LOC102549158 (sorting nexin-1-like) - Rat Genome Database

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Gene: LOC102549158 (sorting nexin-1-like) Rattus norvegicus
Analyze
Symbol: LOC102549158
Name: sorting nexin-1-like
RGD ID: 7624393
Description: Predicted to enable phosphatidylinositol binding activity; protein dimerization activity; and signaling receptor binding activity. Predicted to be involved in several processes, including early endosome to Golgi transport; lamellipodium morphogenesis; and receptor internalization. Predicted to be located in several cellular components, including early endosome membrane; lamellipodium; and lysosome. Predicted to be part of retromer, tubulation complex.
Type: protein-coding (Ensembl: processed_pseudogene)
RefSeq Status: MODEL
Previously known as: LOC100363031
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81140,899,005 - 40,900,744 (+)NCBIGRCr8
mRatBN7.21127,412,769 - 27,414,504 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1127,413,195 - 27,414,109 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01128,056,151 - 28,057,886 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1128,056,131 - 28,057,737 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01131,670,987 - 31,672,313 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41127,948,236 - 27,949,549 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1127,149,132 - 27,150,867 (+)NCBICelera
Cytogenetic Map11q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Genomics

Variants

.
Variants in LOC102549158
3 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598842Glom10Glomerulus QTL 103.4kidney glomerulus morphology trait (VT:0005325)index of glomerular damage (CMO:0001135)11135331169Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11169446234Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)11104193166113562Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11843667453436674Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111647204744285911Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111897620886241447Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112295940367959403Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112328045668280456Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112328045668280456Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112328045668280456Rat


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
Low 3 2 2 2 3 2 2 3 3 3 3
Below cutoff 7 21 9 14 9 1 2 16 25 22 4 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000089651
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1127,413,195 - 27,414,109 (+)Ensembl
Rnor_6.0 Ensembl1128,056,131 - 28,057,737 (+)Ensembl
RefSeq Acc Id: XM_039088768   ⟹   XP_038944696
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81140,899,005 - 40,900,744 (+)NCBI
mRatBN7.21127,412,769 - 27,414,504 (+)NCBI
Protein Sequences
Protein RefSeqs XP_038944696 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000022960.6
Reference Protein Sequences
RefSeq Acc Id: XP_038944696   ⟸   XM_039088768
- UniProtKB: A0A8L2QBU0 (UniProtKB/TrEMBL)
Protein Domains
PX

Transcriptome

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


Additional Information

Database Acc Id Source(s)
BioCyc Gene G2FUF-22034 BioCyc
Ensembl Genes ENSRNOG00000017029 UniProtKB/TrEMBL
  ENSRNOG00000056964 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000022960.7 UniProtKB/TrEMBL
Gene3D-CATH Arfaptin homology (AH) domain/BAR domain UniProtKB/TrEMBL
  Phox-like domain UniProtKB/TrEMBL
InterPro AH/BAR_dom_sf UniProtKB/TrEMBL
  PX_dom UniProtKB/TrEMBL
  PX_dom_sf UniProtKB/TrEMBL
  SNX1_BAR UniProtKB/TrEMBL
  Sorting_nexin_N UniProtKB/TrEMBL
  Vps5_C UniProtKB/TrEMBL
NCBI Gene LOC102549158 ENTREZGENE
PANTHER SORTING NEXIN UniProtKB/TrEMBL
  SORTING NEXIN-1 UniProtKB/TrEMBL
Pfam PF00787 UniProtKB/TrEMBL
  Sorting_nexin UniProtKB/TrEMBL
  Vps5 UniProtKB/TrEMBL
PhenoGen LOC102549158 PhenoGen
PROSITE PS50195 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000017029 RatGTEx
  ENSRNOG00000056964 RatGTEx
SMART SM00312 UniProtKB/TrEMBL
Superfamily-SCOP BAR/IMD domain-like UniProtKB/TrEMBL
  PX domain UniProtKB/TrEMBL
UniProt A0A8L2QBU0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 LOC102549158  sorting nexin-1-like  LOC100363031  sorting nexin-1-like  Data merged from RGD:2323564 737654 PROVISIONAL
2013-12-18 LOC102549158  sorting nexin-1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100363031  sorting nexin-1-like      Symbol and Name status set to provisional 70820 PROVISIONAL