Sfnl1 (stratifin like 1) - Rat Genome Database

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Gene: Sfnl1 (stratifin like 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Sfnl1 (Ensembl: LOC298795)
Name: stratifin like 1 (Ensembl:similar to 14-3-3 protein sigma)
RGD ID: 1359510
Description: Predicted to enable protein kinase binding activity. Predicted to be involved in signal transduction. Predicted to be active in cytoplasm. Human ortholog(s) of this gene implicated in transitional cell carcinoma and vulva squamous cell carcinoma. Orthologous to human SFN (stratifin).
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: 14-3-3 protein sigma-like; hypothetical protein LOC298795; LOC298795; MGC108952; similar to 14-3-3 protein sigma; uncharacterized protein LOC298795
RGD Orthologs
Alliance Genes
More Info homologs ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2622,965,151 - 22,966,436 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl622,965,093 - 22,966,452 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx623,296,519 - 23,297,802 (-)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.0623,612,342 - 23,613,625 (-)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.0623,099,999 - 23,101,273 (-)NCBIRnor_WKY
Rnor_6.0623,757,225 - 23,758,508 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl623,757,225 - 23,758,496 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0633,617,273 - 33,618,556 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4623,095,404 - 23,096,686 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1623,098,367 - 23,099,639 (-)NCBI
Celera622,499,765 - 22,500,992 (-)NCBICelera
Cytogenetic Map6q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA)

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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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.
Additional References at PubMed
PMID:17303654  


Genomics

Variants

.
Variants in Sfnl1
5 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6127574569Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6127574569Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6127574569Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6127574569Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6127574569Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6134235784Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6137618905Rat
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6139036266Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6141223769Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6141223769Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6141223769Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6141223769Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6141223769Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6142487980Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6142487980Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6142487980Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142838846Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6143394190Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449734434305Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)61653614027261739Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat

Markers in Region
DXRat56  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X58,753,434 - 58,753,614 (+)MAPPERmRatBN7.2
Rnor_6.0X63,109,746 - 63,109,925NCBIRnor6.0
Rnor_5.0X63,699,539 - 63,699,718UniSTSRnor5.0
RGSC_v3.4X81,378,219 - 81,378,398UniSTSRGSC3.4
RGSC_v3.4X81,378,218 - 81,378,398RGDRGSC3.4
RGSC_v3.1X81,451,511 - 81,451,690RGD
CeleraX59,189,648 - 59,189,827UniSTS
RH 3.4 Map41029.5RGD
RH 3.4 Map41029.5UniSTS
FHH x ACI MapX21.8699RGD
FHH x ACI MapX21.8699UniSTS
Cytogenetic MapXq31UniSTS
Cytogenetic Map6q13UniSTS
RH135032  
Rat AssemblyChrPosition (strand)SourceJBrowse
Cytogenetic Map6q13UniSTS
Cytogenetic Map5q36UniSTS


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 7
Low 3 17 1 19 1 2 2 18 35 26 11 2
Below cutoff 40 36 36 36 6 9 50 8 6

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000005553   ⟹   ENSRNOP00000066315
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl622,965,093 - 22,966,452 (-)Ensembl
Rnor_6.0 Ensembl623,757,225 - 23,758,496 (+)Ensembl
RefSeq Acc Id: NM_001013941   ⟹   NP_001013963
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2622,965,151 - 22,966,436 (-)NCBI
Rnor_6.0623,757,225 - 23,758,508 (+)NCBI
Rnor_5.0633,617,273 - 33,618,556 (+)NCBI
RGSC_v3.4623,095,404 - 23,096,686 (-)RGD
Celera622,499,765 - 22,500,992 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001013963 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79389 (Get FASTA)   NCBI Sequence Viewer  
  AAH89860 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001013963   ⟸   NM_001013941
- UniProtKB: Q5EBB0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000066315   ⟸   ENSRNOT00000005553
Protein Domains
14_3_3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5EBB0-F1-model_v2 AlphaFold Q5EBB0 1-248 view protein structure

Transcriptome

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

Promoters
RGD ID:13694420
Promoter ID:EPDNEW_R4945
Type:multiple initiation site
Name:LOC298795_1
Description:similar to 14-3-3 protein sigma
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_6.0623,757,198 - 23,757,258EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1359510 AgrOrtholog
BioCyc Gene G2FUF-38398 BioCyc
Ensembl Genes ENSRNOG00000004188 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000066315 ENTREZGENE
  ENSRNOP00000066315.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000005553 ENTREZGENE
  ENSRNOT00000005553.6 UniProtKB/TrEMBL
Gene3D-CATH 1.20.190.20 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7111773 IMAGE-MGC_LOAD
  IMAGE:7112967 IMAGE-MGC_LOAD
InterPro 14-3-3 UniProtKB/TrEMBL
  14-3-3_CS UniProtKB/TrEMBL
  14-3-3_dom_sf UniProtKB/TrEMBL
  14-3-3_domain UniProtKB/TrEMBL
KEGG Report rno:298795 UniProtKB/TrEMBL
MGC_CLONE MGC:108952 IMAGE-MGC_LOAD
  MGC:94904 IMAGE-MGC_LOAD
NCBI Gene 298795 ENTREZGENE
PANTHER 14-3-3 UniProtKB/TrEMBL
Pfam 14-3-3 UniProtKB/TrEMBL
PhenoGen Sfnl1 PhenoGen
PIRSF 14-3-3 UniProtKB/TrEMBL
PRINTS 1433ZETA UniProtKB/TrEMBL
PROSITE 1433_1 UniProtKB/TrEMBL
  1433_2 UniProtKB/TrEMBL
SMART 14_3_3 UniProtKB/TrEMBL
Superfamily-SCOP 14-3-3 UniProtKB/TrEMBL
UniProt Q5EBB0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-28 Sfnl1  stratifin like 1  LOC298795  similar to 14-3-3 protein sigma  Name and Symbol changed 629549 APPROVED
2005-07-29 LOC298795  similar to 14-3-3 protein sigma      Symbol and Name status set to provisional 70820 PROVISIONAL