Eif1a (eukaryotic translation initiation factor 1A)

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Gene: Eif1a (eukaryotic translation initiation factor 1A) Rattus norvegicus

Analyze

Symbol:

Eif1a

Name:

eukaryotic translation initiation factor 1A

RGD ID:

1306331

Description:

Exhibits ribosomal large subunit binding activity. Predicted to be involved in translational initiation. Orthologous to human EIF1AY (eukaryotic translation initiation factor 1A Y-linked); PARTICIPATES IN translation initiation pathway; INTERACTS WITH (+)-schisandrin B; 2,4-dibromophenyl 2,4,5-tribromophenyl ether; 2,4-dinitrotoluene.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Ab1-287; eIF-1A; eIF-4C; eukaryotic translation initiation factor 4C; liver regeneration-related protein LRRG048; LOC317163; X-linked eukaryotic translation initiation factor 1A

RGD Orthologs

Mouse

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	18	39,325,695 - 39,338,043 (+)	NCBI
Rnor_6.0 Ensembl	18	40,586,315 - 40,597,671 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	40,586,315 - 40,598,661 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	40,240,997 - 40,253,343 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	40,808,057 - 40,819,421 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	40,845,597 - 40,856,958 (+)	NCBI
Celera	18	37,577,743 - 37,589,140 (+)	NCBI		Celera
Cytogenetic Map	18	q11	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-schisandrin B (EXP)

1,2-dichloroethane (ISO)

1,2-dimethylhydrazine (ISO)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

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

2,4-diaminotoluene (ISO)

2,4-dibromophenyl 2,4,5-tribromophenyl ether (EXP)

2,4-dinitrotoluene (EXP)

3,3',4,4'-tetrachlorobiphenyl (ISO)

3-methylcholanthrene (ISO)

4-hydroxyphenyl retinamide (ISO)

aflatoxin B1 (ISO)

all-trans-retinoic acid (ISO)

Aroclor 1254 (ISO)

benzo[a]pyrene (ISO)

carbon nanotube (ISO)

clofibrate (ISO)

clopidogrel (ISO)

cocaine (EXP)

dibutyl phthalate (EXP,ISO)

diclofenac (ISO)

endosulfan (EXP)

ethanol (ISO)

fluoranthene (ISO)

flutamide (EXP)

isoprenaline (ISO)

ketamine (EXP)

lipopolysaccharide (ISO)

methamphetamine (EXP)

nefazodone (EXP)

nickel atom (ISO)

nitric oxide (ISO)

paracetamol (ISO)

phenytoin (EXP)

phosgene (ISO)

pirinixic acid (ISO)

pyrogallol (ISO)

S-butyl-DL-homocysteine (S,R)-sulfoximine (ISO)

silicon dioxide (ISO)

sodium dichromate (EXP)

tamoxifen (ISO)

tetrachloromethane (EXP,ISO)

trimellitic anhydride (ISO)

triphenyl phosphate (EXP)

valproic acid (ISO)

vancomycin (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

translational initiation (IEA)

Cellular Component

cellular_component (ND)

Molecular Function

ribosomal large subunit binding (IDA)

translation initiation factor activity (IEA)

Molecular Pathway Annotations Click to see Annotation Detail View

translation initiation pathway (ISO)

References

References - curated


1.	Hinnebusch AG Annu Rev Biochem. 2014;83:779-812. doi: 10.1146/annurev-biochem-060713-035802. Epub 2014 Jan 29.
2.	MGD data from the GO Consortium
3.	RGD automated data pipeline
4.	RGD automated import pipeline for gene-chemical interactions
5.	RGD comprehensive gene curation
6.	Wu X, etal., Biol Chem. 1997 May;378(5):363-72.

Additional References at PubMed

PMID:12477932	PMID:25943107

Genomics

Comparative Map Data

Eif1a
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	18	39,325,695 - 39,338,043 (+)	NCBI
Rnor_6.0 Ensembl	18	40,586,315 - 40,597,671 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	18	40,586,315 - 40,598,661 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	18	40,240,997 - 40,253,343 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	18	40,808,057 - 40,819,421 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	18	40,845,597 - 40,856,958 (+)	NCBI
Celera	18	37,577,743 - 37,589,140 (+)	NCBI		Celera
Cytogenetic Map	18	q11	NCBI

Eif1a
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	18	46,730,771 - 46,743,292 (+)	NCBI	GRCm39		mm39
GRCm39 Ensembl	18	46,730,768 - 46,749,523 (+)	Ensembl
GRCm38	18	46,597,704 - 46,610,225 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	18	46,597,701 - 46,616,456 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	18	46,757,358 - 46,769,879 (+)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	18	46,723,035 - 46,735,539 (+)	NCBI			mm8
Celera	18	47,957,314 - 47,969,746 (+)	NCBI		Celera
Cytogenetic Map	18	C	NCBI

Position Markers

RH137026

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,597,489 - 40,597,656	NCBI	Rnor6.0
Rnor_5.0	18	40,252,171 - 40,252,338	UniSTS	Rnor5.0
RGSC_v3.4	18	40,819,232 - 40,819,399	UniSTS	RGSC3.4
Celera	18	37,588,951 - 37,589,118	UniSTS
Cytogenetic Map	18	q11	UniSTS

RH139172

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,596,604 - 40,596,766	NCBI	Rnor6.0
Rnor_5.0	18	40,251,286 - 40,251,448	UniSTS	Rnor5.0
RGSC_v3.4	18	40,818,347 - 40,818,509	UniSTS	RGSC3.4
Celera	18	37,588,066 - 37,588,228	UniSTS
Cytogenetic Map	18	q11	UniSTS

RH140145

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,597,953 - 40,598,167	NCBI	Rnor6.0
Rnor_5.0	18	40,252,635 - 40,252,849	UniSTS	Rnor5.0
RGSC_v3.4	18	40,819,696 - 40,819,910	UniSTS	RGSC3.4
Celera	18	37,589,415 - 37,589,629	UniSTS
Cytogenetic Map	18	q11	UniSTS

RH141021

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	18	40,597,016 - 40,597,203	NCBI	Rnor6.0
Rnor_5.0	18	40,251,698 - 40,251,885	UniSTS	Rnor5.0
RGSC_v3.4	18	40,818,759 - 40,818,946	UniSTS	RGSC3.4
Celera	18	37,588,478 - 37,588,665	UniSTS
Cytogenetic Map	18	q11	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
2299160	Iddm35	Insulin dependent diabetes mellitus QTL 35	2.79		blood glucose amount (VT:0000188)	age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)	18	4407513	62570466	Rat
2312568	Glom21	Glomerulus QTL 21	2	0.005	kidney glomerulus morphology trait (VT:0005325)	index of glomerular damage (CMO:0001135)	18	5430134	41781619	Rat
2313082	Bss85	Bone structure and strength QTL 85	0.8	0.0001	long bone metaphysis morphology trait (VT:0000133)	tibia midshaft total cross-sectional area (CMO:0001715)	18	14678852	59678852	Rat
1331753	Bp231	Blood pressure QTL 231	3.643		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539427	53861431	Rat
1358358	Sradr6	Stress Responsive Adrenal Weight QTL 6	2.49		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	18	15539427	61499684	Rat
6903359	Bp355	Blood pressure QTL 355	3.6		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	15539671	61985648	Rat
2293708	Bss46	Bone structure and strength QTL 46	8.8	0.0001	lumbar vertebra morphology trait (VT:0010494)	lumbar vertebra cortical cross-sectional area (CMO:0001690)	18	15695872	68524999	Rat
1578661	Bss20	Bone structure and strength QTL 20	3.7		femur morphology trait (VT:0000559)	femoral neck cross-sectional area (CMO:0001697)	18	15695872	87080053	Rat
1578667	Bss21	Bone structure and strength QTL 21	3.5		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	18	15695872	87080053	Rat
1358193	Emca2	Estrogen-induced mammary cancer QTL 2	1.6		mammary gland integrity trait (VT:0010552)	post-insult time to mammary tumor formation (CMO:0000345)	18	19031030	68436105	Rat
1600373	Mamtr6	Mammary tumor resistance QTL 6			mammary gland integrity trait (VT:0010552)	mammary tumor number (CMO:0000343)	18	20285758	87080053	Rat
7387267	Uae42	Urinary albumin excretion QTL 42		0.61	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	14	21639491	66639491	Rat
1331741	Bp232	Blood pressure QTL 232	3.59112		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22603736	87074531	Rat
6903353	Bp353	Blood pressure QTL 353	2.8		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	22604764	61985648	Rat
1641923	Colcr8	Colorectal carcinoma resistance QTL 8	3.1	0.0014	intestine integrity trait (VT:0010554)	poorly differentiated malignant colorectal tumor number (CMO:0002076)	18	23184227	53861431	Rat
1331733	Bp233	Blood pressure QTL 233	3.97196		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	25961026	81761656	Rat
2325839	Bp348	Blood pressure QTL 348		0.001	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	26743404	43659626	Rat
2301413	Bp318	Blood pressure QTL 318		0.002	arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	27743024	48499517	Rat
12904673	Cm127	Cardiac mass QTL 127		0.005	heart right ventricle mass (VT:0007033)	heart right ventricle weight to body weight ratio (CMO:0000914)	18	27743024	48499517	Rat
12904675	Am19	Aortic mass QTL 19		0.001	aorta mass (VT:0002845)	aorta weight to aorta length to body weight ratio (CMO:0002722)	18	27743024	48499517	Rat
12904677	Kidm72	Kidney mass QTL 72		0.001	kidney mass (VT:0002707)	both kidneys wet weight to body weight ratio (CMO:0000340)	18	27743024	48499517	Rat
12904668	Bw188	Body weight QTL 188		0.03	body mass (VT:0001259)	body weight (CMO:0000012)	18	27743024	48499517	Rat
12904669	Cm125	Cardiac mass QTL 125		0.001	heart mass (VT:0007028)	heart wet weight to body weight ratio (CMO:0002408)	18	27743024	48499517	Rat
12904670	Cm126	Cardiac mass QTL 126		0.001	heart left ventricle mass (VT:0007031)	heart left ventricle weight to body weight ratio (CMO:0000530)	18	27743024	48499517	Rat
2300157	Bmd66	Bone mineral density QTL 66	13.1	0.0001	lumbar vertebra mineral mass (VT:0010511)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2300177	Bmd65	Bone mineral density QTL 65	19.7	0.0001	femur mineral mass (VT:0010011)	volumetric bone mineral density (CMO:0001553)	18	30533614	75533614	Rat
2293704	Bss35	Bone structure and strength QTL 35	4.59	0.0002	femur strength trait (VT:0010010)	femur midshaft polar moment of inertia (CMO:0001669)	18	30533614	75533614	Rat
9590318	Scort22	Serum corticosterone level QTL 22	7.64	0.001	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	18	31361341	76361341	Rat
1331754	Bp230	Blood pressure QTL 230	4.61609		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	31361341	76361341	Rat
9589816	Gluco68	Glucose level QTL 68	7.25	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	31361341	76361341	Rat
8694378	Bw157	Body weight QTL 157	3.59	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	18	31361341	76361341	Rat
738005	Anxrr11	Anxiety related response QTL 11	3.4		exploratory behavior trait (VT:0010471)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	18	31608424	76608424	Rat
61383	Bp47	Blood pressure QTL 47	17.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	18	31728373	62570429	Rat
1331776	Bp225	Blood pressure QTL 225	2.829		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	18	32670352	61985812	Rat
1331774	Bp226	Blood pressure QTL 226	4.41065		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331742	Bp228	Blood pressure QTL 228	3.88752		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331798	Bp224	Blood pressure QTL 224	3.53873		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	61985812	Rat
1331727	Bp237	Blood pressure QTL 237	3.053		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670352	63897621	Rat
61429	Cia17	Collagen induced arthritis QTL 17	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	18	32670352	73016546	Rat
2303120	Mamtr8	Mammary tumor resistance QTL 8		0.001	mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	18	32670352	87080053	Rat
6903347	Bp350	Blood pressure QTL 350	4.4		arterial blood pressure trait (VT:2000000)	mean arterial blood pressure (CMO:0000009)	18	32670473	61985648	Rat
631274	Sprol1	Serum protein level QTL 1	5.3		blood total protein amount (VT:0005567)	serum total protein level (CMO:0000661)	18	32704022	80696226	Rat
631518	Bw11	Body weight QTL 11	2.8		body mass (VT:0001259)	body weight (CMO:0000012)	18	38221919	83221919	Rat
61367	Iddm4	Insulin dependent diabetes mellitus QTL 4	2.33	0.0074	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	18	40375769	85375769	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	98
Count of miRNA genes:	77
Interacting mature miRNAs:	91
Transcripts:	ENSRNOT00000041237
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	42	57	41	19	41	5	6	74	35	41	11	5
Low		1					3	5					3
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001008773	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_006254689	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039096934	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AY325156	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC093607	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473971	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000301	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000041237 ⟹ ENSRNOP00000046345

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	40,586,315 - 40,597,671 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000087984 ⟹ ENSRNOP00000069410

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	18	40,596,166 - 40,596,691 (+)	Ensembl

RefSeq Acc Id:

NM_001008773 ⟹ NP_001008773

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	39,325,695 - 39,337,060 (+)	NCBI
Rnor_6.0	18	40,586,315 - 40,597,678 (+)	NCBI
Rnor_5.0	18	40,240,997 - 40,253,343 (+)	NCBI
RGSC_v3.4	18	40,808,057 - 40,819,421 (+)	RGD
Celera	18	37,577,743 - 37,589,140 (+)	RGD

Sequence:

show sequence

GCGTTGTAGTGAGGACGTGGAAGAGCGTGAGGCCTCGGCGTTGCGTGGGCGGCCCTCCTTGGGC
GAGGGGAGGGGGCAGTGCGGGAACTCGACGGGAAGGGGCGTGGCCGGCCGTTGCCTAGGAAGGG
CGCGTGGTCTCGCTGCTCGCCGGGCTGAGACGGTAGAGGGGTTCTGCTGCATTTGTCACTACTG
GGAAGACTAGACCTTCCTGAGAGCCAGGCCAGAAATTTTGTAGCTGTTAGAAGCCAGGACTCTG
GAACACTGTTTGCTGCTTGTGGATCTTCTATACTTACAGTGTCGCTATTCAGTCACTTCAGATC
TGCCACTATTAAGAGACTTCCTGCCACCCATCCTAGCAGTCACAGTCACTGTCAGCAGGGACTC
CTCACCCAACCCCTGTGGTTGCCATCTTCATCATGCCAAAGAATAAAGGCAAAGGAGGCAAAAA
CAGGCGCAGAGGTAAAAATGAAAATGAACCTGAGAAGAGAGAGTTAGTGTTTAAAGAGGATGGG
CAAGAGTATGCTCAGGTGATCAAAATGCTGGGAAACGGACGGTTGGAAGCAATGTGCTTTGACG
GTGTGCGGAGGCTGTGCCACATAAGAGGGAAGTTGAGAAAAAAGGTTTGGATAAACACCTCAGA
CATTATACTGATTGGTCTACGAGACTACCAAGACAACAAGGCTGACGTAATCTTAAAGTACAAT
GCAGACGAAGCAAGAAGTCTGAAGGCATATGGAGAACTTCCAGAACATGCCAAAATCAATGAAA
CGGACACATTTGGTCCTGGGGATGACGATGAAATCCAGTTTGATGATATTGGAGATGATGATGA
AGACATTGATGATATCTAACCTGACCTAAGCACGTTACATTTCAAGTTCTCTGAAGATAGCTCT
ACACAATTGGGATCTTGACGTTCAGCTGTTAAGTAAAACTTCATTTGGCATGTGTATGACTTGT
TAATGCAAATTGATGAATTTTATTTTTTGAAGTATTATATTTCTTTGAAAACCAAAGATGTTGA
GTTATCTTAAGTGACATGTTAACACTTTGTGCTTCTGGATGTAATTGAACTTAGGGCACAGCAG
TGTGCACTGTTAAGAGACTGCCTTTCCATTTGTGATGCTTCATTTCTGGCACGTGAGTGTTTTG
TGTCAGCAGTTCTGCCGGGTGACCACCGTAGGCTGGAGTAAGTCCTGGTCCAGCACACCTGCTT
TAGACGCTAATTGTCCGGCTGCATTTGAGACGTCTCAAAGTTAGACAGGATATGGCTATTTTTG
TATTTATGGAGCCATGCCATTTTATACTTACTACGTGAAGTTCCATACATTCATTTTACCCTAT
AAGTTGTTGTCATCCATAAAAAAAATCTTACAGTGCAATTTTTAAATTTTATGGGTAGCAATTT
TGAGTTTTAAAAATTAGTCATTGCAAAAATTAAATACTTAGAGGAGATAATCCATTATCTTGAC
TTTACAAATAAAGTAGTTGACAATGTTTATATGTAATTTTACTTTTCTAAGGCATACCCAAAAA
ATAGGAAATGAAAATTAAAAGAGAAGTAAATCTGTTCTGATACTTGCATAGAGAAATTTTCAAA
GAAGGTAGTTGTTAATATTTTGTGTTAAGTCATTTTCAAAAAGTTAGCTACTGTATTGAGGCTT
GCATAATTACTATGTATTGATTAAAGTTAGTTACATAATTGTACGAGGGAAGTTTTCCTTAAAC
TAAGCTTAGGTTAAAGGAAAAGGAGCCACAGCTTAATGAAACCGTGGTTCCTATTTTCTAAATG
GAGGAGTCTAGAAACAAACAATAAAAACATGTTGGTATAAAAAAAAAAAAAAAAAAAAAAAAAG
G

hide sequence

RefSeq Acc Id:

XM_006254689 ⟹ XP_006254751

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	39,325,747 - 39,338,043 (+)	NCBI
Rnor_6.0	18	40,586,412 - 40,598,661 (+)	NCBI
Rnor_5.0	18	40,240,997 - 40,253,343 (+)	NCBI

Sequence:

show sequence

GGGGCGTGGCCGGCCGTTGCCTAGGAAGGGCGCGTGGTCTCGCTGCTCGCCGGGCTGAGACGGT
AGAGGGGTTCTGCTGCATTTGTCACTCTGTTAGAAGCCAGGACTCTGGAACACTGTTTGCTGCT
TGTGGATCTTCTATACTTACAGTGTCGCTATTCAGTCACTTCAGATCTGCCACTATTAAGAGAC
TTCCTGCCACCCATCCTAGCAGTCACAGTCACTGTCAGCAGGGACTCCTCACCCAACCCCTGTG
GTTGCCATCTTCATCATGCCAAAGAATAAAGGCAAAGGAGGCAAAAACAGGCGCAGAGGTAAAA
ATGAAAATGAATCTGAGAAGAGAGAGTTAGTGTTTAAAGAGGATGGGCAAGAGTATGCTCAGGT
GATCAAAATGCTGGGAAACGGACGGTTGGAAGCAATGTGCTTTGACGGTGTGCGGAGGCTGTGC
CACATAAGAGGGAAGTTGAGAAAAAAGGTTTGGATAAACACCTCAGACATTATACTGATTGGTC
TACGAGACTACCAAGACAACAAGGCTGACGTAATCTTAAAGTACAATGCAGACGAAGCAAGAAG
TCTGAAGGCATATGGAGAACTTCCAGAACATGCCAAAATCAATGAAACGGACACATTTGGTCCT
GGGGATGACGATGAAATCCAGTTTGATGATATTGGAGATGATGATGAAGACATTGATGATATCT
AACCTGACCTAAGCACGTTACATTTCAAGTTCTCTGAAGATAGCTCTACACAATTGGGATCTTG
ACGTTCAGCTGTTAAGTAAAACTTCATTTGGCATGTGTATGACTTGTTAATGCAAATTGATGAA
TTTTATTTTTTGAAGTATTATATTTCTTTGAAAACCAAAGATGTTGAGTTATCTTAAGTGACAT
GTTAACACTTTGTGCTTCTGGATGTAATTGAACTTAGGGCACAGCAGTGTGCACTGTTAAGAGA
CTGCCTTTCCATTTGTGATGCTTCATTTCTGGCACGTGAGTGTTTTGTGTCAGCAGTTCTGCCG
GGTGACCACCGTAGGCTGGAGTAAGTCCTGGTCCAGCACACCTGCTTTAGACGCTAATTGTCCG
GCTGCATTTGAGACGTCTCAAAGTTAGACAGGATATGGCTATTTTTGTATTTATGGAGCCATGC
CATTTTATACTTACTACGTGAAGTTCCATACATTCATTTTACCCTATAAGTTGTTGTCATCCAT
AAAAAAAATCTTACAGTGCAATTTTTAAATTTTATGGGTAGCAATTTTGAGTTTTAAAAATTAG
TCATTGCAAAAATTAAATACTTAGAGGAGATAATCCATTATCTTGACTTTACAAATAAAGTAGT
TGACAATGTTTATATGTAATTTTACTTTTCTAAGGCATACCCAAAAAATAGGAAATGAAAATTA
AAAGAGAAGTAAATCTGTTCTGATACTTGCATAGAGAAATTTTCAAAGAAGGTAGTTGTTAATA
TTTTGTGTTAAGTCATTTTCAAAAAGTTAGCTACTGTATTGAGGCTTGCATAATTACTATGTAT
TGATTAAAGTTAGTTACATAATTGTACGAGGGAAGTTTTCCTTAAACTAAGCTTAGGTTAAAGG
AAAAGGAGCCACAGCTTAATGAAACCGTGGTTCCTATTTTCTAAATGGAGGAGTCTAGAAACAA
ACAATAAAAACATGTTGGTATAAAAACATTTTTTCTTTTTAATATGTTCATTATATCTCTGGTA
TATAACAAAAATAAATGACTGGATGATTTCTAGTATATCATGAGAGGCTTTTTTTTTTTTTTTA
ATTAGACACTGGGATTTAAGATAAACAACTATTTTCCCATTTAAGTAATGCTGGTATCAGGGTT
CTGCAGTTTAACTCTTGCTGCTTAGGAAGTAAGTATAACCTTGCTATTAGTCCTCAGATGCCTT
TTAAAAGAATAGTTCCTTTCTCAGGCTTTGTTCTAGATACCTTCAAATGGTGCCTGAGCATGAA
AACAACAGTATTCACCTTCACTTTTGTTTTTTGTTTTCCAGTTAGCCCATAATAATGTAGCTTA
AGGAAATTACCCAGTCAAAAAGAAAGAAAAGCAAATAACAGTTTTCTTGATCATTGATTGGTGA
CTCTTCTAGATGCTGATGTAGATCTTTGTAAAGGTTAATTTTGTAAAATGAGCTAGACATGGTG
CCAGATTAGAGTCAGATCCCACCTCCCCAGAAGGACAGTGTGTCTTTAGAAAGAGAACATCACT
GGAGCTTTTTATTGCTATACACAGTGCATCTGAATATACTGTTAACCTAAGATTTATCCCATTG
CTGCCGTACATTTTAGTACAGGAAGAAAATTTGACCATGGGCCAGCTAGCTTGATGCATTCAAC
AGCAAACAAGATTATCTCAAGTTAGGAGGTGAGGACCAGTGCCTGAAGATGTCCTCTCAGTCCA
CAACATGTACACAACATATATGCATCAGACATGTACAAAGTTGCACTTGATGAGGCTATAGTAT
CATGTCTTGGTCATTGCAAACTATCAGAGGCAAACACTGAGGTATTTACATTGCCTGTTTACCA
ATATCTAATTTCAATCACATTCTAGATGAAGGAATGATTCTTTTATAACATGAGTGATTTATGC
TGTAAATGTTGACATAAGTGTTAGAATTAAAATGACTTGTAGTGAAATA

hide sequence

RefSeq Acc Id:

XM_039096934 ⟹ XP_038952862

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	18	39,326,204 - 39,338,043 (+)	NCBI

Protein Sequences


Protein RefSeqs	NP_001008773	(Get FASTA)	NCBI Sequence Viewer
	XP_006254751	(Get FASTA)	NCBI Sequence Viewer
	XP_038952862	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH93607	(Get FASTA)	NCBI Sequence Viewer
	AAP92557	(Get FASTA)	NCBI Sequence Viewer
	EDM14389	(Get FASTA)	NCBI Sequence Viewer
	EDM14390	(Get FASTA)	NCBI Sequence Viewer
	EDM14391	(Get FASTA)	NCBI Sequence Viewer
	Q6VV72	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001008773 ⟸ NM_001008773
- UniProtKB:	Q566D5 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPKNKGKGGKNRRRGKNENEPEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVRRLCHIRGK LRKKVWINTSDIILIGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDE IQFDDIGDDDEDIDDI hide sequence

RefSeq Acc Id:	XP_006254751 ⟸ XM_006254689
- Peptide Label:	isoform X1
- UniProtKB:	Q6VV72 (UniProtKB/Swiss-Prot)
- Sequence:	show sequence MPKNKGKGGKNRRRGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVRRLCHIRGK LRKKVWINTSDIILIGLRDYQDNKADVILKYNADEARSLKAYGELPEHAKINETDTFGPGDDDE IQFDDIGDDDEDIDDI hide sequence

RefSeq Acc Id:

ENSRNOP00000046345 ⟸ ENSRNOT00000041237

RefSeq Acc Id:

ENSRNOP00000069410 ⟸ ENSRNOT00000087984

RefSeq Acc Id:	XP_038952862 ⟸ XM_039096934
- Peptide Label:	isoform X1

Protein Domains

S1-like

Transcriptome

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

Promoters

RGD ID:

13700765

Promoter ID:

EPDNEW_R11289

Type:

initiation region

Name:

Eif1a_1

Description:

eukaryotic translation initiation factor 1A

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_R11290

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	40,586,410 - 40,586,470	EPDNEW

RGD ID:

13700775

Promoter ID:

EPDNEW_R11290

Type:

single initiation site

Name:

Eif1a_2

Description:

eukaryotic translation initiation factor 1A

SO ACC ID:

SO:0000170

Source:

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

Alternative Promoters:

null; see alsoEPDNEW_R11289

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	18	40,596,224 - 40,596,284	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

Damaging Variants

Assembly: Rnor_5.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
18	40251032	40251033	G	A	snv	IS/Kyo (KyushuU), DOB/Oda (KyushuU), IS-Tlk/Kyo (KyushuU), LE/Stm (KyushuU), LEC/Tj (KyushuU)
18	40251102	40251103	G	A	snv	IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), DOB/Oda (KyushuU), LE/Stm (KyushuU), IS/Kyo (KyushuU)
18	40251122	40251123	A	C	snv	DOB/Oda (KyushuU), LEC/Tj (KyushuU), LE/Stm (KyushuU), IS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU)

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
18	40596350	40596351	G	A	snv	LE/Stm (RGD), SHRSP/Gcrc (RGD)
18	40596420	40596421	G	A	snv	LE/Stm (RGD), SHRSP/Gcrc (RGD)
18	40596440	40596441	A	C	snv	LE/Stm (RGD), SHRSP/Gcrc (RGD)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1306331	AgrOrtholog
Ensembl Genes	ENSRNOG00000031421	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000046345	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOP00000069410	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000041237	ENTREZGENE, UniProtKB/Swiss-Prot
	ENSRNOT00000087984	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:7318425	IMAGE-MGC_LOAD
InterPro	NA-bd_OB-fold	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RNA-binding_domain_S1_IF1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TIF_eIF-1A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	TIF_eIF-1A_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:317163	UniProtKB/TrEMBL
MGC_CLONE	MGC:105626	IMAGE-MGC_LOAD
NCBI Gene	317163	ENTREZGENE
PANTHER	PTHR21668	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	eIF-1a	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Eif1a	PhenoGen
PROSITE	IF1A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	S1_IF1_TYPE	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	eIF1a	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF50249	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGRFAMs	eIF-1A	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JVA7_RAT	UniProtKB/TrEMBL
	IF1A_RAT	UniProtKB/Swiss-Prot
	Q566D5	ENTREZGENE, UniProtKB/TrEMBL
	Q6VV72	ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2005-12-06	Eif1a	eukaryotic translation initiation factor 1A	Eif1a_predicted	eukaryotic translation initiation factor 1A (predicted)	Symbol and Name updated	1559027	APPROVED
2005-01-12	Eif1a_predicted	eukaryotic translation initiation factor 1A (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)

RGD Manual Annotations