Tgif1 (TGFB-induced factor homeobox 1) - Rat Genome Database
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Gene: Tgif1 (TGFB-induced factor homeobox 1) Rattus norvegicus
Analyze
Symbol: Tgif1
Name: TGFB-induced factor homeobox 1
RGD ID: 1310517
Description: Exhibits co-SMAD binding activity. Involved in cellular response to growth factor stimulus; negative regulation of gene expression; and response to drug. Localizes to nucleus. Biomarker of muscular atrophy. Human ortholog(s) of this gene implicated in holoprosencephaly and holoprosencephaly 4. Orthologous to human TGIF1 (TGFB induced factor homeobox 1); INTERACTS WITH (+)-schisandrin B; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: homeobox protein TGIF1; LOC316742; MGC109104; MGC156525; Tfig; TG interacting factor; TG interacting factor 1; Tgif
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.09119,181,079 - 119,190,698 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9119,181,083 - 119,190,698 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09118,636,415 - 118,646,034 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49110,043,164 - 110,052,783 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19110,252,647 - 110,262,263 (-)NCBI
Celera9107,878,776 - 107,888,395 (-)NCBICelera
Cytogenetic Map9q38NCBI
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
(+)-schisandrin B  (EXP)
(-)-epigallocatechin 3-gallate  (ISO)
1,1-dichloroethene  (ISO)
1,2-dimethylhydrazine  (ISO)
1,4-dichlorobenzene  (ISO)
1-chloro-2,4-dinitrobenzene  (ISO)
17beta-estradiol  (ISO)
2,2',4,4',5,5'-hexachlorobiphenyl  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2-methylcholine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
9-cis-retinoic acid  (ISO)
acetamide  (EXP)
acetylsalicylic acid  (ISO)
albendazole  (ISO)
all-trans-retinoic acid  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
bisphenol A  (EXP,ISO)
cadmium atom  (ISO)
carbamazepine  (ISO)
chlordecone  (ISO)
choline  (ISO)
ciglitazone  (ISO)
clofibrate  (ISO)
clofibric acid  (EXP)
copper atom  (ISO)
copper(0)  (ISO)
copper(II) sulfate  (ISO)
coumestrol  (ISO)
crocidolite asbestos  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dibutyl phthalate  (EXP,ISO)
dioxygen  (ISO)
disodium selenite  (ISO)
dorsomorphin  (ISO)
Enterolactone  (ISO)
fluoranthene  (ISO)
flusilazole  (ISO)
folic acid  (ISO)
formaldehyde  (ISO)
gentamycin  (EXP)
geraniol  (ISO)
glyphosate  (ISO)
iron atom  (EXP)
iron(0)  (EXP)
ivermectin  (ISO)
L-methionine  (ISO)
leflunomide  (ISO)
LY294002  (ISO)
mercury dichloride  (EXP)
methylparaben  (ISO)
N-acetylsphingosine  (ISO)
N-methyl-N-nitrosourea  (EXP)
N-nitrosodiethylamine  (EXP)
nickel sulfate  (ISO)
oxaliplatin  (ISO)
paracetamol  (ISO)
phenobarbital  (ISO)
phenol  (ISO)
pirinixic acid  (ISO)
piroxicam  (ISO)
potassium chromate  (ISO)
progesterone  (ISO)
resveratrol  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenite  (ISO)
sodium dichromate  (EXP)
Soman  (EXP)
tamibarotene  (ISO)
tetrachloromethane  (EXP,ISO)
theophylline  (ISO)
thioacetamide  (EXP)
trichostatin A  (ISO)
triphenyl phosphate  (EXP)
trovafloxacin  (ISO)
valproic acid  (ISO)
valsartan  (ISO)
vancomycin  (ISO)
wortmannin  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

References

Additional References at PubMed
PMID:10764806   PMID:16428452   PMID:16705179   PMID:16751776   PMID:17082251   PMID:18973577   PMID:20040491   PMID:21503901   PMID:25319900   PMID:25782868   PMID:26599628  


Genomics

Comparative Map Data
Tgif1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.09119,181,079 - 119,190,698 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl9119,181,083 - 119,190,698 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.09118,636,415 - 118,646,034 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.49110,043,164 - 110,052,783 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.19110,252,647 - 110,262,263 (-)NCBI
Celera9107,878,776 - 107,888,395 (-)NCBICelera
Cytogenetic Map9q38NCBI
TGIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl183,411,608 - 3,459,978 (+)EnsemblGRCh38hg38GRCh38
GRCh38183,412,009 - 3,459,978 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37183,411,925 - 3,458,409 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36183,402,072 - 3,448,409 (+)NCBINCBI36hg18NCBI36
Build 34183,402,071 - 3,448,404NCBI
Celera183,291,675 - 3,337,991 (+)NCBI
Cytogenetic Map18p11.31NCBI
HuRef183,376,674 - 3,423,225 (+)NCBIHuRef
CHM1_1183,411,321 - 3,457,803 (+)NCBICHM1_1
Tgif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391771,151,200 - 71,160,527 (-)NCBIGRCm39mm39
GRCm381770,844,205 - 70,853,532 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1770,844,205 - 70,853,546 (-)EnsemblGRCm38mm10GRCm38
MGSCv371771,193,545 - 71,202,872 (-)NCBIGRCm37mm9NCBIm37
MGSCv361770,749,072 - 70,756,055 (-)NCBImm8
Celera1775,106,130 - 75,115,447 (-)NCBICelera
Cytogenetic Map17E1.3NCBI
Tgif1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554027,129,484 - 7,138,340 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554027,130,809 - 7,138,945 (-)NCBIChiLan1.0ChiLan1.0
TGIF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11813,128,354 - 13,139,145 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1813,128,359 - 13,139,145 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01810,819,015 - 10,830,282 (-)NCBIMhudiblu_PPA_v0panPan3
TGIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1770,040,376 - 70,048,346 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Tgif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049366721,128,104 - 1,135,844 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
TGIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl6103,226,397 - 103,235,856 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.16103,226,395 - 103,234,591 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2696,252,966 - 96,261,029 (-)NCBISscrofa10.2Sscrofa10.2susScr3
TGIF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11862,691,705 - 62,698,265 (+)NCBI
Tgif1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477013,506,501 - 13,515,388 (+)NCBI

Position Markers
RH132854  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.09119,181,276 - 119,181,460NCBIRnor6.0
Rnor_5.09118,636,612 - 118,636,796UniSTSRnor5.0
RGSC_v3.49110,043,361 - 110,043,545UniSTSRGSC3.4
Celera9107,878,973 - 107,879,157UniSTS
Cytogenetic Map9q38UniSTS
RH 3.4 Map9870.2UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
1354626Bvd1Brain ventricular dilatation QTL 13.730.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)981411073119983851Rat
7794784Mcs31Mammary carcinoma susceptibility QTL 312.98mammary gland integrity trait (VT:0010552)mammary tumor incidence/prevalence measurement (CMO:0000946)990024661119983851Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:334
Count of miRNA genes:186
Interacting mature miRNAs:212
Transcripts:ENSRNOT00000021534
Prediction methods:Microtar, Miranda, 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 26 46 30 19 30 31 31 41 11
Low 17 11 11 11 8 11 43 4 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021534   ⟹   ENSRNOP00000021534
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl9119,181,083 - 119,190,698 (-)Ensembl
RefSeq Acc Id: NM_001015020   ⟹   NP_001015020
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.09119,181,079 - 119,190,698 (-)NCBI
Rnor_5.09118,636,415 - 118,646,034 (-)NCBI
RGSC_v3.49110,043,164 - 110,052,783 (-)RGD
Celera9107,878,776 - 107,888,395 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001015020 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91264 (Get FASTA)   NCBI Sequence Viewer  
  AAI27462 (Get FASTA)   NCBI Sequence Viewer  
  EDL90939 (Get FASTA)   NCBI Sequence Viewer  
  EDL90940 (Get FASTA)   NCBI Sequence Viewer  
  EDL90941 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001015020   ⟸   NM_001015020
- UniProtKB: Q5BJZ9 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021534   ⟸   ENSRNOT00000021534
Protein Domains
Homeobox

Transcriptome

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

Promoters
RGD ID:13696909
Promoter ID:EPDNEW_R7434
Type:multiple initiation site
Name:Tgif1_1
Description:TGFB-induced factor homeobox 1
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_6.09119,190,771 - 119,190,831EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310517 AgrOrtholog
Ensembl Genes ENSRNOG00000015906 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021534 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021534 ENTREZGENE, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7379061 IMAGE-MGC_LOAD
  IMAGE:7389058 IMAGE-MGC_LOAD
InterPro Homeobox UniProtKB/TrEMBL
  Homeobox_KN_domain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
KEGG Report rno:316742 UniProtKB/TrEMBL
MGC_CLONE MGC:109104 IMAGE-MGC_LOAD
  MGC:156525 IMAGE-MGC_LOAD
NCBI Gene 316742 ENTREZGENE
Pfam Coprinus_mating UniProtKB/TrEMBL
PharmGKB TGIF RGD
PhenoGen Tgif1 PhenoGen
PROSITE HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniGene Rn.154349 ENTREZGENE
UniProt Q5BJZ9 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-23 Tgif1  TGFB-induced factor homeobox 1  Tgif1  TG interacting factor 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-04 Tgif1  TG interacting factor 1  Tgif  TG interacting factor  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 Tgif  TG interacting factor  Tgif_predicted  TG interacting factor (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-12 Tgif_predicted  TG interacting factor (predicted)      Symbol and Name status set to approved 70820 APPROVED