Sptbn1 (spectrin, beta, non-erythrocytic 1) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Sptbn1 (spectrin, beta, non-erythrocytic 1) Rattus norvegicus
Analyze
Symbol: Sptbn1
Name: spectrin, beta, non-erythrocytic 1
RGD ID: 727922
Description: Predicted to have GTPase binding activity and ankyrin binding activity. Predicted to be a structural constituent of cytoskeleton. Predicted to be involved in several processes, including Golgi to plasma membrane protein transport; common-partner SMAD protein phosphorylation; and positive regulation of interleukin-2 production. Localizes to glutamatergic synapse; postsynapse; and protein-containing complex. Orthologous to human SPTBN1 (spectrin beta, non-erythrocytic 1); PARTICIPATES IN transforming growth factor-beta Smad dependent signaling pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: beta II spectrin-like (short form); bSPII-; cytoskeleton protein; non-erythroid spectrin beta; short form of beta II spectrin; spectrin beta 2; spectrin beta chain, brain 1; spectrin beta chain, non-erythrocytic 1; spectrin beta non-erythrocytic 1; Spnb1; Spnb2
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214103,842,684 - 104,008,507 (-)NCBI
Rnor_6.0 Ensembl14114,518,816 - 114,692,764 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014114,517,839 - 114,700,199 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014114,188,053 - 114,356,233 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414111,076,741 - 111,246,286 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114111,255,392 - 111,259,578 (+)NCBI
Celera14102,708,226 - 102,873,561 (-)NCBICelera
Cytogenetic Map14q22NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (EXP,ISO)
1,2-dimethylhydrazine  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
2,3,7,8-Tetrachlorodibenzofuran  (EXP,ISO)
2,4-dinitrotoluene  (EXP)
2,6-dinitrotoluene  (EXP)
2-butoxyethanol  (ISO)
2-methoxyethanol  (EXP)
3,3',4,4',5-pentachlorobiphenyl  (EXP)
3,4-methylenedioxymethamphetamine  (ISO)
4,4'-diaminodiphenylmethane  (ISO)
4-hydroxyphenyl retinamide  (ISO)
4-vinylcyclohexene dioxide  (ISO)
5-aza-2'-deoxycytidine  (ISO)
6-propyl-2-thiouracil  (EXP)
acetohydrazide  (ISO)
acrolein  (ISO)
afimoxifene  (ISO)
aflatoxin B1  (ISO)
aflatoxin B2  (ISO)
all-trans-retinoic acid  (ISO)
alpha-pinene  (ISO)
AM-251  (ISO)
amiodarone  (ISO)
ammonium chloride  (EXP)
apigenin  (ISO)
Aroclor 1254  (ISO)
arsane  (ISO)
arsenic atom  (ISO)
arsenous acid  (ISO)
atrazine  (ISO)
benzene  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
benzo[b]fluoranthene  (ISO)
bis(2-chloroethyl) sulfide  (ISO)
bisphenol A  (EXP,ISO)
bortezomib  (ISO)
Brodifacoum  (EXP)
carbon nanotube  (ISO)
chloroprene  (EXP)
chlorpyrifos  (EXP)
choline  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clobetasol  (ISO)
cocaine  (ISO)
copper atom  (ISO)
copper(0)  (ISO)
CU-O LINKAGE  (ISO)
cyclosporin A  (ISO)
dexamethasone  (ISO)
diarsenic trioxide  (ISO)
dicrotophos  (ISO)
disulfiram  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
enzyme inhibitor  (ISO)
ethanol  (ISO)
fenvalerate  (EXP)
flavonoids  (EXP)
flutamide  (EXP)
folic acid  (ISO)
fonofos  (ISO)
formaldehyde  (ISO)
fumonisin B1  (ISO)
geldanamycin  (ISO)
genistein  (EXP)
gentamycin  (EXP)
L-methionine  (ISO)
lead diacetate  (ISO)
lead(0)  (ISO)
lead(2+)  (ISO)
leflunomide  (ISO)
levonorgestrel  (ISO)
lipopolysaccharide  (ISO)
mercury atom  (ISO)
mercury dichloride  (EXP)
mercury(0)  (ISO)
methapyrilene  (EXP)
methyl methanesulfonate  (ISO)
Methylazoxymethanol acetate  (EXP)
nickel atom  (ISO)
ochratoxin A  (ISO)
oxaliplatin  (ISO)
ozone  (ISO)
p-menthan-3-ol  (ISO)
paracetamol  (ISO)
parathion  (ISO)
phenobarbital  (ISO)
pirinixic acid  (ISO)
progesterone  (ISO)
quercetin  (ISO)
resveratrol  (ISO)
rimonabant  (ISO)
rotenone  (EXP)
silicon dioxide  (ISO)
silver atom  (ISO)
silver(0)  (ISO)
sodium arsenate  (ISO)
sodium arsenite  (EXP,ISO)
sulindac sulfide  (ISO)
terbufos  (ISO)
tert-butyl hydroperoxide  (ISO)
testosterone undecanoate  (ISO)
tetraphene  (ISO)
thapsigargin  (ISO)
thimerosal  (ISO)
titanium dioxide  (ISO)
Tributyltin oxide  (ISO)
triclosan  (ISO)
triptonide  (ISO)
tungsten  (ISO)
ursodeoxycholic acid  (EXP)
valproic acid  (EXP,ISO)
vinclozolin  (EXP)
vorinostat  (ISO)
zinc protoporphyrin  (ISO)
zinc sulfate  (ISO)

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:9537418   PMID:10477754   PMID:10806113   PMID:11274145   PMID:12477932   PMID:14593108   PMID:15262991   PMID:16025302   PMID:17114649   PMID:17620337   PMID:18723693   PMID:18796539  
PMID:19056867   PMID:20458337   PMID:21966409   PMID:22681889   PMID:22871113   PMID:23239625   PMID:24337748   PMID:24625528   PMID:25468996  


Genomics

Comparative Map Data
Sptbn1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.214103,842,684 - 104,008,507 (-)NCBI
Rnor_6.0 Ensembl14114,518,816 - 114,692,764 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.014114,517,839 - 114,700,199 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.014114,188,053 - 114,356,233 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.414111,076,741 - 111,246,286 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.114111,255,392 - 111,259,578 (+)NCBI
Celera14102,708,226 - 102,873,561 (-)NCBICelera
Cytogenetic Map14q22NCBI
SPTBN1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl254,456,317 - 54,671,446 (+)EnsemblGRCh38hg38GRCh38
GRCh38254,456,327 - 54,671,446 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37254,683,464 - 54,898,583 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36254,536,958 - 54,752,087 (+)NCBINCBI36hg18NCBI36
Build 34254,697,181 - 54,799,245NCBI
Celera254,523,740 - 54,739,107 (+)NCBI
Cytogenetic Map2p16.2NCBI
HuRef254,485,674 - 54,631,223 (+)NCBIHuRef
CHM1_1254,613,602 - 54,828,713 (+)NCBICHM1_1
Sptbn1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391130,049,395 - 30,218,384 (-)NCBIGRCm39mm39
GRCm39 Ensembl1130,049,395 - 30,218,175 (-)Ensembl
GRCm381130,099,395 - 30,268,384 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1130,099,395 - 30,268,175 (-)EnsemblGRCm38mm10GRCm38
MGSCv371129,999,395 - 30,119,772 (-)NCBIGRCm37mm9NCBIm37
MGSCv361130,000,434 - 30,119,772 (-)NCBImm8
Celera1132,468,358 - 32,593,393 (-)NCBICelera
Cytogenetic Map11A3.3NCBI
cM Map1117.44NCBI
Sptbn1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544120,248,578 - 20,378,038 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495544120,248,578 - 20,378,038 (+)NCBIChiLan1.0ChiLan1.0
SPTBN1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A55,822,415 - 55,961,925 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A55,822,415 - 55,961,925 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A54,608,711 - 54,816,083 (+)NCBIMhudiblu_PPA_v0panPan3
SPTBN1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11055,429,989 - 55,571,917 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1055,429,940 - 55,571,916 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1055,325,541 - 55,524,492 (+)NCBI
ROS_Cfam_1.01056,373,040 - 56,571,581 (+)NCBI
UMICH_Zoey_3.11056,064,719 - 56,261,769 (+)NCBI
UNSW_CanFamBas_1.01056,353,568 - 56,552,022 (+)NCBI
UU_Cfam_GSD_1.01056,700,647 - 56,842,710 (+)NCBI
Sptbn1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629227,462,919 - 27,650,484 (-)NCBI
SpeTri2.0NW_004936491920,830 - 1,108,374 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTBN1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl386,585,050 - 86,784,107 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1386,585,225 - 86,784,316 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
SPTBN1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11452,266,197 - 52,487,111 (-)NCBI
ChlSab1.1 Ensembl1452,262,416 - 52,487,112 (-)Ensembl
Vero_WHO_p1.0NW_02366604559,248,465 - 59,459,178 (+)NCBI
Sptbn1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248336,947,611 - 7,144,688 (-)NCBI

Position Markers
RH138476  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,915,473 - 103,915,715 (+)MAPPER
Rnor_6.014114,592,356 - 114,592,597NCBIRnor6.0
Rnor_5.014114,260,592 - 114,260,833UniSTSRnor5.0
RGSC_v3.414111,173,182 - 111,173,423UniSTSRGSC3.4
Celera14102,780,741 - 102,780,982UniSTS
Cytogenetic Map14q22UniSTS
RH141179  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.214103,849,330 - 103,849,522 (+)MAPPER
Rnor_6.014114,525,457 - 114,525,648NCBIRnor6.0
Rnor_5.014114,194,700 - 114,194,891UniSTSRnor5.0
RGSC_v3.414111,239,448 - 111,239,639UniSTSRGSC3.4
Celera14102,714,873 - 102,715,064UniSTS
Cytogenetic Map14q22UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1582259Gluco23Glucose level QTL 233.10.0008blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1480049285115493446Rat
1641900Alcrsp11Alcohol response QTL 11alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)1480049285115493446Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:95
Count of miRNA genes:84
Interacting mature miRNAs:86
Transcripts:ENSRNOT00000008210
Prediction methods:Microtar, 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 2
Medium 3 43 57 41 19 41 8 11 74 35 41 9 8
Low
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000008210   ⟹   ENSRNOP00000008210
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl14114,518,816 - 114,692,764 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000083528   ⟹   ENSRNOP00000074766
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl14114,518,943 - 114,649,173 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000084595   ⟹   ENSRNOP00000071233
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl14114,518,940 - 114,583,122 (-)Ensembl
RefSeq Acc Id: NM_001013130   ⟹   NP_001013148
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.214103,842,684 - 104,008,507 (-)NCBI
Rnor_6.014114,518,810 - 114,692,764 (-)NCBI
Rnor_5.014114,188,053 - 114,356,233 (-)NCBI
RGSC_v3.414111,076,741 - 111,246,286 (+)RGD
Celera14102,708,226 - 102,873,561 (-)RGD
Sequence:
RefSeq Acc Id: XM_008770458   ⟹   XP_008768680
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,517,839 - 114,694,298 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770460   ⟹   XP_008768682
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,517,839 - 114,618,310 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770461   ⟹   XP_008768683
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,517,839 - 114,699,643 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770462   ⟹   XP_008768684
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,527,180 - 114,617,871 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008770463   ⟹   XP_008768685
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,525,190 - 114,692,764 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017599259   ⟹   XP_017454748
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,517,839 - 114,700,199 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_001013148   ⟸   NM_001013130
- UniProtKB: Q6XD99 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768683   ⟸   XM_008770461
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768680   ⟸   XM_008770458
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008768682   ⟸   XM_008770460
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: XP_008768685   ⟸   XM_008770463
- Peptide Label: isoform X4
- Sequence:
RefSeq Acc Id: XP_008768684   ⟸   XM_008770462
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017454748   ⟸   XM_017599259
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000008210   ⟸   ENSRNOT00000008210
RefSeq Acc Id: ENSRNOP00000071233   ⟸   ENSRNOT00000084595
RefSeq Acc Id: ENSRNOP00000074766   ⟸   ENSRNOT00000083528
Protein Domains
Calponin-homology (CH)   PH

Transcriptome

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

Promoters
RGD ID:13699548
Promoter ID:EPDNEW_R10063
Type:single initiation site
Name:Sptbn1_1
Description:spectrin, beta, non-erythrocytic 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.014114,583,071 - 114,583,131EPDNEW

Strain Variation

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


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
14 114559810 114559811 T C snv Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:727922 AgrOrtholog
Ensembl Genes ENSRNOG00000005434 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000008210 UniProtKB/TrEMBL
  ENSRNOP00000071233 UniProtKB/TrEMBL
  ENSRNOP00000074766 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000008210 UniProtKB/TrEMBL
  ENSRNOT00000083528 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000084595 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7303580 IMAGE-MGC_LOAD
InterPro Actinin_actin-bd_CS UniProtKB/TrEMBL
  Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  PH_9 UniProtKB/TrEMBL
  PH_dom-spectrin-type UniProtKB/TrEMBL
  PH_like_dom UniProtKB/TrEMBL
  Pleckstrin_homology UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/TrEMBL
  Spectrin_bsu UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/TrEMBL
KEGG Report rno:305614 UniProtKB/TrEMBL
MGC_CLONE MGC:105994 IMAGE-MGC_LOAD
NCBI Gene 305614 ENTREZGENE
Pfam PF00307 UniProtKB/TrEMBL
  PH_9 UniProtKB/TrEMBL
  Spectrin UniProtKB/TrEMBL
PhenoGen Sptbn1 PhenoGen
PIRSF Spectrin_beta_subunit UniProtKB/TrEMBL
PRINTS SPECTRINPH UniProtKB/TrEMBL
PROSITE ACTININ_1 UniProtKB/TrEMBL
  ACTININ_2 UniProtKB/TrEMBL
  PH_DOMAIN UniProtKB/TrEMBL
  PS50021 UniProtKB/TrEMBL
SMART SM00033 UniProtKB/TrEMBL
  SM00233 UniProtKB/TrEMBL
  SPEC UniProtKB/TrEMBL
Superfamily-SCOP Calponin-homology UniProtKB/TrEMBL
UniProt A0A0G2JZY6_RAT UniProtKB/TrEMBL
  A0A0G2K8W9_RAT UniProtKB/TrEMBL
  G3V6S0_RAT UniProtKB/TrEMBL
  Q5D002_RAT UniProtKB/TrEMBL
  Q6XD99 ENTREZGENE, UniProtKB/TrEMBL
  Q9WUX0_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-09-18 Sptbn1  spectrin, beta, non-erythrocytic 1  Spnb2  spectrin beta 2  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-09-04 Spnb2  spectrin beta 2  Spnb1l  beta II spectrin-like (short form)  Data Merged 737654 APPROVED
2008-03-13 Spnb1l  beta II spectrin-like (short form)  Spnb1  short form of beta II spectrin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-07-08 Spnb2  spectrin beta 2      Symbol and Name status set to approved 1299863 APPROVED
2005-01-20 Spnb1  short form of beta II spectrin      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Spnb1  short form of beta II spectrin      Symbol and Name status set to provisional 70820 PROVISIONAL