Shfl (shiftless antiviral inhibitor of ribosomal frameshifting) - Rat Genome Database

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Gene: Shfl (shiftless antiviral inhibitor of ribosomal frameshifting) Rattus norvegicus
Analyze
Symbol: Shfl
Name: shiftless antiviral inhibitor of ribosomal frameshifting
RGD ID: 1565995
Description: Predicted to enable identical protein binding activity; ribosome binding activity; and sequence-specific mRNA binding activity. Predicted to be involved in several processes, including defense response to other organism; regulation of translation; and viral translational frameshifting. Predicted to be located in P-body; cytosol; and nucleoplasm. Orthologous to human SHFL (shiftless antiviral inhibitor of ribosomal frameshifting); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 4,4'-sulfonyldiphenol; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC500956; LOC500956; repressor of yield of DENV protein homolog; RyDEN; shiftless antiviral inhibitor of ribosomal frameshifting protein homolog; UPF0515 protein C19orf66 homolog
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,683,560 - 27,690,269 (+)NCBIGRCr8
mRatBN7.2819,408,298 - 19,414,084 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,408,333 - 19,413,971 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,427,673 - 23,433,448 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,725,519 - 21,731,295 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,638,006 - 19,643,765 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,890,214 - 21,896,045 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,890,319 - 21,896,031 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0821,946,550 - 21,952,295 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4819,893,861 - 19,899,475 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,803,335 - 20,808,975 (+)NCBICelera
Cytogenetic Map8q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA,ISO,ISS)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)
nucleus  (IEA,ISO,ISS)
P-body  (IEA,ISO,ISS)

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
3. 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:26735137   PMID:27974568   PMID:30682371  


Genomics

Comparative Map Data
Shfl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8827,683,560 - 27,690,269 (+)NCBIGRCr8
mRatBN7.2819,408,298 - 19,414,084 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl819,408,333 - 19,413,971 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx823,427,673 - 23,433,448 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0821,725,519 - 21,731,295 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0819,638,006 - 19,643,765 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0821,890,214 - 21,896,045 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl821,890,319 - 21,896,031 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0821,946,550 - 21,952,295 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4819,893,861 - 19,899,475 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera820,803,335 - 20,808,975 (+)NCBICelera
Cytogenetic Map8q13NCBI
SHFL
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381910,086,317 - 10,093,243 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1910,086,122 - 10,093,252 (+)EnsemblGRCh38hg38GRCh38
GRCh371910,196,993 - 10,203,919 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361910,057,806 - 10,064,928 (+)NCBINCBI36Build 36hg18NCBI36
Celera1910,092,297 - 10,099,418 (+)NCBICelera
Cytogenetic Map19p13.2NCBI
HuRef199,777,615 - 9,784,585 (+)NCBIHuRef
CHM1_11910,197,078 - 10,204,203 (+)NCBICHM1_1
T2T-CHM13v2.01910,212,537 - 10,219,461 (+)NCBIT2T-CHM13v2.0
Shfl
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39920,779,914 - 20,785,603 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl920,779,938 - 20,785,603 (+)EnsemblGRCm39 Ensembl
GRCm38920,868,635 - 20,874,307 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl920,868,642 - 20,874,307 (+)EnsemblGRCm38mm10GRCm38
MGSCv37920,673,086 - 20,678,751 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36920,619,098 - 20,624,698 (+)NCBIMGSCv36mm8
Celera918,137,340 - 18,143,005 (+)NCBICelera
Cytogenetic Map9A3NCBI
cM Map97.65NCBI
Shfl
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554951,431,023 - 1,440,821 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554951,431,677 - 1,437,035 (+)NCBIChiLan1.0ChiLan1.0
SHFL
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22015,001,218 - 15,008,351 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11914,001,520 - 14,008,644 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0199,634,718 - 9,641,824 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11910,293,967 - 10,301,067 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1910,293,967 - 10,301,067 (+)Ensemblpanpan1.1panPan2
SHFL
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12050,961,557 - 50,966,261 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2050,961,551 - 50,965,961 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2050,830,673 - 50,835,649 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02051,482,922 - 51,487,898 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2051,483,358 - 51,487,768 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12050,690,819 - 50,695,795 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02051,117,829 - 51,122,806 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02051,358,731 - 51,363,707 (-)NCBIUU_Cfam_GSD_1.0
Shfl
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118209,862,784 - 209,873,772 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936659473,889 - 493,978 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936659480,934 - 491,926 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SHFL
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl268,942,450 - 68,948,989 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1268,942,246 - 68,947,107 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2269,270,421 - 69,275,282 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SHFL
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.169,152,015 - 9,162,883 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl69,152,100 - 9,163,871 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366607410,898,442 - 10,905,492 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Shfl
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248282,287,275 - 2,292,199 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248282,285,577 - 2,293,307 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Shfl
31 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:148
Count of miRNA genes:103
Interacting mature miRNAs:125
Transcripts:ENSRNOT00000027949
Prediction methods:Miranda, Rnahybrid, 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
1558646Swd5Spike wave discharge measurement QTL 53.450.00036brain electrophysiology trait (VT:0010557)brain spike-and-wave discharge frequency (CMO:0001742)81490675159906751Rat
1357398Slep3Serum leptin concentration QTL 33.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
2317030Wbc5White blood cell count QTL 53.210.005leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)8873663553736635Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
12880044Am9Aortic mass QTL 90.007aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)8209764047097640Rat
2317032Ginf2Gastrointestinal inflammation QTL 23.210.005liver integrity trait (VT:0010547)liver granuloma severity score (CMO:0002157)8470581049705810Rat
2301416Bp315Blood pressure QTL 3150.008arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)8767057852670578Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
2317036Livw3Liver weight QTL 32.430.01liver mass (VT:0003402)liver weight to body weight ratio (CMO:0000633)8470581049705810Rat
1598824Memor4Memory QTL 42.5exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)8971222053356647Rat
12880023Bw184Body weight QTL 1840.001body mass (VT:0001259)body weight (CMO:0000012)8209764047097640Rat
9590084Insglur5Insulin/glucose ratio QTL 518.540.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)8124597739Rat
1354595Despr4Despair related QTL 42.160.0036locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)8768895552688955Rat
1354627Despr14Despair related QTL 140.0056locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)8768895552688955Rat
12880028Cm103Cardiac mass QTL 1030.02heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)8209764047097640Rat
2317051Aia18Adjuvant induced arthritis QTL 182.42joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)8873663553736635Rat
2317882Alcrsp24Alcohol response QTL 243.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)8125902202Rat
2317048Ginf1Gastrointestinal inflammation QTL 13.520.005cecum mucosa thickness (VT:0010234)enterocolitis severity score (CMO:0002138)8470581049705810Rat
2302367Slep5Serum leptin concentration QTL 53.43blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)8971246341866876Rat
12880025Cm102Cardiac mass QTL 1020.044heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)8209764047097640Rat
61373Mcs4Mammary carcinoma susceptibility QTL 41.1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)81629044461290444Rat

Markers in Region
RH130656  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2819,413,815 - 19,414,003 (+)MAPPERmRatBN7.2
Rnor_6.0821,895,721 - 21,895,908NCBIRnor6.0
Rnor_5.0821,952,036 - 21,952,223UniSTSRnor5.0
RGSC_v3.4819,899,318 - 19,899,505UniSTSRGSC3.4
Celera820,808,818 - 20,809,005UniSTS
RH 3.4 Map8179.6UniSTS
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
nervous system
renal system
reproductive system
respiratory system
9 11 45 111 91 90 59 25 59 6 214 93 91 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000027949   ⟹   ENSRNOP00000027949
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl819,408,333 - 19,413,971 (+)Ensembl
Rnor_6.0 Ensembl821,890,319 - 21,896,031 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000110950   ⟹   ENSRNOP00000093661
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl819,408,333 - 19,413,971 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117855   ⟹   ENSRNOP00000097519
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl819,408,333 - 19,413,358 (+)Ensembl
RefSeq Acc Id: NM_001394375   ⟹   NP_001381304
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,684,510 - 27,690,269 (+)NCBI
mRatBN7.2819,408,323 - 19,414,082 (+)NCBI
RefSeq Acc Id: XM_008765978   ⟹   XP_008764200
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,683,560 - 27,690,257 (+)NCBI
mRatBN7.2819,408,301 - 19,414,084 (+)NCBI
Rnor_6.0821,890,214 - 21,896,045 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039081925   ⟹   XP_038937853
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,683,560 - 27,690,257 (+)NCBI
mRatBN7.2819,408,298 - 19,414,084 (+)NCBI
RefSeq Acc Id: XM_039081926   ⟹   XP_038937854
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8827,683,560 - 27,690,257 (+)NCBI
mRatBN7.2819,408,300 - 19,413,501 (+)NCBI
RefSeq Acc Id: XP_008764200   ⟸   XM_008765978
- Peptide Label: isoform X2
- UniProtKB: A0A140TAE2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000027949   ⟸   ENSRNOT00000027949
RefSeq Acc Id: XP_038937853   ⟸   XM_039081925
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038937854   ⟸   XM_039081926
- Peptide Label: isoform X3
- UniProtKB: A0A8I6AT40 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000097519   ⟸   ENSRNOT00000117855
Ensembl Acc Id: ENSRNOP00000093661   ⟸   ENSRNOT00000110950
RefSeq Acc Id: NP_001381304   ⟸   NM_001394375
- UniProtKB: A6JNL7 (UniProtKB/TrEMBL),   A0A8I6AM91 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5RJN4-F1-model_v2 AlphaFold Q5RJN4 1-163 view protein structure

Transcriptome

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

Promoters
RGD ID:13695764
Promoter ID:EPDNEW_R6289
Type:initiation region
Name:LOC500956_1
Description:hypothetical protein LOC500956
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_6.0821,890,228 - 21,890,288EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1565995 AgrOrtholog
BioCyc Gene G2FUF-31457 BioCyc
Ensembl Genes ENSRNOG00000020580 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000027949 ENTREZGENE
  ENSRNOT00000110950 ENTREZGENE
  ENSRNOT00000117855 ENTREZGENE
IMAGE_CLONE IMAGE:7300711 IMAGE-MGC_LOAD
InterPro RyDEN UniProtKB/Swiss-Prot
MGC_CLONE MGC:105913 IMAGE-MGC_LOAD
NCBI Gene 500956 ENTREZGENE
PANTHER PTHR16135 UniProtKB/Swiss-Prot
  SHIFTLESS ANTIVIRAL INHIBITOR OF RIBOSOMAL FRAMESHIFTING PROTEIN UniProtKB/Swiss-Prot
Pfam UPF0515 UniProtKB/Swiss-Prot
PhenoGen Shfl PhenoGen
RatGTEx ENSRNOG00000020580 RatGTEx
UniProt A0A140TAE2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AM91 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6AT40 ENTREZGENE, UniProtKB/TrEMBL
  A6JNL7 ENTREZGENE, UniProtKB/TrEMBL
  Q5RJN4 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-08-08 Shfl  shiftless antiviral inhibitor of ribosomal frameshifting  LOC500956  hypothetical protein LOC500956  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC500956  hypothetical protein LOC500956      Symbol and Name status set to provisional 70820 PROVISIONAL