Erlin2 (ER lipid raft associated 2) - Rat Genome Database

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Gene: Erlin2 (ER lipid raft associated 2) Rattus norvegicus
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Symbol: Erlin2
Name: ER lipid raft associated 2
RGD ID: 1309010
Description: Predicted to enable cholesterol binding activity and ubiquitin protein ligase binding activity. Predicted to be involved in ERAD pathway; SREBP signaling pathway; and negative regulation of lipid biosynthetic process. Predicted to be located in several cellular components, including cytosol; endoplasmic reticulum; and membrane raft. Predicted to be part of protein-containing complex. Predicted to be active in endoplasmic reticulum membrane. Human ortholog(s) of this gene implicated in hereditary spastic paraplegia 18. Orthologous to human ERLIN2 (ER lipid raft associated 2); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; acrylamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: endoplasmic reticulum lipid raft-associated protein 2; erlin-2; LOC290823; RGD1309010; similar to CDNA sequence BC036333; SPFH domain family, member 2; SPFH domain-containing protein 2; Spfh2; stomatin-prohibitin-flotillin-HflC/K domain-containing protein 2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81671,720,486 - 71,736,999 (-)NCBIGRCr8
mRatBN7.21665,017,654 - 65,034,184 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1665,018,532 - 65,033,671 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1670,301,813 - 70,316,979 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01673,708,144 - 73,723,311 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01668,953,921 - 68,969,062 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01669,179,005 - 69,195,452 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1669,179,588 - 69,195,097 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01668,853,254 - 68,868,395 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41669,345,708 - 69,360,849 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11669,347,796 - 69,361,094 (-)NCBI
Celera1662,937,899 - 62,953,040 (-)NCBICelera
Cytogenetic Map16q12.3NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

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. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16835267   PMID:17502376   PMID:18468998   PMID:19240031   PMID:21700703   PMID:22771797   PMID:23376485   PMID:24019521   PMID:24217618   PMID:25204797   PMID:29476059  


Genomics

Comparative Map Data
Erlin2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81671,720,486 - 71,736,999 (-)NCBIGRCr8
mRatBN7.21665,017,654 - 65,034,184 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1665,018,532 - 65,033,671 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1670,301,813 - 70,316,979 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01673,708,144 - 73,723,311 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01668,953,921 - 68,969,062 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01669,179,005 - 69,195,452 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1669,179,588 - 69,195,097 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01668,853,254 - 68,868,395 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41669,345,708 - 69,360,849 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11669,347,796 - 69,361,094 (-)NCBI
Celera1662,937,899 - 62,953,040 (-)NCBICelera
Cytogenetic Map16q12.3NCBI
ERLIN2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38837,736,634 - 37,758,422 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl837,736,601 - 37,758,422 (+)EnsemblGRCh38hg38GRCh38
GRCh37837,594,152 - 37,615,940 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36837,713,255 - 37,734,477 (+)NCBINCBI36Build 36hg18NCBI36
Build 34837,713,306 - 37,734,476NCBI
Celera836,546,048 - 36,567,268 (+)NCBICelera
Cytogenetic Map8p11.23NCBI
HuRef836,128,897 - 36,150,116 (+)NCBIHuRef
CHM1_1837,795,543 - 37,816,776 (+)NCBICHM1_1
T2T-CHM13v2.0838,013,033 - 38,034,818 (+)NCBIT2T-CHM13v2.0
Erlin2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39827,513,399 - 27,529,465 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl827,513,289 - 27,530,356 (+)EnsemblGRCm39 Ensembl
GRCm38827,023,371 - 27,039,437 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl827,023,261 - 27,040,328 (+)EnsemblGRCm38mm10GRCm38
MGSCv37828,134,331 - 28,149,896 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36828,489,795 - 28,505,360 (+)NCBIMGSCv36mm8
Celera828,512,703 - 28,528,268 (+)NCBICelera
Cytogenetic Map8A2NCBI
cM Map815.91NCBI
Erlin2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495546313,444,722 - 13,463,132 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495546313,445,468 - 13,460,370 (+)NCBIChiLan1.0ChiLan1.0
ERLIN2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2756,276,392 - 56,316,023 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1831,993,463 - 32,033,113 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0837,034,391 - 37,057,164 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1834,212,610 - 34,233,583 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl834,212,704 - 34,233,583 (+)Ensemblpanpan1.1panPan2
ERLIN2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11627,622,549 - 27,639,807 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1627,625,417 - 27,639,202 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1628,139,650 - 28,156,544 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01629,522,128 - 29,539,021 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1629,521,245 - 29,538,467 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11627,743,568 - 27,760,038 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01628,321,254 - 28,338,103 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01628,360,352 - 28,377,263 (-)NCBIUU_Cfam_GSD_1.0
Erlin2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494350,251,154 - 50,267,575 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367101,193,411 - 1,210,739 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367101,193,679 - 1,210,059 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ERLIN2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1548,643,724 - 48,662,536 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11548,643,722 - 48,662,648 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21555,760,192 - 55,779,099 (-)NCBISscrofa10.2Sscrofa10.2susScr3
ERLIN2
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1835,771,541 - 35,789,848 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl835,771,580 - 35,789,345 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660526,212,314 - 6,233,680 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Erlin2
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247805,843,141 - 5,862,039 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247805,844,473 - 5,861,493 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Erlin2
50 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:589
Count of miRNA genes:279
Interacting mature miRNAs:348
Transcripts:ENSRNOT00000018973
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2300163Bmd64Bone mineral density QTL 645.30.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)163775215682752156Rat
1600378Arunc4Aerobic running capacity QTL 40.03exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)1638024580345693Rat
70215Niddm29Non-insulin dependent diabetes mellitus QTL 293.54blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)161900443575226532Rat
1578768Stresp22Stress response QTL 222.8thymus mass (VT:0004954)thymus wet weight (CMO:0000855)163528887080288870Rat
2302057Pia29Pristane induced arthritis QTL 293.60.001blood autoantibody amount (VT:0003725)serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)162173597566735975Rat
7205510Activ5Activity QTL 53.780.00028locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)164239634584729064Rat
631525Pia14Pristane induced arthritis QTL 144.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)165571108783402471Rat
8694453Bw172Body weight QTL 1728.330.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)162432551369325513Rat
7411648Foco22Food consumption QTL 22150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)165272646484729064Rat
6903294Stl30Serum triglyceride level QTL 302.60.0013blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)162515279370152793Rat
2293690Bss45Bone structure and strength QTL 455.130.0001lumbar vertebra morphology trait (VT:0010494)lumbar vertebra cortical cross-sectional area (CMO:0001690)163775215682752156Rat
8694364Abfw7Abdominal fat weight QTL 712.220.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)165272646484729064Rat
8694429Bw164Body weight QTL 16450.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)165272646484729064Rat
70205Gcr3Gastric cancer resistance QTL 32.3stomach morphology trait (VT:0000470)stomach tumor diameter (CMO:0001889)161769679182635055Rat


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
nervous system
renal system
reproductive system
respiratory system
9 11 49 113 91 90 59 25 59 6 218 97 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000018973   ⟹   ENSRNOP00000018973
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1665,018,532 - 65,033,671 (-)Ensembl
Rnor_6.0 Ensembl1669,179,588 - 69,195,097 (-)Ensembl
RefSeq Acc Id: NM_001106088   ⟹   NP_001099558
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81671,721,362 - 71,736,503 (-)NCBI
mRatBN7.21665,018,530 - 65,033,671 (-)NCBI
Rnor_6.01669,179,881 - 69,195,022 (-)NCBI
Rnor_5.01668,853,254 - 68,868,395 (-)NCBI
RGSC_v3.41669,345,708 - 69,360,849 (-)RGD
Celera1662,937,899 - 62,953,040 (-)RGD
Sequence:
RefSeq Acc Id: XM_008771323   ⟹   XP_008769545
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81671,720,486 - 71,736,453 (-)NCBI
mRatBN7.21665,017,654 - 65,033,613 (-)NCBI
Rnor_6.01669,179,005 - 69,194,974 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008771324   ⟹   XP_008769546
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81671,720,486 - 71,736,999 (-)NCBI
mRatBN7.21665,017,654 - 65,034,184 (-)NCBI
Rnor_6.01669,179,005 - 69,195,452 (-)NCBI
Sequence:
RefSeq Acc Id: NP_001099558   ⟸   NM_001106088
- UniProtKB: B5DEH2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008769546   ⟸   XM_008771324
- Peptide Label: isoform X1
- UniProtKB: B5DEH2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_008769545   ⟸   XM_008771323
- Peptide Label: isoform X1
- UniProtKB: B5DEH2 (UniProtKB/Swiss-Prot)
- Sequence:
Ensembl Acc Id: ENSRNOP00000018973   ⟸   ENSRNOT00000018973

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B5DEH2-F1-model_v2 AlphaFold B5DEH2 1-339 view protein structure

Transcriptome

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

Promoters
RGD ID:13700157
Promoter ID:EPDNEW_R10680
Type:initiation region
Name:Erlin2_1
Description:ER lipid raft associated 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_6.01669,195,051 - 69,195,111EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309010 AgrOrtholog
BioCyc Gene G2FUF-11028 BioCyc
Ensembl Genes ENSRNOG00000013763 Ensembl, UniProtKB/Swiss-Prot
  ENSRNOG00055008213 UniProtKB/Swiss-Prot
  ENSRNOG00060011861 UniProtKB/Swiss-Prot
  ENSRNOG00065002719 UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000018973.7 UniProtKB/Swiss-Prot
  ENSRNOT00055013899 UniProtKB/Swiss-Prot
  ENSRNOT00060020063 UniProtKB/Swiss-Prot
  ENSRNOT00065003699 UniProtKB/Swiss-Prot
Gene3D-CATH 3.30.479.30 UniProtKB/Swiss-Prot
InterPro Band_7 UniProtKB/Swiss-Prot
  Band_7/SPFH_dom_sf UniProtKB/Swiss-Prot
  Erlin1/2 UniProtKB/Swiss-Prot
KEGG Report rno:290823 UniProtKB/Swiss-Prot
NCBI Gene 290823 ENTREZGENE
PANTHER ERLIN-2 UniProtKB/Swiss-Prot
  PTHR15351 UniProtKB/Swiss-Prot
Pfam Band_7 UniProtKB/Swiss-Prot
PhenoGen Erlin2 PhenoGen
RatGTEx ENSRNOG00000013763 RatGTEx
  ENSRNOG00055008213 RatGTEx
  ENSRNOG00060011861 RatGTEx
  ENSRNOG00065002719 RatGTEx
SMART PHB UniProtKB/Swiss-Prot
UniProt B5DEH2 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-07 Erlin2  ER lipid raft associated 2  Spfh2_predicted  SPFH domain family, member 2 (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Spfh2_predicted  SPFH domain family, member 2 (predicted)  RGD1309010_predicted  similar to CDNA sequence BC036333 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1309010_predicted  similar to CDNA sequence BC036333 (predicted)  LOC290823_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC290823_predicted  similar to CDNA sequence BC036333 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL