Hdgfl2 (HDGF like 2) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Hdgfl2 (HDGF like 2) Rattus norvegicus
Analyze
Symbol: Hdgfl2
Name: HDGF like 2
RGD ID: 621013
Description: Predicted to enable several functions, including chromatin binding activity; methylated histone binding activity; and transcription coregulator activity. Predicted to be involved in several processes, including positive regulation of cell growth; regulation of nucleobase-containing compound metabolic process; and skeletal muscle tissue regeneration. Located in cytoplasm and 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
Previously 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
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
mRatBN7.29909,581 - 929,195 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9909,614 - 929,186 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,356,830 - 1,376,171 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.096,703,386 - 6,722,855 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.095,661,867 - 5,681,208 (+)NCBIRnor_WKY
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 Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IDA)
nucleus  (IBA,IDA,IEA,ISO,ISS)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
5. Information Derived from GenBank Report RGD, Sept. 2003
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
7. Hepatoma-derived growth factor-2 is highly expressed during development and in spinal cord injury. Zhuang Z, etal., Mol Med Rep. 2015 Oct;12(4):6140-4. doi: 10.3892/mmr.2015.4195. Epub 2015 Aug 6.
Additional References at PubMed
PMID:16430771   PMID:22212508   PMID:25689719  


Genomics

Comparative Map Data
Hdgfl2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.29909,581 - 929,195 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl9909,614 - 929,186 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx91,356,830 - 1,376,171 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.096,703,386 - 6,722,855 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.095,661,867 - 5,681,208 (+)NCBIRnor_WKY
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
GRCh38194,472,297 - 4,502,207 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl194,472,297 - 4,502,208 (+)EnsemblGRCh38hg38GRCh38
GRCh37194,472,294 - 4,502,219 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36194,423,255 - 4,453,223 (+)NCBINCBI36Build 36hg18NCBI36
Celera194,410,462 - 4,440,415 (+)NCBICelera
Cytogenetic Map19p13.3NCBI
HuRef194,234,125 - 4,263,759 (+)NCBIHuRef
CHM1_1194,471,840 - 4,502,384 (+)NCBICHM1_1
T2T-CHM13v2.0194,455,746 - 4,485,666 (+)NCBIT2T-CHM13v2.0
Hdgfl2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391756,386,601 - 56,407,605 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1756,386,634 - 56,407,607 (+)EnsemblGRCm39 Ensembl
GRCm381756,079,599 - 56,100,605 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1756,079,634 - 56,100,607 (+)EnsemblGRCm38mm10GRCm38
MGSCv371756,219,080 - 56,240,019 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361755,672,950 - 55,693,889 (+)NCBIMGSCv36mm8
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_v0Mhudiblu_PPA_v0panPan3
HDGFL2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12055,204,861 - 55,224,543 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2055,204,868 - 55,224,528 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2054,933,184 - 54,956,226 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02055,863,117 - 55,886,396 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2055,849,820 - 55,886,379 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12054,925,065 - 54,947,720 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02055,405,613 - 55,428,631 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02055,604,586 - 55,627,320 (-)NCBIUU_Cfam_GSD_1.0
Hdgfl2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118215,219,517 - 215,248,069 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365882,590,329 - 2,618,604 (+)EnsemblSpeTri2.0
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 - 74,357,040 (-)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 - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.164,200,031 - 4,230,941 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl64,200,077 - 4,230,731 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660813,962,491 - 3,998,027 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Hdgfl2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248285,227,034 - 5,251,268 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248285,231,497 - 5,251,402 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Hdgfl2
17 total Variants
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.


QTLs in Region (mRatBN7.2)
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)9114209783Rat
70226Eae4Experimental allergic encephalomyelitis QTL 4nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)9125661317Rat
9589055Scfw5Subcutaneous fat weight QTL 55.550.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)9137999212Rat
7411592Foco8Food consumption QTL 87.40.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)9137999212Rat
9589158Gluco65Glucose level QTL 656.820.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)9137999212Rat
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9140594091Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9143718459Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9143718459Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9187073594Rat

Markers in Region
RH132982  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.29929,247 - 929,442 (-)MAPPERmRatBN7.2
Rnor_6.0910,972,086 - 10,972,280NCBIRnor6.0
Rnor_5.099,959,033 - 9,959,227UniSTSRnor5.0
Celera97,577,398 - 7,577,592UniSTS


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
mRatBN7.2 Ensembl9909,614 - 929,183 (+)Ensembl
Rnor_6.0 Ensembl910,972,351 - 10,991,820 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000081441   ⟹   ENSRNOP00000070603
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl9909,619 - 929,186 (+)Ensembl
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
mRatBN7.29909,707 - 929,177 (+)NCBI
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
mRatBN7.29909,586 - 929,195 (+)NCBI
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
mRatBN7.29909,585 - 929,195 (+)NCBI
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
mRatBN7.29909,586 - 929,195 (+)NCBI
Rnor_6.0910,972,342 - 10,991,938 (-)NCBI
Rnor_5.099,959,289 - 9,978,889 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039082995   ⟹   XP_038938923
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.29909,581 - 927,258 (+)NCBI
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
- UniProtKB: A0A8L2QVL5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000064555   ⟸   ENSRNOT00000073011
RefSeq Acc Id: ENSRNOP00000070603   ⟸   ENSRNOT00000081441
RefSeq Acc Id: XP_038938923   ⟸   XM_039082995
- Peptide Label: isoform X4
Protein Domains
PWWP

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q925G1-F1-model_v2 AlphaFold Q925G1 1-669 view protein structure

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621013 AgrOrtholog
BioCyc Gene G2FUF-28564 BioCyc
Ensembl Genes ENSRNOG00000049142 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000064555 ENTREZGENE
  ENSRNOP00000064555.2 UniProtKB/TrEMBL
  ENSRNOP00000070603 ENTREZGENE
  ENSRNOP00000070603.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000073011 ENTREZGENE
  ENSRNOT00000073011.3 UniProtKB/TrEMBL
  ENSRNOT00000081441 ENTREZGENE
  ENSRNOT00000081441.2 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
UniProt A0A0G2JYC7_RAT UniProtKB/TrEMBL
  A0A8L2QVL5 ENTREZGENE, 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