Snrpf (small nuclear ribonucleoprotein polypeptide F) - Rat Genome Database

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Gene: Snrpf (small nuclear ribonucleoprotein polypeptide F) Rattus norvegicus
Analyze
Symbol: Snrpf
Name: small nuclear ribonucleoprotein polypeptide F
RGD ID: 1588229
Description: Predicted to enable RNA binding activity. Predicted to be involved in spliceosomal snRNP assembly. Predicted to be located in cytosol and nucleus. Predicted to be part of several cellular components, including methylosome; nucleus; and pICln-Sm protein complex. Orthologous to human SNRPF (small nuclear ribonucleoprotein polypeptide F); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC680737; similar to Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF); small nuclear ribonucleoprotein F
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
GRCr8730,017,460 - 30,024,162 (-)NCBIGRCr8
mRatBN7.2728,130,427 - 28,137,129 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl728,130,427 - 28,137,129 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx730,120,802 - 30,127,504 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0732,283,015 - 32,289,717 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0732,057,661 - 32,064,355 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0734,478,331 - 34,485,034 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl734,478,331 - 34,485,034 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0734,543,253 - 34,549,956 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4730,644,564 - 30,651,266 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera725,229,126 - 25,235,828 (-)NCBICelera
Cytogenetic Map7q13NCBI
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

Biological Process

Molecular Function
protein binding  (ISO)
RNA binding  (IBA,ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

References - curated
# Reference Title Reference Citation
1. Proteomic analysis of in vivo-assembled pre-mRNA splicing complexes expands the catalog of participating factors. Chen YI, etal., Nucleic Acids Res. 2007;35(12):3928-44. Epub 2007 May 30.
2. ToP: a trend-of-disease-progression procedure works well for identifying cancer genes from multi-state cohort gene expression data for human colorectal cancer. Chung FH, etal., PLoS One. 2013 Jun 14;8(6):e65683. doi: 10.1371/journal.pone.0065683. Print 2013.
3. 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.
4. Low-molecular-mass secretome profiling identifies C-C motif chemokine 5 as a potential plasma biomarker and therapeutic target for nasopharyngeal carcinoma. Lin SJ, etal., J Proteomics. 2013 Dec 6;94:186-201. doi: 10.1016/j.jprot.2013.09.013. Epub 2013 Sep 27.
5. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
6. GOA pipeline RGD automated data pipeline
7. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
9. Comprehensive gene review and curation RGD comprehensive gene curation
10. The spliceosome: design principles of a dynamic RNP machine. Wahl MC, etal., Cell. 2009 Feb 20;136(4):701-18. doi: 10.1016/j.cell.2009.02.009.
Additional References at PubMed
PMID:7744013   PMID:11574479   PMID:11991638   PMID:15146077   PMID:18984161   PMID:21113136   PMID:21516107   PMID:25555158   PMID:26912367   PMID:28076346   PMID:28781166   PMID:35352799  


Genomics

Comparative Map Data
Snrpf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8730,017,460 - 30,024,162 (-)NCBIGRCr8
mRatBN7.2728,130,427 - 28,137,129 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl728,130,427 - 28,137,129 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx730,120,802 - 30,127,504 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0732,283,015 - 32,289,717 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0732,057,661 - 32,064,355 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0734,478,331 - 34,485,034 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl734,478,331 - 34,485,034 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0734,543,253 - 34,549,956 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4730,644,564 - 30,651,266 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera725,229,126 - 25,235,828 (-)NCBICelera
Cytogenetic Map7q13NCBI
SNRPF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381295,858,952 - 95,866,140 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1295,858,952 - 95,903,828 (+)EnsemblGRCh38hg38GRCh38
GRCh371296,252,730 - 96,259,918 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361294,776,840 - 94,784,369 (+)NCBINCBI36Build 36hg18NCBI36
Build 341294,755,206 - 94,762,385NCBI
Celera1295,921,842 - 95,929,371 (+)NCBICelera
Cytogenetic Map12q23.1NCBI
HuRef1293,317,251 - 93,324,785 (+)NCBIHuRef
CHM1_11296,218,303 - 96,225,832 (+)NCBICHM1_1
T2T-CHM13v2.01295,835,373 - 95,842,560 (+)NCBIT2T-CHM13v2.0
Snrpf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391093,418,891 - 93,425,520 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1093,418,891 - 93,425,568 (-)EnsemblGRCm39 Ensembl
GRCm381093,583,029 - 93,589,658 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1093,583,029 - 93,589,706 (-)EnsemblGRCm38mm10GRCm38
MGSCv371093,045,774 - 93,052,403 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361093,012,491 - 93,022,251 (-)NCBIMGSCv36mm8
Celera1095,569,839 - 95,576,455 (-)NCBICelera
Cytogenetic Map10C2NCBI
cM Map1048.57NCBI
Snrpf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540532,236,876 - 32,242,716 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495540532,236,876 - 32,242,716 (+)NCBIChiLan1.0ChiLan1.0
SNRPF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v210103,933,905 - 103,941,144 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan112103,930,295 - 103,937,539 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01293,452,446 - 93,459,691 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11296,841,638 - 96,848,864 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1296,841,638 - 96,886,039 (+)Ensemblpanpan1.1panPan2
SNRPF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11535,691,071 - 35,698,734 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1536,077,729 - 36,085,397 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01536,356,099 - 36,363,772 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1536,356,802 - 36,389,943 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11535,628,828 - 35,636,491 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01535,723,194 - 35,730,847 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01535,986,761 - 35,994,428 (+)NCBIUU_Cfam_GSD_1.0
Snrpf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494524,255,072 - 24,261,639 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493650711,973,564 - 11,982,283 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493650711,973,818 - 11,980,370 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SNRPF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl587,604,596 - 87,622,879 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1587,614,934 - 87,622,863 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2591,818,173 - 91,826,105 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SNRPF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11191,244,619 - 91,251,805 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666037153,888,691 - 153,896,152 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Snrpf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475011,430,311 - 11,436,204 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462475011,430,311 - 11,436,223 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Snrpf
32 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:313
Count of miRNA genes:191
Interacting mature miRNAs:213
Transcripts:ENSRNOT00000007351
Prediction methods:Microtar, 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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354644Spl4Serum phospholipid level QTL 44.9blood phospholipid amount (VT:0006084)blood phospholipid level (CMO:0001169)71965431749753746Rat
7411569Bw137Body weight QTL 1370.001body mass (VT:0001259)body weight gain (CMO:0000420)72192119566921195Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1578652Bmd15Bone mineral density QTL 155.2femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)7986646760460686Rat
9590102Sffal5Serum free fatty acids level QTL 58.620.001blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)7532901950329019Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7144822433Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7352928048529280Rat
2298547Neuinf5Neuroinflammation QTL 53.7nervous system integrity trait (VT:0010566)spinal cord Cd74 protein level (CMO:0002131)7946224658265113Rat
10059592Kidm45Kidney mass QTL 453.950.025kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)7757398552573985Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7135342956Rat
10755440Coatc10Coat color QTL 100coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7749649952496499Rat
1354637Scl30Serum cholesterol level QTL 303.7blood cholesterol amount (VT:0000180)blood total cholesterol level (CMO:0000051)71965431749753746Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7134000259Rat
1354639Spl5Serum phospholipid level QTL 53.9blood LDL phospholipid amount (VT:0010505)blood low density lipoprotein phospholipid level (CMO:0001568)71965431752888450Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7131962314Rat
10755451Coatc11Coat color QTL 110coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)71794435762944357Rat
2317059Aia15Adjuvant induced arthritis QTL 152.46joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)71700459862004598Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7144782185Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
2290372Gluco33Glucose level QTL 332.71blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)72055570529891047Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1582260Bw72Body weight QTL 723.20.0043body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7131962314Rat
1582261Bw69Body weight QTL 693.20.0048body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
1582262Bw75Body weight QTL 7530.0038body mass (VT:0001259)body weight (CMO:0000012)71579556538073970Rat
70190Mcs6Mammary carcinoma susceptibility QTL 62.29mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)72673740163902784Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
61369Mcs2Mammary carcinoma susceptibility QTL 23.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)71903280735526300Rat
738033Anxrr6Anxiety related response QTL 64.1exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)71557388960573889Rat

Markers in Region
RH139206  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2728,135,180 - 28,135,301 (+)MAPPERmRatBN7.2
Rnor_6.0734,483,086 - 34,483,206NCBIRnor6.0
Rnor_5.0734,548,008 - 34,548,128UniSTSRnor5.0
RGSC_v3.4730,649,318 - 30,649,438UniSTSRGSC3.4
Celera725,233,880 - 25,234,000UniSTS
RH 3.4 Map7189.3UniSTS
Cytogenetic Map7q13UniSTS


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: ENSRNOT00000007351   ⟹   ENSRNOP00000007351
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl728,130,427 - 28,137,129 (-)Ensembl
Rnor_6.0 Ensembl734,478,331 - 34,485,034 (-)Ensembl
RefSeq Acc Id: NM_001126091   ⟹   NP_001119563
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8730,017,460 - 30,024,162 (-)NCBI
mRatBN7.2728,130,427 - 28,137,129 (-)NCBI
Rnor_6.0734,478,331 - 34,485,034 (-)NCBI
Rnor_5.0734,543,253 - 34,549,956 (-)NCBI
RGSC_v3.4730,644,564 - 30,651,266 (-)RGD
Celera725,229,126 - 25,235,828 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001119563 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM16907 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000007351.4
RefSeq Acc Id: NP_001119563   ⟸   NM_001126091
- UniProtKB: D4AAT4 (UniProtKB/TrEMBL),   A6IFZ1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000007351   ⟸   ENSRNOT00000007351
Protein Domains
Sm

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4AAT4-F1-model_v2 AlphaFold D4AAT4 1-86 view protein structure

Transcriptome

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

Promoters
RGD ID:13695148
Promoter ID:EPDNEW_R5673
Type:multiple initiation site
Name:Snrpf_1
Description:small nuclear ribonucleoprotein polypeptide F
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_6.0734,484,956 - 34,485,016EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1588229 AgrOrtholog
BioCyc Gene G2FUF-34386 BioCyc
Ensembl Genes ENSRNOG00000005556 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000007351.6 UniProtKB/TrEMBL
Gene3D-CATH 2.30.30.100 UniProtKB/TrEMBL
InterPro IPR047575 UniProtKB/TrEMBL
  LSM_domain UniProtKB/TrEMBL
  LSM_related_domain UniProtKB/TrEMBL
  Sm_F UniProtKB/TrEMBL
  snRNP_SmF UniProtKB/TrEMBL
KEGG Report rno:680737 UniProtKB/TrEMBL
NCBI Gene 680737 ENTREZGENE
PANTHER PTHR11021 UniProtKB/TrEMBL
  SMALL NUCLEAR RIBONUCLEOPROTEIN F UniProtKB/TrEMBL
Pfam LSM UniProtKB/TrEMBL
PhenoGen Snrpf PhenoGen
PIRSF snRNP_SmF UniProtKB/TrEMBL
PROSITE PS52002 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000005556 RatGTEx
SMART SM00651 UniProtKB/TrEMBL
Superfamily-SCOP Sm_like_riboprot UniProtKB/TrEMBL
UniProt A6IFZ1 ENTREZGENE, UniProtKB/TrEMBL
  D4AAT4 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-03-05 Snrpf  small nuclear ribonucleoprotein polypeptide F  LOC680737  similar to Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-11-19 LOC680737  similar to Small nuclear ribonucleoprotein F (snRNP-F) (Sm protein F) (Sm-F) (SmF)      Symbol and Name status set to provisional 70820 PROVISIONAL