Shcbp1 (SHC binding and spindle associated 1)

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Gene: Shcbp1 (SHC binding and spindle associated 1) Rattus norvegicus

Analyze

Symbol:

Shcbp1

Name:

SHC binding and spindle associated 1

RGD ID:

1590844

Description:

Predicted to have SH2 domain binding activity. Predicted to be involved in fibroblast growth factor receptor signaling pathway and regulation of neural precursor cell proliferation. Orthologous to human SHCBP1 (SHC binding and spindle associated 1); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; 2-amino-2-deoxy-D-glucopyranose.

Type:

protein-coding

RefSeq Status:

MODEL

Also known as:

LOC364648; SHC SH2 domain-binding protein 1; Shc SH2-domain binding protein 1; similar to Shc SH2-domain binding protein 1

Orthologs:

Homo sapiens (human) : SHCBP1 (SHC binding and spindle associated 1) HGNC Alliance
Mus musculus (house mouse) : Shcbp1 (Shc SH2-domain binding protein 1) MGI Alliance
Chinchilla lanigera (long-tailed chinchilla) : Shcbp1 (SHC binding and spindle associated 1)
Pan paniscus (bonobo/pygmy chimpanzee) : SHCBP1 (SHC binding and spindle associated 1)
Canis lupus familiaris (dog) : SHCBP1 (SHC binding and spindle associated 1)
Ictidomys tridecemlineatus (thirteen-lined ground squirrel) : Shcbp1 (SHC binding and spindle associated 1)
Sus scrofa (pig) : SHCBP1 (SHC binding and spindle associated 1)
Chlorocebus sabaeus (African green monkey) : SHCBP1 (SHC binding and spindle associated 1)
Heterocephalus glaber (naked mole-rat) : Shcbp1 (SHC binding and spindle associated 1)

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
Rnor_6.0	16	90,613,826 - 90,642,683 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	90,613,870 - 90,641,420 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	89,996,147 - 90,027,873 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	90,002,645 - 90,022,167 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	16	82,361,107 - 82,392,376 (+)	NCBI		Celera
Cytogenetic Map	16	q12.5	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

Experimental Liver Cirrhosis (ISO)

synovial sarcoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,1-dichloroethene (ISO)

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (ISO)

17beta-estradiol (ISO)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

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

2,4-diaminotoluene (ISO)

2-amino-2-deoxy-D-glucopyranose (EXP)

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

3-methylcholanthrene (ISO)

4,4'-diaminodiphenylmethane (EXP,ISO)

6-propyl-2-thiouracil (EXP)

aflatoxin B1 (ISO)

aldehydo-D-glucosamine (EXP)

azathioprine (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

benzo[b]fluoranthene (ISO)

beta-D-glucosamine (EXP)

bisphenol A (EXP,ISO)

cadmium dichloride (EXP)

calcitriol (ISO)

carbon nanotube (ISO)

chloropicrin (ISO)

choline (ISO)

cisplatin (ISO)

cobalt dichloride (ISO)

copper atom (ISO)

copper(0) (ISO)

copper(II) sulfate (ISO)

coumestrol (ISO)

cyclosporin A (ISO)

DDT (ISO)

deoxynivalenol (ISO)

dexamethasone (ISO)

dibenz[a,h]anthracene (ISO)

dioxygen (ISO)

Enterolactone (ISO)

erythromycin estolate (EXP)

folic acid (ISO)

furan (EXP)

hydrogen peroxide (ISO)

indometacin (ISO)

kojic acid (ISO)

L-methionine (ISO)

lucanthone (ISO)

MeIQx (ISO)

methamphetamine (EXP,ISO)

methotrexate (ISO)

methylparaben (ISO)

N-nitrosodimethylamine (EXP)

N-Nitrosopyrrolidine (ISO)

ozone (ISO)

paracetamol (ISO)

phenethyl isothiocyanate (ISO)

phenobarbital (ISO)

phytoestrogen (ISO)

pirinixic acid (ISO)

piroxicam (ISO)

pregnenolone 16alpha-carbonitrile (ISO)

progesterone (ISO)

propanal (ISO)

resveratrol (ISO)

silicon dioxide (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

tamoxifen (ISO)

testosterone (ISO)

tetrachloromethane (ISO)

thioacetamide (EXP)

titanium dioxide (EXP,ISO)

trichloroethene (ISO)

trimellitic anhydride (ISO)

valproic acid (ISO)

zaragozic acid A (EXP,ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

fibroblast growth factor receptor signaling pathway (IBA,ISO)

regulation of neural precursor cell proliferation (ISO)

Molecular Function

protein binding (ISO)

SH2 domain 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.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3.	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:10086341	PMID:22508726

Genomics

Comparative Map Data

Shcbp1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Rnor_6.0	16	90,613,826 - 90,642,683 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	16	90,613,870 - 90,641,420 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	16	89,996,147 - 90,027,873 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	16	90,002,645 - 90,022,167 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	16	82,361,107 - 82,392,376 (+)	NCBI		Celera
Cytogenetic Map	16	q12.5	NCBI

SHCBP1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	16	46,578,591 - 46,621,379 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	16	46,578,591 - 46,621,379 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	16	46,614,466 - 46,655,311 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	16	45,171,968 - 45,212,785 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	16	45,171,967 - 45,212,785	NCBI
Celera	16	31,122,631 - 31,163,484 (-)	NCBI
Cytogenetic Map	16	q11.2	NCBI
HuRef	16	32,503,090 - 32,544,039 (-)	NCBI		HuRef
CHM1_1	16	48,019,417 - 48,062,248 (-)	NCBI		CHM1_1

Shcbp1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	8	4,785,976 - 4,829,567 (-)	NCBI
GRCm38	8	4,735,976 - 4,779,567 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	8	4,735,976 - 4,779,567 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	8	4,735,980 - 4,779,534 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	8	4,735,980 - 4,779,534 (-)	NCBI			mm8
Celera	8	4,929,794 - 4,973,513 (-)	NCBI		Celera
Cytogenetic Map	8	A1.1	NCBI

Shcbp1
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955448	72,191 - 141,588 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955448	74,969 - 141,627 (-)	NCBI	ChiLan1.0	ChiLan1.0

SHCBP1
(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	16	45,741,706 - 45,783,226 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	16	45,741,101 - 45,783,632 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	16	26,847,164 - 26,890,762 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

SHCBP1
(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	15	8,465,409 - 8,490,214 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	15	8,465,366 - 8,491,085 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Shcbp1
(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_004936597	440,126 - 442,842 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

SHCBP1
(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	38,029,572 - 38,063,859 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	6	38,029,869 - 38,063,773 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	6	33,218,790 - 33,224,681 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

SHCBP1
(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 Ensembl	5	32,438,361 - 32,480,284 (-)	Ensembl
ChlSab1.1	5	32,438,918 - 32,480,410 (-)	NCBI

Shcbp1
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624914	39,197 - 107,922 (-)	NCBI

Position Markers

AI502109

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	16	90,641,194 - 90,641,395	NCBI	Rnor6.0
Rnor_5.0	16	90,026,384 - 90,026,585	UniSTS	Rnor5.0
Celera	16	82,390,886 - 82,391,087	UniSTS
Cytogenetic Map	16	q12.5	UniSTS

AW534701

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	16	90,641,840 - 90,642,000	NCBI	Rnor6.0
Rnor_5.0	16	90,027,030 - 90,027,190	UniSTS	Rnor5.0
Celera	16	82,391,533 - 82,391,693	UniSTS
Cytogenetic Map	16	q12.5	UniSTS
RH 3.4 Map	16	794.8	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
7205510	Activ5	Activity QTL 5	3.78	0.00028	locomotor behavior trait (VT:0001392)	number of entries into a discrete space in an experimental apparatus (CMO:0000960)	16	46558188	90668790	Rat
7411648	Foco22	Food consumption QTL 22	15	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	16	57816357	90668790	Rat
8694429	Bw164	Body weight QTL 164	5	0.001	body lean mass (VT:0010483)	lean tissue morphological measurement (CMO:0002184)	16	57816357	90668790	Rat
8694364	Abfw7	Abdominal fat weight QTL 7	12.22	0.001	visceral adipose mass (VT:0010063)	abdominal fat pad weight to body weight ratio (CMO:0000095)	16	57816357	90668790	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	79
Count of miRNA genes:	65
Interacting mature miRNAs:	67
Transcripts:	ENSRNOT00000071993
Prediction methods:	Microtar, Miranda, Rnahybrid
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	2	26	26	20	14	20			30	18	35
Low	1	12	24	15	5	15	4	4	44	12	6	11	4
Below cutoff		5	7	6		6	4	7		5			4

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008773569	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_017600413	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AABR07026727	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01089493	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	AAHX01089494	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000079334 ⟹ ENSRNOP00000072261

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	16	90,613,870 - 90,641,420 (+)	Ensembl

RefSeq Acc Id:

XM_008773569 ⟹ XP_008771791

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Celera	16	82,361,107 - 82,392,376 (+)	NCBI

Sequence:

show sequence

TCATCGCGTTCCGGTTTGTGACAGCCGCCCGCGTAAATTCGAAATGGCTGATGATTTGCAGGCG
GGTGTAGTTCTGGAACCTGACGCTATGGTTCCACCGAGACCTGAGTTGGCGGCGGAGGAGGAAC
CGGCGTCCTGGAAGGAAGGTTTATTCCAGGATACAGATCCATGCAGTGATTGTGGCTATCATGC
TAATCCAGGTGCTACTGTAAAAACTCTAATGCCAGAAGGAAAAATTCTTTTTCCACAAATTATC
CAAACAAATGAACTTCTGTTTTATGAGCGATTCAGAGCCTATCAGGATTACATTTTAGCTGACT
GTAAGGCCTCTGAAGTAAAGGAATTCACAGTCAGCTTCTTGGAAAAGGTCCTTGAACCATCTGG
ATGGTGGGCAGTCTGGCACACTAATGTGTTTGAGGTGTTGGTTGAGGTAAGTAGAGCTTTTGGA
CCGAAGGAGTTTCATCTGCCTCTGCAGGAGCTGTGGGTGGTATCAGATGACTCACATGAAGTTC
ACCAGATGGCCCTTGCGATCGAGCACGTCAGATTTTTCTACAAAAACATCTGGAGAAGTTGGGA
TGAAGAAGAGGAGGATGAGTATGATTATTTTGTCAGATGTGTTGAACCTCGATTGAGATTGTAT
TATGATATACTTGAAGATCGAGTTCCCTCAGGACTTATCGTTGACTACCACAATCTGTTGTCTC
AATGTGAAGAGAGTTACAGGAAATTTTTAAATCTGAGAAGCAGTTTGTCAAGTTGTAATTCTGA
CTCTGAGCAGGAAAATATCTCCATGGTGGAAGGGTTAAATTTGTATTCAGAAATTGAACAGTTG
AAGCAAAAGCTAAAACTTATTGAGAATCCTTTGTTGAGATACGTTTTTGGTTATCAGAAAAACT
CTAATATCCAAGCAAAGGGTACTCGTCAAAATGGCCAGAAGGTCATCCATGTGGTTTCCTCCAC
CATGAAGACAGGTCTGCTTCGGTCTCTATTTAGGGACAGGTTTTGTGAGGAGTCTTGCAAAGAA
GAAACGGAAATTCAGTTCCATAGTGATCTGTTGTCTGGTATAAATGCCTGCTATGATGGTGACA
CTGTCATTGTTTGTCCTGGCCATTATGTAGTTCATGGCACCTGCTGCATAGCTGACTCCATTGA
GTTGGAAGGATACGGTCCCCCAGATGATATCATCATTGAAAAGAGGGGCAAAGGAGATACTTTT
GTGGATTGCACGGGTATGGATGTTAAAATTTCAGGCGTAAAATTTATTCAGCATGATTCTGTAG
AAGGAATCTTAATTATTCACCATGGCAAGACCACCCTGGAAAACTGTGTACTGCAATGTGAAAC
TACAGGAGTCACAGTGCGCACATCAGCAGAACTTTTTATGAAAAACTCAGATGTATATGGTGCC
AAGGGTGCTGGTATAGAAATATATCCTGGAAGTAAATGTACCCTGACTGACAATGGAATCCATC
ATTGCAAGGAAGGAATCCTCATTAAGGACTTCCTTGATGAGCATTACGATATTCCCAAAATATC
TATGATAAATAACGTCATACATAATAATGAAGGTTATGGTGTTGTTTTGGTGAAGCCTACAATT
TTCTGTGACCTACTGGAACATGCCCAAGATGAAACTAATGACAATACAGTTCAGAAAAATAAAG
AGGCAGATGTCACTGAAGGATTAGATCTGGAAGAAATGCTTCAGTGTGTGTCTAACAAAATGGA
GCCTTATGCCACAGCAGACTTTAATGAACAAGCTAAGGGAAACTGTGAAATTATAAATGAACTG
CTTGCTATTTCCATGCAAAAAGGCCGGATGAAGAAAAGACTGAGTGAACTTGGGATCGTACAAG
CTGACGACGACTTAATGTCACAGGAGATGTTTATTGAAATTGTGGGGAACCAGTTTAAGTGGAA
TGGCAAGGGGAGTTTTGGCACCTTTCTTTATTAGCTACAATGAGACCAATAGCTCACAAAGTAT
TGTGTTTTGACATGTCCTAAGCACGCTACTTATATACGTTGCTTCATTTGCTTCATAACTGTAT
ATTATATAAAGTGTACTTGATTAAGCTCGTGTGAAATATGGGTTTATTTCTACCTAAATGTATT
ATATACAGAGCACACCTTTGTAGGAAAGCCATAAAAAACAGAAAAATATGAATGTACATGTAGC
TCAATAGTAGAGCATTTGTCTAACACGTCCAAGGCCCAAGGTTCAATACCCAGCTCTCCCCCTC
GCTTCCCTCCCCAAAAAGAAAGAAAACTAATTGGAGATTTCTTATCTAGAAAATCCCCTTTTTT
AACGGAATAGCTCTGCTATATTGAGCCTTCTAGTACTTTTTTTTTCTTGTAAATACCCTTTAGC
ATTGAAGGTGAAAGAGAAAGAGGTGCAAGATGTGAGAGTAAGTGTGCAGTAGGTGTCATGTGTT
CAGTGTCCTTTGTTTGTTTGTGATAGTGTCTCTCTAGAAACTCAGTGTGTAAACCATGCTGGTC
TCAGGCTCATTGACTCGCCTTACCTCTGCCTCCCATGTGCTGAGATTAGAGACACATGCCACCA
TACCTAGTTTGAATGGGATACTTTTTTAATTGAAATTATTGTCATTAAATAGGTCACAGGTATG
TGTTCAGAGCCAGTATTGAATATAAATGATTATAAGAATATTTAATTGCATGTAAAACTTTTGA
AGTATGCAAAAGTATGTTACAGTTAACATTTTTTTCCTGACTTTTTAGGCATGTGAAAATTTCA
TAAAACTGTTGTTTGAAATTTTTCTATTTTCTCTGCTCATCAGCTAAAACCTCTCAAAGCCTCT
TCCCACAGGTAAAGCTTAATGAGCTGGGTCAACAATGCTCCCATCCAGGTGGTCCAAATGCAGT
GAGACCAGGACCTGAGATATTGGGATTTAGACATCACATGGTGAAAGCTCAGAGTAACCTGATT
TGATGAGTTTGAATTGAGGGATAAATGTGTAGCAGGACAGGTCTTTCTTGTTTTGTATATGAAG
GCTTCAAACTACCAGGGTATCACAATTAAAGACCAGTTTTGAAATGTACTGGCCCAATGGACTG
AGGATTAGGGAGACAAAATATATAAATATATTTATTACAGTTCCTCGCATTGTGGTGACCTATA
ACCATAAATAATATAAAATAAAAATTAGAAAAATTAATAATATATCACATTTAATAAAAATAAT
GTCTTTCCTTGAAATTCA

hide sequence

RefSeq Acc Id:

XM_017600413 ⟹ XP_017455902

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	16	90,613,826 - 90,642,683 (+)	NCBI

Sequence:

show sequence

GTCATCGCGTTCCGGTTTGTGACAGCCGCCCGCGTAAATTCGAAATGGCTGATGATTTGCAGGC
GGGTGTAGTTCTGGAACCTGACGCTATGGTTCCACCGAGACCTGAGTTGGCGGCGGAGGAGGAA
CCGGCGTCCTGGAAGGAAGGTTTATTCCAGGATACAGATCCATGCAGTGATTGTGGCTATCATG
CTAATCCAGGTGCTACTGTAAAAACTCTAATGCCAGAAGGAAAAATTCTTTTTCCACAAATTAT
CCAAACAAATGAACTTCTGTTTTATGAGCGATTCAGAGCCTATCAGGATTACATTTTAGCTGAC
TGTAAGGCCTCTGAAGTAAAGGAATTCACAGTCAGCTTCTTGGAAAAGGTCCTTGAACCATCTG
GATGGTGGGCAGTCTGGCACACTAATGTGTTTGAGGTGTTGGTTGAGGTAAGTAGATATTTAAG
CCACACCTCCATCCTTTTGAGCCAGTGGTTGAATTTTATTGATATTAAGCTTCTTTTCAGATTT
TTCTACAAAAACATCTGGAGAAGTTGGGATGAAGAAGAGGAGGATGAGTATGATTATTTTGTCA
GATGTGTTGAACCTCGATTGAGATTGTATTATGATATACTTGAAGATCGAGTTCCCTCAGGACT
TATCGTTGACTACCACAATCTGTTGTCTCAATGTGAAGAGAGTTACAGGAAATTTTTAAATCTG
AGAAGCAGTTTGTCAAGTTGTAATTCTGACTCTGAGCAGGAAAATATCTCCATGGTGGAAGGGT
TAAATTTGTATTCAGAAATTGAACAGTTGAAGCAAAAGCTAAAACTTATTGAGAATCCTTTGTT
GAGATACGTTTTTGGTTATCAGAAAAACTCTAATATCCAAGCAAAGGGTACTCGTCAAAATGGC
CAGAAGGTCATCCATGTGGTTTCCTCCACCATGAAGACAGGTCTGCTTCGGTCTCTATTTAGGG
ACAGGTTTTGTGAGGAGTCTTGCAAAGAAGAAACGGAAATTCAGTTCCATAGTGATCTGTTGTC
TGGTATAAATGCCTGCTATGATGGTGACACTGTCATTGTTTGTCCTGGCCATTATGTAGTTCAT
GGCACCTGCTGCATAGCTGACTCCATTGAGTTGGAAGGATACGGTCCCCCAGATGATATCATCA
TTGAAAAGAGGGGCAAAGGAGATACTTTTGTGGATTGCACGGGTATGGATGTTAAAATTTCAGG
CGTAAAATTTATTCAGCATGATTCTGTAGAAGGAATCTTAATTATTCACCATGGCAAGACCACC
CTGGAAAACTGTGTACTGCAATGTGAAACTACAGGAGTCACAGTGCGCACATCAGCAGAACTTT
TTATGAAAAACTCAGATGTATATGGTGCCAAGGGTGCTGGTATAGAAATATATCCTGGAAGTAA
ATGTACCCTGACTGACAATGGAATCCATCATTGCAAGGAAGGAATCCTCATTAAGGACTTCCTT
GATGAGCATTACGATATTCCCAAAATATCTATGATAAATAACGTCATACATAATAATGAAGGTT
ATGGTGTTGTTTTGGTGAAGCCTACAATTTTCTGTGACCTACTGGAACATGCCCAAGATGAAAC
TAATGACAATACAGTTCAGAAAAATAAAGAGGCAGATGTCACTGAAGGATTAGATCTGGAAGAA
ATGCTTCAGTGTGTGTCTAACAAAATGGAGCCTTATGCCACAGCAGACTTTAATGAACAAGCTA
AGGGAAACTGTGAAATTATAAATGAACTGCTTGCTATTTCCATGCAAAAAGGCCGGATGAAGAA
AAGACTGAGTGAACTTGGGATCGTACAAGCTGACGACGACTTAATGTCACAGGAGATGTTTATT
GAAATTGTGGGGAACCAGTTTAAGTGGAATGGCAAGGGGAGTTTTGGCACCTTTCTTTATTAGC
TACAATGAGACCAATAGCTCACAAAGTATTGTGTTTTGACATGTCCTAAGCACGCTACTTATAT
ACGTTGCTTCATTTGCTTCATAACTGTATATTATATAAAGTGTACTTGATTAAGCTCGTGTGAA
ATATGGGTTTATTTCTACCTAAATGTATTATATACAGAGCACACCTTTGTAGGAAAGCCATAAA
AAACAGAAAATATGAATGTACATGTAGCTCAATAGTAGAGCATTTGTCTAACACGTCCAAGGCC
CAAGGTTCAATACCCAGCTCTCCCCCTCGCTTCCCTCCCCAAAAAGAAAGAAAACTAATTGGAG
ATTTCTTATCTAGAAAATCCCCTTTTTTAACGGAATAGCTCTGCTATATTGAGCCTTCTAGTAC
TTTTTTTTTCTTGTAAATACCCTTTAGCATTGAAGGTGAAAGAGAAAGAGGTGCAAGATGTGAG
AGTAAGTGTGCAGTAGGTGTCATGTGTTCAGTGTCCTTTGTTTGTTTGTGATAGTGTCTCTCTA
GAAACTCAGTGTGTAAACCATGCTGGTCTCAGGCTCATTGACTCGCCTTACCTCTGCCTCCCAT
GTGCTGAGATTAGAGACACATGCCACCATACCTAGTTTGAATGGGATACTTTTTTAATTGAAAT
TATTGTCATTAAATAGGTCACAGGTATGTGTTCAGAGCCAGTATTGAATATAAATGATTATAAG
AATATTTAATTGCATGTAAAACTTTTGAAGTATGCAAAAGTATGTTACAGTTAACATTTTTTTC
CTGACTTTTTAGGCATGTGAAAATTTCATAAAACTGTTGTTTGAAATTTTTCTATTTTCTCTGC
TCATCAGCTAAAACCTCTCAAAGCCTCTTCCCACAGGTAAAGCTTAATGAGCTGGGTCAACAAT
GCTCCCATCCAGGTGGTCCAAATGCAGTGAGACCAGGACCTGAGATATTGGGATTTAGACATCA
CATGGTGAAAGCTCAGAGTAACCTGATTTGATGAGTTTGAATTGAGGGATAAATGTGTAGCAGG
ACAGGTCTTTCTTGTTTTGTATATGAAGGCTTCAAACTACCAGGGTATCACAATTAAAGACCAG
TTTTGAAATGTACTGGCCCAATGGACTGAGGATTAGGGAGACAAAATATATAAATATATTTATT
ACAGTTCCTCGCATTGTGGTGACCTATAACCATAAATAATATAAAATAAAAATTAGAAAAATTA
ATAATATATCACATTTAATAAAAATAATGTCTTTCCTTGAAATTCA

hide sequence

Protein Sequences


Protein RefSeqs	XP_008771791	(Get FASTA)	NCBI Sequence Viewer
	XP_017455902	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

XP_008771791 ⟸ XM_008773569

- Peptide Label:

isoform X2

- Sequence:

show sequence

MADDLQAGVVLEPDAMVPPRPELAAEEEPASWKEGLFQDTDPCSDCGYHANPGATVKTLMPEGK
ILFPQIIQTNELLFYERFRAYQDYILADCKASEVKEFTVSFLEKVLEPSGWWAVWHTNVFEVLV
EVSRAFGPKEFHLPLQELWVVSDDSHEVHQMALAIEHVRFFYKNIWRSWDEEEEDEYDYFVRCV
EPRLRLYYDILEDRVPSGLIVDYHNLLSQCEESYRKFLNLRSSLSSCNSDSEQENISMVEGLNL
YSEIEQLKQKLKLIENPLLRYVFGYQKNSNIQAKGTRQNGQKVIHVVSSTMKTGLLRSLFRDRF
CEESCKEETEIQFHSDLLSGINACYDGDTVIVCPGHYVVHGTCCIADSIELEGYGPPDDIIIEK
RGKGDTFVDCTGMDVKISGVKFIQHDSVEGILIIHHGKTTLENCVLQCETTGVTVRTSAELFMK
NSDVYGAKGAGIEIYPGSKCTLTDNGIHHCKEGILIKDFLDEHYDIPKISMINNVIHNNEGYGV
VLVKPTIFCDLLEHAQDETNDNTVQKNKEADVTEGLDLEEMLQCVSNKMEPYATADFNEQAKGN
CEIINELLAISMQKGRMKKRLSELGIVQADDDLMSQEMFIEIVGNQFKWNGKGSFGTFLY

hide sequence

RefSeq Acc Id:

XP_017455902 ⟸ XM_017600413

- Peptide Label:

isoform X1

- Sequence:

show sequence

MADDLQAGVVLEPDAMVPPRPELAAEEEPASWKEGLFQDTDPCSDCGYHANPGATVKTLMPEGK
ILFPQIIQTNELLFYERFRAYQDYILADCKASEVKEFTVSFLEKVLEPSGWWAVWHTNVFEVLV
EVSRYLSHTSILLSQWLNFIDIKLLFRFFYKNIWRSWDEEEEDEYDYFVRCVEPRLRLYYDILE
DRVPSGLIVDYHNLLSQCEESYRKFLNLRSSLSSCNSDSEQENISMVEGLNLYSEIEQLKQKLK
LIENPLLRYVFGYQKNSNIQAKGTRQNGQKVIHVVSSTMKTGLLRSLFRDRFCEESCKEETEIQ
FHSDLLSGINACYDGDTVIVCPGHYVVHGTCCIADSIELEGYGPPDDIIIEKRGKGDTFVDCTG
MDVKISGVKFIQHDSVEGILIIHHGKTTLENCVLQCETTGVTVRTSAELFMKNSDVYGAKGAGI
EIYPGSKCTLTDNGIHHCKEGILIKDFLDEHYDIPKISMINNVIHNNEGYGVVLVKPTIFCDLL
EHAQDETNDNTVQKNKEADVTEGLDLEEMLQCVSNKMEPYATADFNEQAKGNCEIINELLAISM
QKGRMKKRLSELGIVQADDDLMSQEMFIEIVGNQFKWNGKGSFGTFLY

hide sequence

RefSeq Acc Id:

ENSRNOP00000072261 ⟸ ENSRNOT00000079334

Protein Domains

Beta_helix

Transcriptome

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

Promoters

RGD ID:

13700268

Promoter ID:

EPDNEW_R10778

Type:

multiple initiation site

Name:

Shcbp1_1

Description:

SHC binding and spindle associated 1

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	16	90,613,846 - 90,613,906	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_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
16	90626141	90626142	T	C	snv	WKY/N (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1590844	AgrOrtholog
Ensembl Genes	ENSRNOG00000053026	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000072261	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000079334	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.160.20.10	UniProtKB/TrEMBL
InterPro	Beta_helix	UniProtKB/TrEMBL
	PbH1	UniProtKB/TrEMBL
	Pectin_lyas_fold	UniProtKB/TrEMBL
	Pectin_lyase_fold/virulence	UniProtKB/TrEMBL
NCBI Gene	364648	ENTREZGENE
Pfam	Beta_helix	UniProtKB/TrEMBL
PhenoGen	Shcbp1	PhenoGen
SMART	PbH1	UniProtKB/TrEMBL
Superfamily-SCOP	Pectin_lyas_like	UniProtKB/TrEMBL
UniProt	A0A0G2K2J0_RAT	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2016-04-27	Shcbp1	SHC binding and spindle associated 1	Shcbp1	Shc SH2-domain binding protein 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2013-05-24	Shcbp1	Shc SH2-domain binding protein 1	LOC687121	similar to Shc SH2-domain binding protein 1	Data Merged	1643240	APPROVED
2008-03-05	Shcbp1	Shc SH2-domain binding protein 1	LOC364648	similar to Shc SH2-domain binding protein 1	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2006-11-20	LOC364648	similar to Shc SH2-domain binding protein 1			Symbol and Name status set to provisional	70820	PROVISIONAL
2006-11-19	LOC687121	similar to Shc SH2-domain binding protein 1			Symbol and Name status set to provisional	70820	PROVISIONAL

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 - CTD