Scaf4 (SR-related CTD-associated factor 4) - Rat Genome Database

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Gene: Scaf4 (SR-related CTD-associated factor 4) Rattus norvegicus
Analyze
Symbol: Scaf4
Name: SR-related CTD-associated factor 4
RGD ID: 727896
Description: Exhibits protein C-terminus binding activity. Involved in mRNA processing. Predicted to localize to nucleoplasm. Orthologous to human SCAF4 (SR-related CTD associated factor 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; acrylamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: CTD-binding SR-like protein rA4; LOC245924; serine/arginine-rich splicing factor 15; Sfrs15; splicing factor, arginine/serine-rich 15; SR-related and CTD-associated factor 4; Srsf15
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21129,460,479 - 29,521,153 (-)NCBI
Rnor_6.0 Ensembl1130,371,713 - 30,428,073 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01130,371,713 - 30,428,073 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01133,987,199 - 34,047,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41129,751,872 - 29,807,911 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11129,751,869 - 29,807,911 (+)NCBI
Celera1129,152,167 - 29,208,170 (-)NCBICelera
Cytogenetic Map11q11NCBI
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

Cellular Component
nucleoplasm  (IEA,ISO)
nucleus  (ISO,ISS)

Molecular Function

References

Additional References at PubMed
PMID:22681889   PMID:31104839  


Genomics

Comparative Map Data
Scaf4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21129,460,479 - 29,521,153 (-)NCBI
Rnor_6.0 Ensembl1130,371,713 - 30,428,073 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01130,371,713 - 30,428,073 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01133,987,199 - 34,047,580 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41129,751,872 - 29,807,911 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11129,751,869 - 29,807,911 (+)NCBI
Celera1129,152,167 - 29,208,170 (-)NCBICelera
Cytogenetic Map11q11NCBI
SCAF4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2131,671,000 - 31,732,118 (-)EnsemblGRCh38hg38GRCh38
GRCh382131,668,987 - 31,732,118 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372133,043,313 - 33,104,431 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362131,965,416 - 32,026,133 (-)NCBINCBI36hg18NCBI36
Celera2118,226,630 - 18,287,746 (-)NCBI
Cytogenetic Map21q22.11NCBI
HuRef2118,453,341 - 18,514,530 (-)NCBIHuRef
CHM1_12132,605,296 - 32,666,386 (-)NCBICHM1_1
Scaf4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391690,021,504 - 90,082,074 (-)NCBIGRCm39mm39
GRCm39 Ensembl1690,022,568 - 90,081,391 (-)Ensembl
GRCm381690,228,950 - 90,286,140 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1690,225,680 - 90,284,503 (-)EnsemblGRCm38mm10GRCm38
MGSCv371690,229,384 - 90,284,670 (-)NCBIGRCm37mm9NCBIm37
MGSCv361690,229,384 - 90,284,670 (-)NCBImm8
Celera1690,424,774 - 90,479,985 (-)NCBICelera
Cytogenetic Map16C3.3NCBI
Scaf4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540731,270,035 - 31,303,823 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540731,269,673 - 31,303,823 (-)NCBIChiLan1.0ChiLan1.0
SCAF4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12131,421,160 - 31,482,543 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2131,421,160 - 31,482,543 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02118,039,507 - 18,101,700 (-)NCBIMhudiblu_PPA_v0panPan3
SCAF4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.13126,546,801 - 26,583,040 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl3126,547,108 - 26,636,811 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha3126,538,227 - 26,597,009 (-)NCBI
ROS_Cfam_1.03126,665,041 - 26,723,881 (-)NCBI
UMICH_Zoey_3.13126,610,942 - 26,669,751 (-)NCBI
UNSW_CanFamBas_1.03126,622,773 - 26,681,555 (-)NCBI
UU_Cfam_GSD_1.03127,129,000 - 27,187,809 (-)NCBI
Scaf4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440497127,123,792 - 27,168,322 (-)NCBI
SpeTri2.0NW_00493650010,307,868 - 10,342,952 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCAF4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl13195,315,309 - 195,396,199 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.113195,335,178 - 195,396,246 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.213205,632,094 - 205,690,676 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCAF4
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1260,397,173 - 60,459,295 (+)NCBI
ChlSab1.1 Ensembl260,397,233 - 60,458,553 (+)Ensembl
Scaf4
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474520,040,416 - 20,097,764 (-)NCBI

Position Markers
D11Rat15  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,528,418 - 29,528,587 (+)MAPPER
Rnor_6.01130,435,339 - 30,435,507NCBIRnor6.0
Rnor_5.01134,054,821 - 34,054,989UniSTSRnor5.0
RGSC_v3.41129,744,438 - 29,744,606UniSTSRGSC3.4
RGSC_v3.41129,744,366 - 29,744,736RGDRGSC3.4
RGSC_v3.11129,744,438 - 29,744,606RGD
Celera1129,215,379 - 29,215,547UniSTS
RH 3.4 Map11167.8RGD
RH 3.4 Map11167.8UniSTS
RH 2.0 Map11469.5RGD
SHRSP x BN Map118.2299RGD
FHH x ACI Map1112.19RGD
Cytogenetic Map11q11UniSTS
D11Wox13  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,465,920 - 29,466,112 (+)MAPPER
Rnor_6.01130,372,528 - 30,372,719NCBIRnor6.0
Rnor_5.01133,992,010 - 33,992,201UniSTSRnor5.0
RGSC_v3.41129,806,905 - 29,807,096UniSTSRGSC3.4
Celera1129,152,982 - 29,153,173UniSTS
Cytogenetic Map11q11UniSTS
D11Wox12  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,479,193 - 29,479,495 (+)MAPPER
Rnor_6.01130,385,801 - 30,386,102NCBIRnor6.0
Rnor_5.01134,005,283 - 34,005,584UniSTSRnor5.0
RGSC_v3.41129,793,522 - 29,793,823UniSTSRGSC3.4
Celera1129,166,237 - 29,166,538UniSTS
Cytogenetic Map11q11UniSTS
RH141768  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,464,340 - 29,464,554 (+)MAPPER
Rnor_6.01130,370,948 - 30,371,161NCBIRnor6.0
Rnor_5.01133,990,430 - 33,990,643UniSTSRnor5.0
RGSC_v3.41129,808,463 - 29,808,676UniSTSRGSC3.4
Celera1129,151,402 - 29,151,615UniSTS
RH 3.4 Map11179.5UniSTS
Cytogenetic Map11q11UniSTS
Sra4-pending  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,494,350 - 29,495,160 (+)MAPPER
Rnor_6.01130,400,958 - 30,401,767NCBIRnor6.0
Rnor_5.01134,020,440 - 34,021,249UniSTSRnor5.0
RGSC_v3.41129,777,862 - 29,778,671UniSTSRGSC3.4
Celera1129,181,391 - 29,182,200UniSTS
Cytogenetic Map11q11UniSTS
G15982  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21129,489,064 - 29,489,119 (+)MAPPER
Rnor_6.01130,395,674 - 30,395,728NCBIRnor6.0
Rnor_5.01134,015,156 - 34,015,210UniSTSRnor5.0
Celera1129,176,107 - 29,176,161UniSTS
Cytogenetic Map11q11UniSTS


QTLs in Region (Rnor_6.0)
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)11133867429Rat
1300147Bp187Blood pressure QTL 1873.67arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)11172720192Rat
1558659Tescar1Testicular tumor resistance QTL 13.9testis integrity trait (VT:0010572)percentage of study population developing testis tumors during a period of time (CMO:0001261)1132503169342559Rat
1641927Alcrsp10Alcohol response QTL 10alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)11935127454351274Rat
2290451Scl58Serum cholesterol level QTL 583.48blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)111136730644444347Rat
724517Uae18Urinary albumin excretion QTL 183.7urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)111632197346583360Rat
724554Iddm17Insulin dependent diabetes mellitus QTL 170.001blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)111901627290463843Rat
10755497Bp388Blood pressure QTL 3882.76arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)111947517979734728Rat
1598811Bp291Blood pressure QTL 2911.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)112194422966944229Rat
1598841Memor7Memory QTL 7exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)112194422966944229Rat
634341Bw121Body weight QTL 1213.56abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)112204314944444112Rat
10058952Gmadr6Adrenal mass QTL 62.290.0072adrenal gland mass (VT:0010420)both adrenal glands wet weight to body weight ratio (CMO:0002411)112540112970401129Rat
9590313Scort20Serum corticosterone level QTL 206.510.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)112572003870720038Rat
9589032Epfw10Epididymal fat weight QTL 109.290.001epididymal fat pad mass (VT:0010421)epididymal fat pad weight to body weight ratio (CMO:0000658)112572003870720038Rat
8694376Bw156Body weight QTL 1562.250.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
8694424Bw162Body weight QTL 1623.80.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)112572003870720038Rat
724563Uae10Urinary albumin excretion QTL 106urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)112831466586994795Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:301
Count of miRNA genes:196
Interacting mature miRNAs:225
Transcripts:ENSRNOT00000002881, ENSRNOT00000047741
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.


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 26 17 16 7 16 66 27 35 3
Low 17 40 25 12 25 8 11 8 8 6 8 8
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001037347 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087959 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087960 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087961 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087962 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087963 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087965 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087966 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087967 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087968 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087969 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039087970 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AY387086 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473989 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000222 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  U49058 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000002881   ⟹   ENSRNOP00000002881
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1130,381,426 - 30,412,143 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000047741   ⟹   ENSRNOP00000047258
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1130,371,713 - 30,428,073 (-)Ensembl
RefSeq Acc Id: NM_001037347   ⟹   NP_001032424
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,465,106 - 29,521,153 (-)NCBI
Rnor_6.01130,371,713 - 30,428,073 (-)NCBI
Rnor_5.01133,987,199 - 34,047,580 (-)NCBI
RGSC_v3.41129,751,872 - 29,807,911 (+)RGD
Celera1129,152,167 - 29,208,170 (-)RGD
Sequence:
RefSeq Acc Id: XM_039087959   ⟹   XP_038943887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,465,103 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087960   ⟹   XP_038943888
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,465,103 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087961   ⟹   XP_038943889
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,465,103 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087962   ⟹   XP_038943890
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,465,103 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087963   ⟹   XP_038943891
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,460,479 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087965   ⟹   XP_038943893
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,476,744 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087966   ⟹   XP_038943894
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,476,744 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087967   ⟹   XP_038943895
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,476,744 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087968   ⟹   XP_038943896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,476,744 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087969   ⟹   XP_038943897
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,468,823 - 29,521,065 (-)NCBI
RefSeq Acc Id: XM_039087970   ⟹   XP_038943898
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21129,468,823 - 29,521,065 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001032424   ⟸   NM_001037347
- UniProtKB: Q6TUE4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000047258   ⟸   ENSRNOT00000047741
RefSeq Acc Id: ENSRNOP00000002881   ⟸   ENSRNOT00000002881
RefSeq Acc Id: XP_038943891   ⟸   XM_039087963
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038943890   ⟸   XM_039087962
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038943888   ⟸   XM_039087960
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038943889   ⟸   XM_039087961
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038943887   ⟸   XM_039087959
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038943898   ⟸   XM_039087970
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038943897   ⟸   XM_039087969
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038943896   ⟸   XM_039087968
- Peptide Label: isoform X9
RefSeq Acc Id: XP_038943895   ⟸   XM_039087967
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038943894   ⟸   XM_039087966
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038943893   ⟸   XM_039087965
- Peptide Label: isoform X6
Protein Domains
CID   RRM

Transcriptome

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

Promoters
RGD ID:13698044
Promoter ID:EPDNEW_R8569
Type:initiation region
Name:Scaf4_1
Description:SR-related CTD-associated factor 4
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_6.01130,428,134 - 30,428,194EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727896 AgrOrtholog
Ensembl Genes ENSRNOG00000002104 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000002881 UniProtKB/TrEMBL
  ENSRNOP00000047258 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000002881 UniProtKB/TrEMBL
  ENSRNOT00000047741 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.25.40.90 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  3.30.70.330 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro CID_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ENTH_VHS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SCAF4_RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:245924 UniProtKB/TrEMBL
NCBI Gene 245924 ENTREZGENE
Pfam CTD_bind UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scaf4 PhenoGen
PROSITE CID UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART RPR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  RRM UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48464 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF54928 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt F1M994_RAT UniProtKB/TrEMBL
  Q63627 ENTREZGENE
  Q6TUE4 ENTREZGENE, UniProtKB/TrEMBL
  SFR15_RAT UniProtKB/Swiss-Prot
UniProt Secondary F1LSM7 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-01 Scaf4  SR-related CTD-associated factor 4  Sfrs15  splicing factor, arginine/serine-rich 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-22 Sfrs15  splicing factor, arginine/serine-rich 15  Scaf4  SR-related CTD-associated factor 4   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-13 Srsf15  serine/arginine-rich splicing factor 15  Sfrs15  splicing factor, arginine/serine-rich 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2011-07-13 Scaf4  SR-related CTD-associated factor 4   Srsf15  serine/arginine-rich splicing factor 15  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Sfrs15  splicing factor, arginine/serine-rich 15  LOC245924  CTD-binding SR-like protein rA4  Symbol and Name updated 1299863 APPROVED