Hdgfl2 (HDGF like 2) - Rat Genome Database
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Gene: Hdgfl2 (HDGF like 2) Rattus norvegicus
Analyze
Symbol: Hdgfl2
Name: HDGF like 2
RGD ID: 621013
Description: Predicted to have chromatin binding activity; double-stranded DNA binding activity; and transcription coregulator activity. Predicted to be involved in positive regulation of cell growth and regulation of transcription by RNA polymerase II. Predicted to localize to nucleus. Orthologous to human HDGFL2 (HDGF like 2); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: HDGF-3; Hdgf2; Hdgfrp2; hepatoma-derived growth factor 3; hepatoma-derived growth factor, related protein 2; hepatoma-derived growth factor-related protein 2; HRP-2; MGC105333
Orthologs:
Homo sapiens (human) : HDGFL2 (HDGF like 2)  HGNC  Alliance
Mus musculus (house mouse) : Hdgfl2 (HDGF like 2)  MGI  Alliance
Chinchilla lanigera (long-tailed chinchilla) : Hdgfl2 (HDGF like 2)
Pan paniscus (bonobo/pygmy chimpanzee) : HDGFL2 (HDGF like 2)
Canis lupus familiaris (dog) : HDGFL2 (HDGF like 2)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Hdgfl2 (HDGF like 2)
Sus scrofa (pig) : HDGFL2 (HDGF like 2)
Chlorocebus sabaeus (African green monkey) : HDGFL2 (HDGF like 2)
Heterocephalus glaber (naked mole-rat) : Hdgfl2 (HDGF like 2)
more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0910,972,342 - 10,991,938 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,972,351 - 10,991,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,959,289 - 9,978,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,577,663 - 7,597,323 (-)NCBICelera
Cytogenetic Map9q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Biological Process

Cellular Component
nucleus  (IBA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:16430771   PMID:22212508   PMID:25689719   PMID:26252862  


Genomics

Comparative Map Data
Hdgfl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rnor_6.0910,972,342 - 10,991,938 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl910,972,351 - 10,991,927 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.099,959,289 - 9,978,889 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera97,577,663 - 7,597,323 (-)NCBICelera
Cytogenetic Map9q12NCBI
HDGFL2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl194,472,297 - 4,502,208 (+)EnsemblGRCh38hg38GRCh38
GRCh38194,472,297 - 4,502,220 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37194,472,255 - 4,502,223 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,423,255 - 4,453,223 (+)NCBINCBI36hg18NCBI36
Celera194,410,462 - 4,440,415 (+)NCBI
Cytogenetic Map19p13.3NCBI
HuRef194,234,125 - 4,263,759 (+)NCBIHuRef
CHM1_1194,471,778 - 4,502,393 (+)NCBICHM1_1
Hdgfl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,386,601 - 56,407,605 (+)NCBI
GRCm381756,079,599 - 56,100,605 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,079,634 - 56,100,607 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,219,080 - 56,240,019 (+)NCBIGRCm37mm9NCBIm37
MGSCv361755,672,950 - 55,693,889 (+)NCBImm8
Celera1759,498,318 - 59,519,257 (+)NCBICelera
Cytogenetic Map17DNCBI
Hdgfl2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554954,425,325 - 4,447,917 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554954,426,929 - 4,447,276 (-)NCBIChiLan1.0ChiLan1.0
HDGFL2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1194,439,561 - 4,471,421 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl194,440,491 - 4,471,212 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0193,489,986 - 3,521,935 (+)NCBIMhudiblu_PPA_v0panPan3
HDGFL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2055,204,868 - 55,224,528 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12055,204,861 - 55,224,543 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Hdgfl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365882,590,557 - 2,615,241 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HDGFL2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,332,106 - 74,357,016 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,331,891 - 74,357,037 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2274,824,918 - 74,850,041 (-)NCBISscrofa10.2Sscrofa10.2susScr3
HDGFL2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1 Ensembl64,200,077 - 4,230,731 (+)Ensembl
ChlSab1.164,200,031 - 4,230,941 (+)NCBI
Hdgfl2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248285,231,497 - 5,251,402 (-)NCBI

Position Markers
RH132982  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0910,972,086 - 10,972,280NCBIRnor6.0
Rnor_5.099,959,033 - 9,959,227UniSTSRnor5.0
Celera97,577,398 - 7,577,592UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
10054141Gmadr4Adrenal mass QTL 42.450.0074adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)9116520166Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9129467098Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9140383872Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9140383872Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9140383872Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1578675Bss17Bone structure and strength QTL 173.8femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)9190783415555026Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
61450Ciaa3CIA Autoantibody QTL 36.5blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)9572425425692342Rat
1331757Cdexp1CD45RC expression in CD8 T cells QTL 14.3CD8-positive T cell quantity (VT:0008077)blood CD45RChigh CD8 T cell count to CD45RClow CD8 T cell count ratio (CMO:0001990)91086939115509311Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:209
Count of miRNA genes:149
Interacting mature miRNAs:170
Transcripts:ENSRNOT00000073011
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 42 55 39 19 39 6 9 74 35 41 11 6
Low 1 2 2 2 2 2 2
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000073011   ⟹   ENSRNOP00000064555
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,972,351 - 10,991,820 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081441   ⟹   ENSRNOP00000070603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl910,972,804 - 10,991,927 (-)Ensembl
RefSeq Acc Id: NM_133548   ⟹   NP_598232
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,972,351 - 10,991,820 (-)NCBI
Rnor_5.099,959,289 - 9,978,889 (-)NCBI
Celera97,577,663 - 7,597,323 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244289   ⟹   XP_006244351
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,972,346 - 10,991,938 (-)NCBI
Rnor_5.099,959,289 - 9,978,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244290   ⟹   XP_006244352
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,972,346 - 10,991,938 (-)NCBI
Rnor_5.099,959,289 - 9,978,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244291   ⟹   XP_006244353
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0910,972,342 - 10,991,938 (-)NCBI
Rnor_5.099,959,289 - 9,978,889 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_598232   ⟸   NM_133548
- UniProtKB: Q925G1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006244353   ⟸   XM_006244291
- Peptide Label: isoform X3
- UniProtKB: Q925G1 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006244352   ⟸   XM_006244290
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_006244351   ⟸   XM_006244289
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000064555   ⟸   ENSRNOT00000073011
RefSeq Acc Id: ENSRNOP00000070603   ⟸   ENSRNOT00000081441
Protein Domains
PWWP

Transcriptome

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

Promoters
RGD ID:13696469
Promoter ID:EPDNEW_R6994
Type:multiple initiation site
Name:Hdgfl2_1
Description:HDGF like 2
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_6.0910,991,913 - 10,991,973EPDNEW

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
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
9 9959933 9959934 C T snv IS-Tlk/Kyo (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621013 AgrOrtholog
Ensembl Genes ENSRNOG00000049142 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064555 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000070603 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073011 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000081441 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.930.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7100147 IMAGE-MGC_LOAD
  IMAGE:7312553 IMAGE-MGC_LOAD
InterPro HDGF-rel_PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  HIVI-bd_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LEDGF_IBD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PWWP_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TFIIS/LEDGF_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:171073 UniProtKB/Swiss-Prot
MGC_CLONE MGC:105333 IMAGE-MGC_LOAD
  MGC:91504 IMAGE-MGC_LOAD
NCBI Gene 171073 ENTREZGENE
Pfam LEDGF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Hdgfl2 PhenoGen
PROSITE PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PWWP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF140576 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniGene Rn.29462 ENTREZGENE
UniProt A0A0G2JYC7_RAT UniProtKB/TrEMBL
  HDGR2_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q5PPH2 UniProtKB/Swiss-Prot
  Q68G63 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2017-05-02 Hdgfl2  HDGF like 2  Hdgfrp2  hepatoma-derived growth factor-related protein 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-08-02 Hdgfrp2  hepatoma-derived growth factor-related protein 2  Hdgf2  hepatoma-derived growth factor-related protein 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-04-29 Hdgf2  hepatoma-derived growth factor-related protein 2  Hdgfrp2  hepatoma-derived growth factor, related protein 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 Hdgfrp2  hepatoma-derived growth factor, related protein 2      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Hdgfrp2  hepatoma-derived growth factor, related protein 2      Symbol and Name status set to provisional 70820 PROVISIONAL