Sptb (spectrin, beta, erythrocytic) - Rat Genome Database
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Gene: Sptb (spectrin, beta, erythrocytic) Rattus norvegicus
Analyze
Symbol: Sptb
Name: spectrin, beta, erythrocytic
RGD ID: 1303243
Description: Predicted to have actin filament binding activity and ankyrin binding activity. Predicted to be involved in hemopoiesis; plasma membrane organization; and porphyrin-containing compound biosynthetic process. Predicted to localize to several cellular components, including cell surface; cytoskeleton; and cytosol. Human ortholog(s) of this gene implicated in hereditary spherocytosis and hereditary spherocytosis type 2. Orthologous to human SPTB (spectrin beta, erythrocytic); INTERACTS WITH 17beta-estradiol; 2,3,7,8-Tetrachlorodibenzofuran; acetamide.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: erythroid spectrin beta; hypothetical protein LOC679700; LOC314251; LOC679700; spectrin beta 1; spectrin beta chain, erythrocyte; spectrin beta chain, erythrocytic; Spnb1
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
mRatBN7.2695,310,342 - 95,437,221 (-)NCBI
Rnor_6.0 Ensembl699,659,651 - 99,783,047 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0699,657,144 - 99,783,189 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06109,055,163 - 109,181,316 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4699,194,202 - 99,315,691 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1699,197,658 - 99,319,147 (-)NCBI
Celera693,748,706 - 93,857,362 (-)NCBICelera
Cytogenetic Map6q24NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:379653   PMID:658175   PMID:6234993   PMID:8159688   PMID:9373263   PMID:9373273   PMID:10867799   PMID:14627610   PMID:16060676   PMID:18723693   PMID:20585040   PMID:21297961  
PMID:26514267   PMID:31505169  


Genomics

Comparative Map Data
Sptb
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2695,310,342 - 95,437,221 (-)NCBI
Rnor_6.0 Ensembl699,659,651 - 99,783,047 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0699,657,144 - 99,783,189 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.06109,055,163 - 109,181,316 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4699,194,202 - 99,315,691 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1699,197,658 - 99,319,147 (-)NCBI
Celera693,748,706 - 93,857,362 (-)NCBICelera
Cytogenetic Map6q24NCBI
SPTB
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1464,746,283 - 64,879,907 (-)EnsemblGRCh38hg38GRCh38
GRCh381464,744,106 - 64,879,907 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371465,213,001 - 65,346,625 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361464,282,754 - 64,359,619 (-)NCBINCBI36hg18NCBI36
Build 341464,302,870 - 64,416,308NCBI
Celera1445,270,736 - 45,347,605 (-)NCBI
Cytogenetic Map14q23.3NCBI
HuRef1445,384,969 - 45,462,806 (-)NCBIHuRef
CHM1_11465,152,596 - 65,229,440 (-)NCBICHM1_1
Sptb
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391276,627,262 - 76,757,321 (-)NCBIGRCm39mm39
GRCm39 Ensembl1276,627,262 - 76,757,321 (-)Ensembl
GRCm381276,580,488 - 76,710,547 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1276,580,488 - 76,710,547 (-)EnsemblGRCm38mm10GRCm38
MGSCv371277,681,475 - 77,811,534 (-)NCBIGRCm37mm9NCBIm37
MGSCv361277,499,328 - 77,629,387 (-)NCBImm8
Celera1277,672,725 - 77,802,629 (-)NCBICelera
Cytogenetic Map12C3NCBI
cM Map1233.73NCBI
Sptb
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554665,097,116 - 5,167,596 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554665,013,963 - 5,170,186 (+)NCBIChiLan1.0ChiLan1.0
SPTB
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11464,209,453 - 64,289,073 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1464,209,453 - 64,288,851 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01445,329,658 - 45,466,597 (-)NCBIMhudiblu_PPA_v0panPan3
SPTB
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl839,158,795 - 39,221,193 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1839,156,388 - 39,300,908 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sptb
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049364958,415,950 - 8,540,590 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPTB
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl788,812,715 - 88,954,306 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1788,812,717 - 88,954,471 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2795,193,318 - 95,335,373 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SPTB
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12441,957,438 - 42,038,522 (-)NCBI
ChlSab1.1 Ensembl2441,978,595 - 42,038,516 (-)Ensembl
Sptb
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473436,151,701 - 36,272,058 (+)NCBI

Position Markers
D6Got123  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0699,757,445 - 99,757,614NCBIRnor6.0
Rnor_5.06109,155,582 - 109,155,751UniSTSRnor5.0
RGSC_v3.4699,289,184 - 99,289,354RGDRGSC3.4
RGSC_v3.4699,289,185 - 99,289,354UniSTSRGSC3.4
RGSC_v3.1699,292,641 - 99,292,810RGD
Celera693,830,892 - 93,831,051UniSTS
RH 3.4 Map6676.1UniSTS
RH 3.4 Map6676.1RGD
Cytogenetic Map6q24UniSTS
D6Got206  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0699,692,158 - 99,692,325NCBIRnor6.0
Rnor_5.06109,090,178 - 109,090,345UniSTSRnor5.0
RGSC_v3.4699,211,276 - 99,211,444RGDRGSC3.4
RGSC_v3.4699,211,277 - 99,211,444UniSTSRGSC3.4
RGSC_v3.1699,214,733 - 99,214,900RGD
Celera693,765,781 - 93,765,931UniSTS
RH 3.4 Map6669.8UniSTS
RH 3.4 Map6669.8RGD
Cytogenetic Map6q24UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)648432758108268790Rat
1558641Cm47Cardiac mass QTL 472.90.001heart mass (VT:0007028)heart wet weight (CMO:0000069)660606431108154445Rat
6893332Cm74Cardiac mass QTL 740.40.64heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)660606431108154445Rat
70176Mcsm1Mammary carcinoma susceptibility modifier QTL 1mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)662263348107263348Rat
12801471Schws9Schwannoma susceptibility QTL 9nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)666129520111129520Rat
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)668781170147991367Rat
1641904Alcrsp4Alcohol response QTL 4response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)671206251116206251Rat
1300075Glom7Glomerulus QTL 75.60.0000002kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)675449871120449871Rat
1331789Rf37Renal function QTL 373.224kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)675623277120276465Rat
70196BpQTLcluster7Blood pressure QTL cluster 76.82arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)675623277120623277Rat
724536Uae7Urinary albumin excretion QTL 73.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)675623277136143011Rat
1331799Bp211Blood pressure QTL 2113.66407arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)675623277136426962Rat
1581550Pur8Proteinuria QTL 8total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)675623393136142742Rat
1581563Uae33Urinary albumin excretion QTL 33urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)675623393136142742Rat
724524Uae2Urinary albumin excretion QTL 22.70.0005urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)676902247114203334Rat
2293837Kiddil1Kidney dilation QTL 13.7kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
2293842Kiddil3Kidney dilation QTL 34.3kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)684763275108464097Rat
737827Hcar11Hepatocarcinoma resistance QTL 114.4liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)686422697115379601Rat
1576302Schws4Schwannoma susceptibility QTL 40.0078nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)687418448111129520Rat
738034Anxrr5Anxiety related response QTL 55.9exploratory behavior trait (VT:0010471)percentage of entries into a discrete space in an experimental apparatus (CMO:0000961)688507712133507712Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)688996335139410483Rat
10054138Gmadr3Adrenal mass QTL 33.680.00045adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)689631358134631358Rat
10054123Srcrt6Stress Responsive Cort QTL 62.50.0043blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)689631358134631358Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)691703409136703409Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (VE) (CMO:0000132)692879510137879510Rat
1331722Thshl1Thyroid stimulating hormone level QTL 111.70.0001blood thyroid-stimulating hormone amount (VT:0005119)serum thyroid stimulating hormone level (CMO:0001248)693706176111134673Rat
1331725Bp212Blood pressure QTL 2123.52475arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)697949772133849286Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)699273921144273921Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)699273921144792678Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:185
Count of miRNA genes:129
Interacting mature miRNAs:142
Transcripts:ENSRNOT00000009028
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 43 24 24 11 24 8 11 46 18 3 8
Low 3 29 13 8 13 28 35 23 8
Below cutoff 4 4 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009028   ⟹   ENSRNOP00000009028
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl699,659,651 - 99,783,047 (-)Ensembl
RefSeq Acc Id: NM_212522   ⟹   NP_997687
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2695,328,287 - 95,437,118 (-)NCBI
Rnor_6.0699,675,083 - 99,783,069 (-)NCBI
Rnor_5.06109,055,163 - 109,181,316 (-)NCBI
RGSC_v3.4699,194,202 - 99,315,691 (-)RGD
Celera693,748,706 - 93,857,362 (-)RGD
Sequence:
RefSeq Acc Id: XM_006240244   ⟹   XP_006240306
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2695,313,049 - 95,437,221 (-)NCBI
Rnor_6.0699,657,144 - 99,783,189 (-)NCBI
Rnor_5.06109,055,163 - 109,181,316 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594142   ⟹   XP_017449631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2695,313,049 - 95,437,221 (-)NCBI
Rnor_6.0699,657,144 - 99,783,189 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017594143   ⟹   XP_017449632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2695,313,049 - 95,437,221 (-)NCBI
Rnor_6.0699,657,144 - 99,783,189 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039112276   ⟹   XP_038968204
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2695,310,342 - 95,380,142 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_997687   ⟸   NM_212522
- UniProtKB: Q6XDA0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006240306   ⟸   XM_006240244
- Peptide Label: isoform X1
- UniProtKB: A0A140UHX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449632   ⟸   XM_017594143
- Peptide Label: isoform X1
- UniProtKB: A0A140UHX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017449631   ⟸   XM_017594142
- Peptide Label: isoform X1
- UniProtKB: A0A140UHX6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009028   ⟸   ENSRNOT00000009028
RefSeq Acc Id: XP_038968204   ⟸   XM_039112276
- Peptide Label: isoform X1
Protein Domains
Calponin-homology (CH)   PH

Transcriptome

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

Promoters
RGD ID:13694678
Promoter ID:EPDNEW_R5203
Type:initiation region
Name:Sptb_1
Description:spectrin, beta, erythrocytic
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_6.0699,783,084 - 99,783,144EPDNEW

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)
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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
6 109095271 109095272 G T snv DOB/Oda (KyushuU)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1303243 AgrOrtholog
Ensembl Genes ENSRNOG00000006911 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000009028 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000009028 UniProtKB/TrEMBL
Gene3D-CATH 1.10.418.10 UniProtKB/TrEMBL
  2.30.29.30 UniProtKB/TrEMBL
InterPro Actinin_actin-bd_CS UniProtKB/TrEMBL
  Calponin-like_dom_sf UniProtKB/TrEMBL
  CH-domain UniProtKB/TrEMBL
  PH_9 UniProtKB/TrEMBL
  PH_dom-like UniProtKB/TrEMBL
  PH_dom-spectrin-type UniProtKB/TrEMBL
  PH_domain UniProtKB/TrEMBL
  Spectrin/alpha-actinin UniProtKB/TrEMBL
  Spectrin_bsu UniProtKB/TrEMBL
  Spectrin_repeat UniProtKB/TrEMBL
KEGG Report rno:314251 UniProtKB/TrEMBL
NCBI Gene 314251 ENTREZGENE
Pfam PF00307 UniProtKB/TrEMBL
  PH_9 UniProtKB/TrEMBL
  Spectrin UniProtKB/TrEMBL
PhenoGen Sptb 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 A0A140UHX6 ENTREZGENE, UniProtKB/TrEMBL
  Q6XDA0 ENTREZGENE, UniProtKB/TrEMBL
UniProt Secondary F1MAL3 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Sptb  spectrin, beta, erythrocytic  LOC679700  hypothetical protein LOC679700  Data Merged 737654 PROVISIONAL
2008-09-18 Sptb  spectrin, beta, erythrocytic  Spnb1  spectrin beta 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-13 Spnb1  spectrin beta 1  LOC314251  erythroid spectrin beta  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-01-09 LOC679700  hypothetical protein LOC679700  LOC687997  hypothetical protein LOC687997  Data Merged 1643240 APPROVED
2006-11-20 LOC687997  hypothetical protein LOC687997      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC679700  hypothetical protein LOC679700      Symbol and Name status set to provisional 70820 PROVISIONAL
2005-10-12 LOC314251        Symbol and Name status set to provisional 70820 PROVISIONAL