LOC681325 (hypothetical protein LOC681325) - Rat Genome Database

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Gene: LOC681325 (hypothetical protein LOC681325) Rattus norvegicus
Analyze
No known orthologs.
Symbol: LOC681325
Name: hypothetical protein LOC681325 (Ensembl:predicted gene 6377)
RGD ID: 1596765
Description: Predicted to be involved in regulation of lysosomal lumen pH.
Type: protein-coding
RefSeq Status: PREDICTED
Previously known as: uncharacterized protein LOC681325
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X78,392,551 - 78,396,164 (+)NCBIGRCr8
mRatBN7.2X74,312,698 - 74,316,311 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX74,312,661 - 74,316,635 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX75,828,294 - 75,831,907 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X79,301,331 - 79,304,944 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X76,869,211 - 76,872,824 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X80,359,555 - 80,363,168 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX80,359,555 - 80,363,168 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X80,538,523 - 80,542,136 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X97,611,715 - 97,615,328 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX75,584,410 - 75,588,023 (+)NCBICelera
Cytogenetic MapXq22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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.

Genomics

Variants

.
Variants in LOC681325
8 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:709
Count of miRNA genes:300
Interacting mature miRNAs:386
Transcripts:ENSRNOT00000030692
Prediction methods:Microtar, Miranda, Pita, 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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat

Markers in Region
AW534334  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X74,314,578 - 74,314,738 (+)MAPPERmRatBN7.2
Rnor_6.0X80,361,436 - 80,361,595NCBIRnor6.0
Rnor_5.0X80,540,404 - 80,540,563UniSTSRnor5.0
RGSC_v3.4X97,613,596 - 97,613,755UniSTSRGSC3.4
CeleraX75,586,291 - 75,586,450UniSTS
RH 3.4 MapX720.34UniSTS
Cytogenetic MapXq31UniSTS


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 11 5
Low 2 32 18 8 18 8 6 6
Below cutoff 1 33 25 23 23 8 8 39 25 26 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000030692   ⟹   ENSRNOP00000030641
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX74,312,661 - 74,316,635 (+)Ensembl
Rnor_6.0 EnsemblX80,359,555 - 80,363,168 (+)Ensembl
RefSeq Acc Id: NM_001109439   ⟹   NP_001102909
RefSeq Status: PREDICTED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X78,392,551 - 78,396,164 (+)NCBI
mRatBN7.2X74,312,698 - 74,316,311 (+)NCBI
Rnor_6.0X80,359,555 - 80,363,168 (+)NCBI
Rnor_5.0X80,538,523 - 80,542,136 (+)NCBI
RGSC_v3.4X97,611,715 - 97,615,328 (+)RGD
CeleraX75,584,410 - 75,588,023 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102909 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM07097 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000030641
  ENSRNOP00000030641.2
Reference Protein Sequences
RefSeq Acc Id: NP_001102909   ⟸   NM_001109439
- UniProtKB: D4A907 (UniProtKB/TrEMBL),   A6IV83 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000030641   ⟸   ENSRNOT00000030692

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A907-F1-model_v2 AlphaFold D4A907 1-303 view protein structure

Transcriptome

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

Promoters
RGD ID:13701910
Promoter ID:EPDNEW_R12434
Type:initiation region
Name:LOC681325_1
Description:hypothetical protein LOC681325
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_6.0X80,359,522 - 80,359,582EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1596765 AgrOrtholog
BioCyc Gene G2FUF-1873 BioCyc
Ensembl Genes ENSRNOG00000023005 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000030692 ENTREZGENE
  ENSRNOT00000030692.5 UniProtKB/TrEMBL
InterPro DUF4569 UniProtKB/TrEMBL
KEGG Report rno:681325 UniProtKB/TrEMBL
NCBI Gene 681325 ENTREZGENE
PANTHER GENE 6377-RELATED UniProtKB/TrEMBL
  PTHR14889 UniProtKB/TrEMBL
Pfam DUF4569 UniProtKB/TrEMBL
PhenoGen LOC681325 PhenoGen
RatGTEx ENSRNOG00000023005 RatGTEx
UniProt A6IV83 ENTREZGENE, UniProtKB/TrEMBL
  D4A907 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-01-09 LOC681325  hypothetical protein LOC681325  LOC682243  hypothetical protein LOC682243  Data merged from RGD:1585747 1643240 APPROVED
2006-11-20 LOC681325  hypothetical protein LOC681325      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC682243  hypothetical protein LOC682243      Symbol and Name status set to provisional 70820 PROVISIONAL