Herpud2 (HERPUD family member 2) - Rat Genome Database

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Gene: Herpud2 (HERPUD family member 2) Rattus norvegicus
Analyze
Symbol: Herpud2
Name: HERPUD family member 2
RGD ID: 1307343
Description: Predicted to be involved in endoplasmic reticulum unfolded protein response and spermatogenesis. Predicted to be located in membrane. Orthologous to human HERPUD2 (HERPUD family member 2); INTERACTS WITH 4,4'-sulfonyldiphenol; bisphenol A; bisphenol F.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: homocysteine-responsive endoplasmic reticulum-resident ubiquitin-like domain member 2 protein; LOC300463; RGD1307343; similar to RIKEN cDNA 5031400M07
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8831,849,216 - 31,894,219 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl831,849,216 - 31,894,219 (-)EnsemblGRCr8
mRatBN7.2823,573,374 - 23,618,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl823,573,379 - 23,617,874 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx827,631,491 - 27,676,822 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0825,928,777 - 25,974,108 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0823,800,662 - 23,845,177 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0826,266,571 - 26,311,528 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl826,266,760 - 26,311,350 (-)Ensemblrn6Rnor6.0
Rnor_5.0826,289,918 - 26,335,435 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4824,777,333 - 24,821,665 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera825,143,615 - 25,187,927 (-)NCBICelera
RGSC_v3.1824,777,334 - 24,821,665 (-)NCBI
Cytogenetic Map8q13NCBI
JBrowse:




Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
membrane  (IEA)

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. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:14581517   PMID:15489334  


Genomics

Comparative Map Data
Herpud2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8831,849,216 - 31,894,219 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl831,849,216 - 31,894,219 (-)EnsemblGRCr8
mRatBN7.2823,573,374 - 23,618,380 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl823,573,379 - 23,617,874 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx827,631,491 - 27,676,822 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0825,928,777 - 25,974,108 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0823,800,662 - 23,845,177 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0826,266,571 - 26,311,528 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl826,266,760 - 26,311,350 (-)Ensemblrn6Rnor6.0
Rnor_5.0826,289,918 - 26,335,435 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4824,777,333 - 24,821,665 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera825,143,615 - 25,187,927 (-)NCBICelera
RGSC_v3.1824,777,334 - 24,821,665 (-)NCBI
Cytogenetic Map8q13NCBI
HERPUD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38735,632,659 - 35,695,135 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl735,632,659 - 35,697,459 (-)Ensemblhg38GRCh38
GRCh37735,672,269 - 35,734,745 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36735,638,794 - 35,701,254 (-)NCBIBuild 36Build 36hg18NCBI36
Celera735,656,891 - 35,718,541 (-)NCBICelera
Cytogenetic Map7p14.2NCBI
HuRef735,553,138 - 35,615,558 (-)NCBIHuRef
CHM1_1735,671,879 - 35,734,370 (-)NCBICHM1_1
T2T-CHM13v2.0735,773,637 - 35,840,411 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2735,711,081 - 35,772,820 (-)NCBI
Herpud2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39925,012,412 - 25,063,109 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl925,019,428 - 25,063,116 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38925,108,126 - 25,151,813 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl925,108,132 - 25,151,820 (-)Ensemblmm10GRCm38
MGSCv37924,912,574 - 24,956,280 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36924,858,540 - 24,901,918 (-)NCBIMGSCv36mm8
Celera922,367,443 - 22,411,134 (-)NCBICelera
Cytogenetic Map9A4NCBI
cM Map910.25NCBI
Herpud2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554607,461,025 - 7,497,495 (+)Ensembl
ChiLan1.0NW_0049554607,461,025 - 7,495,242 (+)NCBIChiLan1.0ChiLan1.0
HERPUD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2640,458,013 - 40,524,425 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1788,782,747 - 88,849,160 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0736,259,315 - 36,321,705 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1736,494,568 - 36,556,481 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl736,494,153 - 36,556,481 (-)EnsemblpanPan2panpan1.1
HERPUD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11447,251,733 - 47,284,519 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1447,210,672 - 47,284,529 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1446,692,169 - 46,726,648 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01447,191,023 - 47,224,976 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1447,191,023 - 47,225,438 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11447,298,029 - 47,331,495 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01446,974,656 - 47,008,409 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01447,348,381 - 47,381,841 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Herpud2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511892,082,462 - 92,123,510 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647811,293,134 - 11,335,241 (-)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493647811,294,193 - 11,335,241 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HERPUD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1838,284,520 - 38,326,311 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11838,284,520 - 38,326,323 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21842,181,620 - 42,212,621 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HERPUD2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12122,728,816 - 22,785,202 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2122,729,346 - 22,788,250 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366604282,069,835 - 82,129,258 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Herpud2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474025,264,399 - 25,307,272 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462474025,179,684 - 25,306,874 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Herpud2
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1821,043,542 - 21,082,167 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Herpud2
370 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:238
Count of miRNA genes:157
Interacting mature miRNAs:187
Transcripts:ENSRNOT00000046432
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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)81699464261994642Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)81038254055382540Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)81595227960952279Rat
631842Inf1Infertility severity QTL 14.10.001seminal gland mass (VT:0010524)seminal vesicle wet weight (CMO:0001603)83154366176543661Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)81296416557964165Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)81296416557964165Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)81799386262252873Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)81038254055382540Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8132882639Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)81699464261994642Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)81038254055382540Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)81296416557964165Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)81799410550763951Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)81038254055382540Rat

Markers in Region
AA900889  
Rat AssemblyChrPosition (strand)SourceJBrowse
GRCr8831,852,895 - 31,853,109 (+)Marker Load Pipeline
mRatBN7.2823,577,055 - 23,577,269 (+)MAPPERmRatBN7.2
Rnor_6.0826,270,251 - 26,270,464NCBIRnor6.0
Rnor_5.0826,293,598 - 26,293,811UniSTSRnor5.0
RGSC_v3.4824,780,826 - 24,781,040UniSTSRGSC3.4
Celera825,147,108 - 25,147,321UniSTS
Cytogenetic Map8q13UniSTS
AA850837  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2823,573,404 - 23,573,537 (+)MAPPERmRatBN7.2
Rnor_6.0826,266,600 - 26,266,732NCBIRnor6.0
Rnor_5.0826,289,947 - 26,290,079UniSTSRnor5.0
RGSC_v3.4824,777,175 - 24,777,307UniSTSRGSC3.4
Celera825,143,457 - 25,143,589UniSTS
RH 3.4 Map8216.9UniSTS
Cytogenetic Map8q13UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000046432   ⟹   ENSRNOP00000049139
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl831,849,216 - 31,893,575 (-)Ensembl
mRatBN7.2 Ensembl823,573,379 - 23,617,874 (-)Ensembl
Rnor_6.0 Ensembl826,266,760 - 26,311,350 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000170862   ⟹   ENSRNOP00000100555
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl831,849,216 - 31,894,219 (-)Ensembl
RefSeq Acc Id: NM_001024988   ⟹   NP_001020159
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8831,849,216 - 31,894,219 (-)NCBI
mRatBN7.2823,573,376 - 23,618,380 (-)NCBI
Rnor_6.0826,266,758 - 26,311,350 (-)NCBI
Rnor_5.0826,289,918 - 26,335,435 (-)NCBI
RGSC_v3.4824,777,333 - 24,821,665 (-)RGD
Celera825,143,615 - 25,187,927 (-)RGD
Sequence:
RefSeq Acc Id: XM_017595533   ⟹   XP_017451022
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8831,850,540 - 31,893,376 (-)NCBI
mRatBN7.2823,573,374 - 23,617,625 (-)NCBI
Rnor_6.0826,266,571 - 26,311,528 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081017   ⟹   XP_038936945
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8831,849,216 - 31,893,331 (-)NCBI
mRatBN7.2823,573,563 - 23,617,512 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001020159 (Get FASTA)   NCBI Sequence Viewer  
  XP_017451022 (Get FASTA)   NCBI Sequence Viewer  
  XP_038936945 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH81861 (Get FASTA)   NCBI Sequence Viewer  
  EDL83359 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000100555
GenBank Protein Q66HH4 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001020159   ⟸   NM_001024988
- UniProtKB: Q66HH4 (UniProtKB/Swiss-Prot),   A0A8L2UM88 (UniProtKB/TrEMBL),   A6JYB6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451022   ⟸   XM_017595533
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000049139   ⟸   ENSRNOT00000046432
RefSeq Acc Id: XP_038936945   ⟸   XM_039081017
- Peptide Label: isoform X2
- UniProtKB: Q66HH4 (UniProtKB/Swiss-Prot)
Ensembl Acc Id: ENSRNOP00000100555   ⟸   ENSRNOT00000170862
Protein Domains
Ubiquitin-like

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q66HH4-F1-model_v2 AlphaFold Q66HH4 1-401 view protein structure

Transcriptome

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

Promoters
RGD ID:13695815
Promoter ID:EPDNEW_R6338
Type:initiation region
Name:Herpud2_1
Description:HERPUD family member 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_6.0826,311,260 - 26,311,320EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307343 AgrOrtholog
BioCyc Gene G2FUF-31339 BioCyc
Ensembl Genes ENSRNOG00000029995 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000170862 ENTREZGENE
Gene3D-CATH Phosphatidylinositol 3-kinase Catalytic Subunit, Chain A, domain 1 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7134757 IMAGE-MGC_LOAD
InterPro HERPUD1/2 UniProtKB/Swiss-Prot
  Ubiquitin-like_domsf UniProtKB/Swiss-Prot
  Ubiquitin_dom UniProtKB/Swiss-Prot
KEGG Report rno:300463 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93672 IMAGE-MGC_LOAD
NCBI Gene 300463 ENTREZGENE
PANTHER HOMOCYSTEINE-RESPONSIVE ENDOPLASMIC RETICULUM-RESIDENT UBIQUITIN-LIKE DOMAIN MEMBER 2 PROTEIN UniProtKB/Swiss-Prot
  PTHR12943 UniProtKB/Swiss-Prot
Pfam ubiquitin UniProtKB/Swiss-Prot
PhenoGen Herpud2 PhenoGen
PROSITE UBIQUITIN_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000029995 RatGTEx
SMART UBQ UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54236 UniProtKB/Swiss-Prot
UniProt A0A8L2UM88 ENTREZGENE, UniProtKB/TrEMBL
  A0ABK0L9D6_RAT UniProtKB/TrEMBL
  A6JYB6 ENTREZGENE, UniProtKB/TrEMBL
  HERP2_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Herpud2  HERPUD family member 2  RGD1307343  similar to RIKEN cDNA 5031400M07  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1307343  similar to RIKEN cDNA 5031400M07  RGD1307343_predicted  similar to RIKEN cDNA 5031400M07 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1307343_predicted  similar to RIKEN cDNA 5031400M07 (predicted)  LOC300463_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300463_predicted  similar to RIKEN cDNA 5031400M07 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL