020)
Visual CSV TAB Printer
Platform: GSPMC-Illumina-NovaSeq6000
Secondary Analysis: BWA_mem_v.0.7.17,_GATK_v.4.1.3.0
Breeder: NIH
Description: Dr. Mindy Dwinell - Hybrid rat diversity program
Damaging Variants


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 72898588 72898589 C G snv SS/JrHsdMcwi (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620289 AgrOrtholog
BioCyc Gene G2FUF-60692 BioCyc
Ensembl Genes ENSRNOG00000027487 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000031061 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000029996 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.920.10 UniProtKB/Swiss-Prot
  3.30.40.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9028761 IMAGE-MGC_LOAD
InterPro Bbox_C UniProtKB/Swiss-Prot
  Bromodomain UniProtKB/Swiss-Prot
  Bromodomain-like_sf UniProtKB/Swiss-Prot
  KAP1 UniProtKB/Swiss-Prot
  TIF1beta_RING-HC UniProtKB/Swiss-Prot
  Zinc_finger_PHD-type_CS UniProtKB/Swiss-Prot
  Znf_B-box UniProtKB/Swiss-Prot
  Znf_FYVE_PHD UniProtKB/Swiss-Prot
  Znf_PHD UniProtKB/Swiss-Prot
  Znf_PHD-finger UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
KEGG Report rno:116698 UniProtKB/Swiss-Prot
MGC_CLONE MGC:188735 IMAGE-MGC_LOAD
NCBI Gene 116698 ENTREZGENE
PANTHER PTHR25462:SF274 UniProtKB/Swiss-Prot
Pfam PHD UniProtKB/Swiss-Prot
  zf-B_box UniProtKB/Swiss-Prot
  zf-RING_5 UniProtKB/Swiss-Prot
PhenoGen Trim28 PhenoGen
PROSITE ZF_BBOX UniProtKB/Swiss-Prot
  ZF_PHD_1 UniProtKB/Swiss-Prot
  ZF_PHD_2 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
SMART BBC UniProtKB/Swiss-Prot
  BBOX UniProtKB/Swiss-Prot
  BROMO UniProtKB/Swiss-Prot
  PHD UniProtKB/Swiss-Prot
  RING UniProtKB/Swiss-Prot
Superfamily-SCOP SSF57903 UniProtKB/Swiss-Prot
UniProt O08629 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary B2RYN5 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-31 Trim28  tripartite motif-containing 28  Trim28  tripartite motif protein 28  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-02-26 Trim28  tripartite motif protein 28      Symbol and Name status set to approved 625702 APPROVED
2002-08-07 Trim28  tripartite motif protein 28      Symbol and Name status set to provisional 70820 PROVISIONAL