TRIM28 (tripartite motif containing 28) - Rat Genome Database

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Gene: TRIM28 (tripartite motif containing 28) Canis lupus familiaris
Analyze
Symbol: TRIM28
Name: tripartite motif containing 28
RGD ID: 12149260
Description: ENCODES a protein that exhibits chromatin binding (ortholog); chromo shadow domain binding (ortholog); DNA binding (ortholog); INVOLVED IN convergent extension involved in axis elongation (ortholog); DNA methylation involved in embryo development (ortholog); DNA repair (ortholog); PARTICIPATES IN p53 signaling pathway; ASSOCIATED WITH atherosclerosis (ortholog); Colorectal Neoplasms (ortholog); nephroblastoma (ortholog); FOUND IN chromatin (ortholog); euchromatin (ortholog); heterochromatin (ortholog)
Type: protein-coding
RefSeq Status: MODEL
Also known as: LOW QUALITY PROTEIN: transcription intermediary factor 1-beta; TIF1BETA; TIF1beta transcription factor; transcription intermediary factor 1-beta
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
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
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
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

Cellular Component

Molecular Pathway Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:10964405  


Genomics

Comparative Map Data
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
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
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1958,544,064 - 58,550,722 (+)EnsemblGRCh38hg38GRCh38
GRCh381958,544,064 - 58,550,722 (+)NCBIGRCh38GRCh38hg38GRCh38
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
(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
(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
(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 (+)NCBI
ChlSab1.1 Ensembl650,819,833 - 50,827,010 (+)Ensembl
Vero_WHO_p1.0NW_0236660454,125,654 - 4,132,206 (+)NCBI
Trim28
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462483249,324 - 56,113 (-)NCBI


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 reproductive system respiratory system adipose tissue
High
Medium 5 5 22 6 6 6 6 6 12 8 10 6
Low
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_014114858 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038466706 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038466707 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038466708 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038527428 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038527429 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038527430 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038591726 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038591727 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038591728 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038615494 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038615504 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038615529 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038655520 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038655521 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038655522 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AJ388515 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AY514779 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000010 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000354 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000001 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSCAFT00000003688
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl199,408,925 - 99,415,146 (-)Ensembl
RefSeq Acc Id: XM_014114858   ⟹   XP_013970333
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1199,408,920 - 99,415,432 (-)NCBI
Sequence:
RefSeq Acc Id: XM_038466706   ⟹   XP_038322634
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1199,667,398 - 99,673,683 (-)NCBI
RefSeq Acc Id: XM_038466707   ⟹   XP_038322635
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1199,667,398 - 99,673,683 (-)NCBI
RefSeq Acc Id: XM_038466708   ⟹   XP_038322636
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.1199,646,919 - 99,673,683 (-)NCBI
RefSeq Acc Id: XM_038527428   ⟹   XP_038383356
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01100,134,869 - 100,141,157 (-)NCBI
RefSeq Acc Id: XM_038527429   ⟹   XP_038383357
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01100,134,869 - 100,141,157 (-)NCBI
RefSeq Acc Id: XM_038527430   ⟹   XP_038383358
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.01100,114,388 - 100,141,157 (-)NCBI
RefSeq Acc Id: XM_038591726   ⟹   XP_038447654
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0199,380,228 - 99,386,515 (-)NCBI
RefSeq Acc Id: XM_038591727   ⟹   XP_038447655
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0199,380,228 - 99,386,515 (-)NCBI
RefSeq Acc Id: XM_038591728   ⟹   XP_038447656
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.0199,359,536 - 99,386,515 (-)NCBI
RefSeq Acc Id: XM_038615494   ⟹   XP_038471422
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha199,807,190 - 99,813,478 (-)NCBI
RefSeq Acc Id: XM_038615504   ⟹   XP_038471432
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha199,807,190 - 99,813,478 (-)NCBI
RefSeq Acc Id: XM_038615529   ⟹   XP_038471457
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
Dog10K_Boxer_Tasha199,786,699 - 99,813,478 (-)NCBI
RefSeq Acc Id: XM_038655520   ⟹   XP_038511448
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01100,022,035 - 100,028,322 (-)NCBI
RefSeq Acc Id: XM_038655521   ⟹   XP_038511449
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01100,022,035 - 100,028,322 (-)NCBI
RefSeq Acc Id: XM_038655522   ⟹   XP_038511450
RefSeq Status:
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.01100,001,554 - 100,028,322 (-)NCBI
Reference Sequences
RefSeq Acc Id: XP_013970333   ⟸   XM_014114858
- Sequence:
RefSeq Acc Id: XP_038322636   ⟸   XM_038466708
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038322635   ⟸   XM_038466707
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038322634   ⟸   XM_038466706
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038447656   ⟸   XM_038591728
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038447655   ⟸   XM_038591727
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038447654   ⟸   XM_038591726
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038511450   ⟸   XM_038655522
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038511449   ⟸   XM_038655521
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038511448   ⟸   XM_038655520
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038471457   ⟸   XM_038615529
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038471432   ⟸   XM_038615504
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038471422   ⟸   XM_038615494
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038383358   ⟸   XM_038527430
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038383357   ⟸   XM_038527429
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038383356   ⟸   XM_038527428
- Peptide Label: isoform X1

Promoters
RGD ID:13682133
Promoter ID:EPDNEW_C200
Type:multiple initiation site
Name:TRIM28_1
Description:tripartite motif containing 28
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1199,415,152 - 99,415,212EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000002354 Ensembl, ENTREZGENE
NCBI Gene TRIM28 ENTREZGENE
VGNC ID VGNC:47811 ENTREZGENE