U2af1l4 (U2 small nuclear RNA auxiliary factor 1-like 4)

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Gene: U2af1l4 (U2 small nuclear RNA auxiliary factor 1-like 4) Rattus norvegicus

Analyze

Symbol:

U2af1l4

Name:

U2 small nuclear RNA auxiliary factor 1-like 4

RGD ID:

1305600

Description:

Predicted to have metal ion binding activity. Predicted to localize to cytoplasm and nuclear speck. Orthologous to human U2AF1L4 (U2 small nuclear RNA auxiliary factor 1 like 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 2,6-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Cb2-807; liver regeneration-related protein LRRG157/LRRG158; LOC361542; splicing factor U2AF 26 kDa subunit; U2 auxiliary factor 26; U2 small nuclear RNA auxiliary factor 1-like protein 4; U2AF1-like 4

RGD Orthologs

Human

Mouse

Bonobo

Dog

Squirrel

Pig

Green Monkey

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	85,816,225 - 85,818,462 (+)	NCBI
Rnor_6.0 Ensembl	1	89,017,479 - 89,019,937 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	89,017,414 - 89,019,651 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	90,172,229 - 90,174,953 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	85,608,372 - 85,610,419 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	85,686,482 - 85,688,530 (+)	NCBI
Celera	1	80,187,746 - 80,189,793 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

dystonia (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2,4-dinitrotoluene (EXP)

2,6-dinitrotoluene (EXP)

3,4-methylenedioxymethamphetamine (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

4,4'-sulfonyldiphenol (ISO)

atrazine (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

clofibrate (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

diazinon (ISO)

dimethyl sulfoxide (ISO)

doxorubicin (ISO)

flutamide (EXP)

folic acid (ISO)

indometacin (ISO)

methyl methanesulfonate (ISO)

N-ethyl-N-nitrosourea (ISO)

pirinixic acid (EXP)

sunitinib (ISO)

thapsigargin (ISO)

tunicamycin (ISO)

valproic acid (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

mRNA splicing, via spliceosome (IBA)

Cellular Component

cytoplasm (IEA)

nuclear speck (IEA)

spliceosomal complex (IBA)

U2AF complex (IBA)

Molecular Function

metal ion binding (IEA)

pre-mRNA 3'-splice site binding (IBA)

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5.	RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data

U2af1l4
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	1	85,816,225 - 85,818,462 (+)	NCBI
Rnor_6.0 Ensembl	1	89,017,479 - 89,019,937 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	1	89,017,414 - 89,019,651 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	1	90,172,229 - 90,174,953 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	85,608,372 - 85,610,419 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	1	85,686,482 - 85,688,530 (+)	NCBI
Celera	1	80,187,746 - 80,189,793 (+)	NCBI		Celera
Cytogenetic Map	1	q21	NCBI

U2AF1L4
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	19	35,742,464 - 35,745,445 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	19	35,742,464 - 35,745,418 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	19	36,233,365 - 36,236,319 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	40,925,268 - 40,928,176 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	19	40,925,272 - 40,928,146	NCBI
Celera	19	32,946,905 - 32,949,813 (-)	NCBI
Cytogenetic Map	19	q13.12	NCBI
HuRef	19	32,738,416 - 32,741,324 (-)	NCBI		HuRef
CHM1_1	19	36,234,748 - 36,237,653 (-)	NCBI		CHM1_1

U2af1l4
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	7	30,262,765 - 30,264,789 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	7	30,262,726 - 30,264,790 (+)	Ensembl
GRCm39 Ensembl	7	30,262,769 - 30,267,385 (+)	Ensembl
GRCm38	7	30,563,340 - 30,565,364 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	7	30,563,301 - 30,565,365 (+)	Ensembl	GRCm38		mm10	GRCm38
GRCm38.p6 Ensembl	7	30,563,344 - 30,567,960 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	7	31,348,359 - 31,350,383 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	7	30,272,100 - 30,274,124 (+)	NCBI			mm8
Celera	7	25,155,101 - 25,157,125 (+)	NCBI		Celera
Cytogenetic Map	7	B1	NCBI

U2AF1L4
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	19	41,406,661 - 41,409,548 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	41,406,661 - 41,409,548 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	19	32,672,304 - 32,675,256 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

U2AF1L4
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	1	116,888,720 - 116,890,923 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	1	116,888,680 - 116,890,911 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

U2af1l4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936570	578,088 - 580,321 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

U2AF1L4
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	6	45,167,557 - 45,172,336 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	45,167,556 - 45,172,382 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	40,625,562 - 40,627,833 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

U2AF1L4
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	30,652,352 - 30,655,077 (-)	NCBI

Position Markers

RH128813

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	89,019,476 - 89,019,630	NCBI	Rnor6.0
Rnor_5.0	1	90,174,291 - 90,174,445	UniSTS	Rnor5.0
RGSC_v3.4	1	85,610,434 - 85,610,588	UniSTS	RGSC3.4
Celera	1	80,189,808 - 80,189,962	UniSTS
RH 3.4 Map	1	846.3	UniSTS
Cytogenetic Map	1	q21	UniSTS

RH134336

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	89,016,585 - 89,017,126	NCBI	Rnor6.0
Rnor_5.0	1	90,171,400 - 90,171,941	UniSTS	Rnor5.0
RGSC_v3.4	1	85,607,543 - 85,608,084	UniSTS	RGSC3.4
Celera	1	80,186,917 - 80,187,458	UniSTS
RH 3.4 Map	1	844.0	UniSTS
Cytogenetic Map	1	q21	UniSTS

RH125642

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	1	89,019,486 - 89,019,644	NCBI	Rnor6.0
Rnor_5.0	1	90,174,301 - 90,174,459	UniSTS	Rnor5.0
RGSC_v3.4	1	85,610,444 - 85,610,602	UniSTS	RGSC3.4
Celera	1	80,189,818 - 80,189,976	UniSTS
Cytogenetic Map	1	q21	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
631688	Hcas2	Hepatocarcinoma susceptibility QTL 2	3	0.0001	liver integrity trait (VT:0010547)	liver tumorous lesion number (CMO:0001068)	1	5655769	122614963	Rat
631495	Bp96	Blood pressure QTL 96	4.52		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	23406428	108057505	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	25951907	130917265	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34993530	173445086	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	35377508	94364229	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	35377692	217372257	Rat
2313051	Bss57	Bone structure and strength QTL 57	3.7	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	43579208	126240667	Rat
2313059	Bss55	Bone structure and strength QTL 55	3.2	0.0001	tibia size trait (VT:0100001)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313072	Bss53	Bone structure and strength QTL 53	4.3	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	43579208	126240667	Rat
2313078	Bss54	Bone structure and strength QTL 54	3.5	0.0001	tibia area (VT:1000281)	tibia midshaft cross-sectional area (CMO:0001717)	1	43579208	126240667	Rat
2313094	Bss58	Bone structure and strength QTL 58	3.7	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	43579208	126240667	Rat
2313098	Bmd70	Bone mineral density QTL 70	3.6	0.0001	tibia mineral mass (VT:1000283)	cortical volumetric bone mineral density (CMO:0001730)	1	43579208	126240667	Rat
2313099	Bss56	Bone structure and strength QTL 56	2.4	0.0001	tibia size trait (VT:0100001)	tibia midshaft endosteal cross-sectional area (CMO:0001716)	1	43579208	126240667	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	49147799	156446783	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	49578577	94578577	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	49578577	169852184	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	49578693	217054291	Rat
6903308	Scl36	Serum cholesterol QTL 36	2	0.0125	blood cholesterol amount (VT:0000180)	plasma total cholesterol level (CMO:0000585)	1	50522714	94225616	Rat
61342	Bp27	Blood pressure QTL 27	3.4	0.0006	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	57761301	104391981	Rat
2300164	Bmd44	Bone mineral density QTL 44	5.4	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	1	58209327	103209327	Rat
2298545	Neuinf8	Neuroinflammation QTL 8	4.6		nervous system integrity trait (VT:0010566)	spinal cord beta-2 microglobulin mRNA level (CMO:0002125)	1	58354072	161711996	Rat
7421628	Bp361	Blood pressure QTL 361		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	1	64588516	125875986	Rat
1300121	Hrtrt1	Heart rate QTL 1	3.7		heart pumping trait (VT:2000009)	heart rate (CMO:0000002)	1	66113339	122614963	Rat
631512	Scl6	Serum cholesterol level QTL 6	9.6		blood cholesterol amount (VT:0000180)	serum total cholesterol level (CMO:0000363)	1	67227683	94201552	Rat
1549903	Bp267	Blood pressure QTL 267			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	79134941	113593716	Rat
7411712	Strs4	Sensitivity to stroke QTL 4	8.7		cerebrum integrity trait (VT:0010549)	percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)	1	79689548	124689548	Rat
61433	Cia2	Collagen induced arthritis QTL 2	5		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	1	79689765	94909507	Rat
1578780	Cm52	Cardiac mass QTL 52	3.3	0.0001	heart mass (VT:0007028)	heart wet weight (CMO:0000069)	1	82788437	239853971	Rat
10054135	Gmadr2	Adrenal mass QTL 2	1.97	0.0129	adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	83502376	128502376	Rat
2313083	Bmd74	Bone mineral density QTL 74	4	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	83656882	126240667	Rat
61344	Bp29	Blood pressure QTL 29	7.5		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	85779320	130779320	Rat
1582234	Gluco18	Glucose level QTL 18	3.4	0.0003	blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	85917265	130917265	Rat
4889494	Scort2	Serum corticosterone level QTL 2	4.2		blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	1	86776571	131776571	Rat
2300324	Fetw1	Fetal weight QTL 1	12.1	0.005	fetal growth trait (VT:0004201)	fetal body weight (CMO:0002080)	1	88634585	106002500	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	66
Count of miRNA genes:	31
Interacting mature miRNAs:	33
Transcripts:	ENSRNOT00000038154, ENSRNOT00000046569
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.

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	43	39	23	19	23	8	11	74	35	41	11	8
Low			18	18		18
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008775	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006228776	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006228777	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081930	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081934	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081940	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081942	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039081944	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC141526	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY325237	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AY325238	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473979	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000033	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000038154 ⟹ ENSRNOP00000030286

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	1	89,017,479 - 89,019,937 (+)	Ensembl

RefSeq Acc Id:

NM_001008775 ⟹ NP_001008775

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,225 - 85,818,272 (+)	NCBI
Rnor_6.0	1	89,017,414 - 89,019,461 (+)	NCBI
Rnor_5.0	1	90,172,229 - 90,174,953 (+)	NCBI
RGSC_v3.4	1	85,608,372 - 85,610,419 (+)	RGD
Celera	1	80,187,746 - 80,189,793 (+)	RGD

Sequence:

show sequence

AAGGCAAGTTGGCCTTCAACACGCGTGCGCAATCGCGTCAATGGCTGAATATTTAGCTTCGATA
TTCGGGACTGAGAAGGACAAGGTTAACTGCTCTTTTTACTTTAAGATTGGGGCCTGCCGGCACG
GGGACCGGTGCTCCCGACTTCACAACAAACCGACTTTCAGCCAGACCATAGTCCTGCTCAACTT
GTACCGGAACCCACAGAACACAGCCCAAACTGCAGATGGATCACACTGTCACGTGAGCGATGTG
GAGGTGCAAGAACACTATGATAACTTCTTTGAGGAGGTATTCACAGAACTGCAGGAGAAGTATG
GAGAAATTGAAGAGATGAATGTGTGTGATAACCTCGGGGACCACCTCGTGGGCAATGTCTATGT
TAAGTTCCGGCGGGAGGAGGATGCAGAGCGGGCTGTGGCGGAACTCAATAACCGCTGGTTCAAC
GGGCAGGCTGTGCATGCTGAGCTGTCTCCGGTCACTGACTTCCGAGAGTCATGCTGCCGACAGT
ATGAGATGGGGGAATGTACCCGAGGTGGCTTCTGCAACTTTATGCACCTGCGACCCATATCCAG
GAACTTGCGCCGGCAGCTCTATGGGCGAGGACCCAGGCATAGGTCACCTCCAAGGTCCCATACA
GGTCACCGACCCCGAGAAAGGAACCGACGCCGTTCCCCAGACCACCGGCATGGTCGCTTCTGAA
ATAAA

hide sequence

RefSeq Acc Id:

XM_006228776 ⟹ XP_006228838

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,268 - 85,818,462 (+)	NCBI
Rnor_6.0	1	89,017,492 - 89,019,651 (+)	NCBI
Rnor_5.0	1	90,172,229 - 90,174,953 (+)	NCBI

Sequence:

show sequence

AACGGAAGTGACGTAAGGAGCAGGCGCGTTGGAGTGTTCGGGTAAAAAATGGCTGAATATTTAG
CTTCGATATTCGGGACTGAGAAGGACAAGGTTAACTGCTCTTTTTACTTTAAGATTGGGGCCTG
CCGGCACGGGGACCGGTGCTCCCGACTTCACAACAAACCGACTTTCAGCCAGACCATAGTCCTG
CTCAACTTGTACCGGAACCCACAGAACACAGCCCAAACTGCAGATGGATCACACTGTCACGTGA
GCGATGTGGAGGTGCAAGAACACTATGATAACTTCTTTGAGGAGGTATTCACAGAACTGCAGGA
GAAGTATGGAGAAATTGAAGAGATGAATGTGTGTGATAACCTCGGGGACCACCTCGTGGGCAAT
GTCTATGTTAAGTTCCGGCGGGAGGAGGATGCAGAGCGGGCTGTGGCGGAACTCAATAACCGCT
GGTTCAACGGGCAGGCTGTGCATGCTGAGCTGTCTCCGGTCACTGACTTCCGAGAGTCATGCTG
CCGACAGTATGAGATGGGGGAATGTACCCGAGGTGGCTTCTGCAACTTTATGCACCTGCGACCC
ATATCCAGGAACTTGCGCCGGCAGCTCTATGGGCGAGGACCCAGGCATAGGTCACCTCCAAGGT
CCCATACAGGTCACCGACCCCGAGAAAGGAACCGACGCCGTTCCCCAGACCACCGGCATGGTCG
CTTCTGAGACTGGTGCCCTTGCTCTTCACCCAAGGGCATAGATGTTCCTGTCTAGCATCCCTTC
TCAAAGCGCTCTACACGTTCCAGTCCCATCACCCCCAGGCTTCAGAGCTTCATAACACAATGTT
CGATACAGGAACCTCCTCCTCCTCCTTTTGTCCCTCCTCCAATAAAGCTTAAGAAGTTTGTCAA
CCAAA

hide sequence

RefSeq Acc Id:

XM_006228777 ⟹ XP_006228839

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,337 - 85,818,462 (+)	NCBI
Rnor_6.0	1	89,017,521 - 89,019,651 (+)	NCBI
Rnor_5.0	1	90,172,229 - 90,174,953 (+)	NCBI

Sequence:

show sequence

TGGAGTGTTCGGGTAAAAAATGGCTGAATATTTAGCTTCGATATTCGGGACTGAGAAGGACAAG
TGAGAATGATTGGGGCCTGCCGGCACGGGGACCGGTGCTCCCGACTTCACAACAAACCGACTTT
CAGCCAGACCATAGTCCTGCTCAACTTGTACCGGAACCCACAGAACACAGCCCAAACTGCAGAT
GGATCACACTGTCACGTGAGCGATGTGGAGGTGCAAGAACACTATGATAACTTCTTTGAGGAGG
TATTCACAGAACTGCAGGAGAAGTATGGAGAAATTGAAGAGATGAATGTGTGTGATAACCTCGG
GGACCACCTCGTGGGCAATGTCTATGTTAAGTTCCGGCGGGAGGAGGATGCAGAGCGGGCTGTG
GCGGAACTCAATAACCGCTGGTTCAACGGGCAGGCTGTGCATGCTGAGCTGTCTCCGGTCACTG
ACTTCCGAGAGTCATGCTGCCGACAGTATGAGATGGGGGAATGTACCCGAGGTGGCTTCTGCAA
CTTTATGCACCTGCGACCCATATCCAGGAACTTGCGCCGGCAGCTCTATGGGCGAGGACCCAGG
CATAGGTCACCTCCAAGGTCCCATACAGGTCACCGACCCCGAGAAAGGAACCGACGCCGTTCCC
CAGACCACCGGCATGGTCGCTTCTGAGACTGGTGCCCTTGCTCTTCACCCAAGGGCATAGATGT
TCCTGTCTAGCATCCCTTCTCAAAGCGCTCTACACGTTCCAGTCCCATCACCCCCAGGCTTCAG
AGCTTCATAACACAATGTTCGATACAGGAACCTCCTCCTCCTCCTTTTGTCCCTCCTCCAATAA
AGCTTAAGAAGTTTGTCAACCAAA

hide sequence

RefSeq Acc Id:

XM_039081930 ⟹ XP_038937858

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,268 - 85,818,462 (+)	NCBI

RefSeq Acc Id:

XM_039081934 ⟹ XP_038937862

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,268 - 85,818,462 (+)	NCBI

RefSeq Acc Id:

XM_039081940 ⟹ XP_038937868

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,268 - 85,818,462 (+)	NCBI

RefSeq Acc Id:

XM_039081942 ⟹ XP_038937870

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,339 - 85,818,462 (+)	NCBI

RefSeq Acc Id:

XM_039081944 ⟹ XP_038937872

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	1	85,816,317 - 85,818,462 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001008775	(Get FASTA)	NCBI Sequence Viewer
	XP_006228838	(Get FASTA)	NCBI Sequence Viewer
	XP_006228839	(Get FASTA)	NCBI Sequence Viewer
	XP_038937858	(Get FASTA)	NCBI Sequence Viewer
	XP_038937862	(Get FASTA)	NCBI Sequence Viewer
	XP_038937868	(Get FASTA)	NCBI Sequence Viewer
	XP_038937870	(Get FASTA)	NCBI Sequence Viewer
	XP_038937872	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAP92638	(Get FASTA)	NCBI Sequence Viewer
	AAP92639	(Get FASTA)	NCBI Sequence Viewer
	EDM07736	(Get FASTA)	NCBI Sequence Viewer
	EDM07737	(Get FASTA)	NCBI Sequence Viewer
	EDM07738	(Get FASTA)	NCBI Sequence Viewer
	EDM07739	(Get FASTA)	NCBI Sequence Viewer
	EDM07740	(Get FASTA)	NCBI Sequence Viewer
	EDM07741	(Get FASTA)	NCBI Sequence Viewer
	EDM07742	(Get FASTA)	NCBI Sequence Viewer
	Q7TP17	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_001008775 ⟸ NM_001008775

- UniProtKB:

Q7TP17 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MAEYLASIFGTEKDKVNCSFYFKIGACRHGDRCSRLHNKPTFSQTIVLLNLYRNPQNTAQTADG
SHCHVSDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVA
ELNNRWFNGQAVHAELSPVTDFRESCCRQYEMGECTRGGFCNFMHLRPISRNLRRQLYGRGPRH
RSPPRSHTGHRPRERNRRRSPDHRHGRF

hide sequence

RefSeq Acc Id:	XP_006228838 ⟸ XM_006228776
- Peptide Label:	isoform X1
- UniProtKB:	Q7TP17 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MAEYLASIFGTEKDKVNCSFYFKIGACRHGDRCSRLHNKPTFSQTIVLLNLYRNPQNTAQTADG SHCHVSDVEVQEHYDNFFEEVFTELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVA ELNNRWFNGQAVHAELSPVTDFRESCCRQYEMGECTRGGFCNFMHLRPISRNLRRQLYGRGPRH RSPPRSHTGHRPRERNRRRSPDHRHGRF hide sequence

RefSeq Acc Id:

XP_006228839 ⟸ XM_006228777

- Peptide Label:

isoform X2

- Sequence:

show sequence

MIGACRHGDRCSRLHNKPTFSQTIVLLNLYRNPQNTAQTADGSHCHVSDVEVQEHYDNFFEEVF
TELQEKYGEIEEMNVCDNLGDHLVGNVYVKFRREEDAERAVAELNNRWFNGQAVHAELSPVTDF
RESCCRQYEMGECTRGGFCNFMHLRPISRNLRRQLYGRGPRHRSPPRSHTGHRPRERNRRRSPD
HRHGRF

hide sequence

RefSeq Acc Id:

ENSRNOP00000030286 ⟸ ENSRNOT00000038154

RefSeq Acc Id:	XP_038937858 ⟸ XM_039081930
- Peptide Label:	isoform X3

RefSeq Acc Id:	XP_038937862 ⟸ XM_039081934
- Peptide Label:	isoform X4

RefSeq Acc Id:	XP_038937868 ⟸ XM_039081940
- Peptide Label:	isoform X5

RefSeq Acc Id:	XP_038937872 ⟸ XM_039081944
- Peptide Label:	isoform X6

RefSeq Acc Id:	XP_038937870 ⟸ XM_039081942
- Peptide Label:	isoform X6

Protein Domains

RRM

Transcriptome

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

Promoters

RGD ID:

13689923

Promoter ID:

EPDNEW_R447

Type:

multiple initiation site

Name:

U2af1l4_1

Description:

U2 small nuclear RNA auxiliary factor 1-like 4

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	1	89,017,513 - 89,017,573	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/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)

ACI/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

ACI/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

BBDP/Wor (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

BN/SsN (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

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

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1305600	AgrOrtholog
Ensembl Genes	ENSRNOG00000024497	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000030286	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000038154	UniProtKB/Swiss-Prot
Gene3D-CATH	3.30.70.330	UniProtKB/Swiss-Prot
InterPro	Nucleotide-bd_a/b_plait_sf	UniProtKB/Swiss-Prot
	RBD_domain_sf	UniProtKB/Swiss-Prot
	RRM_dom	UniProtKB/Swiss-Prot
	RRM_dom_euk	UniProtKB/Swiss-Prot
	U2AF_small	UniProtKB/Swiss-Prot
	Znf_CCCH	UniProtKB/Swiss-Prot
KEGG Report	rno:361542	UniProtKB/Swiss-Prot
NCBI Gene	361542	ENTREZGENE
PANTHER	PTHR12620	UniProtKB/Swiss-Prot
Pfam	RRM_1	UniProtKB/Swiss-Prot
	zf-CCCH	UniProtKB/Swiss-Prot
PhenoGen	U2af1l4	PhenoGen
PRINTS	U2AUXFACTOR	UniProtKB/Swiss-Prot
PROSITE	RRM	UniProtKB/Swiss-Prot
	ZF_C3H1	UniProtKB/Swiss-Prot
SMART	RRM	UniProtKB/Swiss-Prot
	RRM_1	UniProtKB/Swiss-Prot
	ZnF_C3H1	UniProtKB/Swiss-Prot
Superfamily-SCOP	SSF54928	UniProtKB/Swiss-Prot
UniProt	Q7TP17	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	Q7TP18	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-12-06	U2af1l4	U2 small nuclear RNA auxiliary factor 1-like 4	U2af1l4_predicted	U2 small nuclear RNA auxiliary factor 1-like 4 (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	U2af1l4_predicted	U2 small nuclear RNA auxiliary factor 1-like 4 (predicted)			Symbol and Name status set to approved	70820	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

Imported Disease Annotations - ClinVar