Necab1 (N-terminal EF-hand calcium binding protein 1) - Rat Genome Database

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Gene: Necab1 (N-terminal EF-hand calcium binding protein 1) Rattus norvegicus
Analyze
Symbol: Necab1
Name: N-terminal EF-hand calcium binding protein 1
RGD ID: 708548
Description: Predicted to have identical protein binding activity. Predicted to be involved in blastocyst hatching and regulation of amyloid precursor protein biosynthetic process. Localizes to cytoplasm. Orthologous to human NECAB1 (N-terminal EF-hand calcium binding protein 1); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: EF hand calcium binding protein 1; EF-hand calcium-binding protein 1; Efcbp1; N-terminal EF-hand calcium-binding protein 1; neuronal Ca(2+)-binding protein 1; neuronal calcium-binding protein 1; Stip-1; synaptotagmin interacting protein 1; synaptotagmin-interacting protein 1
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
mRatBN7.2528,357,859 - 28,578,642 (-)NCBI
Rnor_6.0 Ensembl528,504,558 - 28,737,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0528,507,596 - 28,737,556 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0533,184,793 - 33,414,358 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,427,273 - 29,664,037 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1529,427,272 - 29,664,037 (-)NCBI
Celera527,607,138 - 27,808,811 (-)NCBICelera
Cytogenetic Map5q13NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cytoplasm  (IBA,IDA)
cytosol  (IEA,ISO)
nucleoplasm  (IEA,ISO)

Molecular Function

References

Additional References at PubMed
PMID:27869233  


Genomics

Comparative Map Data
Necab1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2528,357,859 - 28,578,642 (-)NCBI
Rnor_6.0 Ensembl528,504,558 - 28,737,719 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0528,507,596 - 28,737,556 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0533,184,793 - 33,414,358 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4529,427,273 - 29,664,037 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1529,427,272 - 29,664,037 (-)NCBI
Celera527,607,138 - 27,808,811 (-)NCBICelera
Cytogenetic Map5q13NCBI
NECAB1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl890,791,741 - 90,959,393 (+)EnsemblGRCh38hg38GRCh38
GRCh38890,791,768 - 90,959,393 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37891,804,003 - 91,971,621 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36891,872,954 - 92,040,806 (+)NCBINCBI36hg18NCBI36
Build 34891,872,953 - 92,040,806NCBI
Celera887,998,620 - 88,166,361 (+)NCBI
Cytogenetic Map8q21.3NCBI
HuRef887,013,523 - 87,181,552 (+)NCBIHuRef
CHM1_1891,844,508 - 92,012,293 (+)NCBICHM1_1
Necab1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39414,952,245 - 15,149,804 (-)NCBIGRCm39mm39
GRCm39 Ensembl414,952,245 - 15,149,794 (-)Ensembl
GRCm38414,952,245 - 15,149,804 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl414,952,245 - 15,149,794 (-)EnsemblGRCm38mm10GRCm38
MGSCv37414,879,392 - 15,076,278 (-)NCBIGRCm37mm9NCBIm37
MGSCv36414,879,395 - 15,076,261 (-)NCBImm8
Celera414,753,853 - 14,952,324 (-)NCBICelera
Cytogenetic Map4A2NCBI
Necab1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554177,573,861 - 7,737,913 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554177,573,861 - 7,737,920 (+)NCBIChiLan1.0ChiLan1.0
NECAB1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1889,405,495 - 89,573,788 (+)NCBIpanpan1.1PanPan1.1panPan2
Mhudiblu_PPA_v0887,453,523 - 87,622,800 (+)NCBIMhudiblu_PPA_v0panPan3
NECAB1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12936,154,555 - 36,332,111 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2936,154,510 - 36,329,460 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2936,299,409 - 36,484,455 (+)NCBI
ROS_Cfam_1.02936,348,024 - 36,533,389 (+)NCBI
UMICH_Zoey_3.12936,346,899 - 36,553,590 (+)NCBI
UNSW_CanFamBas_1.02936,349,439 - 36,535,346 (+)NCBI
UU_Cfam_GSD_1.02936,788,023 - 36,973,627 (+)NCBI
Necab1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440530343,201,181 - 43,352,967 (-)NCBI
SpeTri2.0NW_0049365444,439,739 - 4,589,060 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NECAB1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl445,982,106 - 46,239,729 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1445,981,777 - 46,239,673 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2449,754,887 - 49,826,195 (-)NCBISscrofa10.2Sscrofa10.2susScr3
NECAB1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1885,851,899 - 86,027,993 (+)NCBI
Necab1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247441,021,362 - 1,211,739 (-)NCBI

Position Markers
D8Got25  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,493,998 - 28,494,213 (+)MAPPER
Rnor_6.0528,651,323 - 28,651,537NCBIRnor6.0
Rnor_5.0533,327,771 - 33,327,985UniSTSRnor5.0
RGSC_v3.4529,576,836 - 29,577,051RGDRGSC3.4
RGSC_v3.4529,576,837 - 29,577,051UniSTSRGSC3.4
RGSC_v3.1529,576,837 - 29,577,051RGD
Celera527,724,449 - 27,724,654UniSTS
RH 3.4 Map5158.91RGD
RH 3.4 Map5158.91UniSTS
Cytogenetic Map5q13UniSTS
RH141013  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2528,473,660 - 28,473,859 (+)MAPPER
mRatBN7.2627,884,774 - 27,884,972 (-)MAPPER
mRatBN7.2627,884,774 - 27,884,972 (+)MAPPER
mRatBN7.2528,473,660 - 28,473,859 (-)MAPPER
Rnor_6.0528,629,109 - 28,629,306NCBIRnor6.0
Rnor_6.0628,969,993 - 28,970,190NCBIRnor6.0
Rnor_5.0533,306,053 - 33,306,250UniSTSRnor5.0
Rnor_5.0640,916,940 - 40,917,137UniSTSRnor5.0
RGSC_v3.4529,557,427 - 29,557,624UniSTSRGSC3.4
RGSC_v3.4628,184,821 - 28,185,018UniSTSRGSC3.4
Celera627,353,356 - 27,353,553UniSTS
Celera527,704,391 - 27,704,546UniSTS
Cytogenetic Map6q14UniSTS
Cytogenetic Map5q13UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1331771Rf35Renal function QTL 354.36965kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5189432042Rat
1331756Rf34Renal function QTL 344.16275kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)5193273395Rat
70212Niddm25Non-insulin dependent diabetes mellitus QTL 253.54blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)51136640934Rat
2312562Pur18Proteinuria QTL 182.60.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)5152509833001026Rat
1576314Eutr1Estrogen induced uterine response QTL 1uterus integrity trait (VT:0010575)pyometritis severity score (CMO:0002009)5152509878720537Rat
8662454Vetf3Vascular elastic tissue fragility QTL 327.4artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)5166658771552720Rat
1300117Hrtrt8Heart rate QTL 83.49heart pumping trait (VT:2000009)heart rate (CMO:0000002)5325132948722188Rat
61462Niddm10Non-insulin dependent diabetes mellitus QTL 103.90.001blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)5452573847978104Rat
2293666Bmd38Bone mineral density QTL 384.4femur size trait (VT:1000369)femoral neck cortical cross-sectional area (CMO:0001702)5863228553632285Rat
7394712Emca13Estrogen-induced mammary cancer QTL 13mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)59514842103580403Rat
634305Mamtr1Mammary tumor resistance QTL 10.0001mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)512651967117554267Rat
1641903Alcrsp3Alcohol response QTL 3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)51328888858288888Rat
1600358Mamtr5Mammary tumor resistance QTL 5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)51884791363847913Rat
1358353Srcrtb2Stress Responsive Cort Basal QTL 23.480.003blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)51884791376608178Rat
8552954Pigfal14Plasma insulin-like growth factor 1 level QTL 149blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)52190436366904363Rat
1549901Neudeg2Neurodegradation QTL 240nervous system integrity trait (VT:0010566)mononuclear cell count (CMO:0002119)52495621244747071Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:37
Count of miRNA genes:35
Interacting mature miRNAs:37
Transcripts:ENSRNOT00000009718
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 46 1
Low 3 19 38 22 17 22 8 9 24 25 29 11 8
Below cutoff 24 19 19 1 19 2 4 10 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000009718   ⟹   ENSRNOP00000009718
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl528,504,558 - 28,737,719 (-)Ensembl
RefSeq Acc Id: NM_022302   ⟹   NP_071638
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2528,357,859 - 28,578,642 (-)NCBI
Rnor_6.0528,507,596 - 28,737,556 (-)NCBI
Rnor_5.0533,184,793 - 33,414,358 (-)NCBI
RGSC_v3.4529,427,273 - 29,664,037 (-)RGD
Celera527,607,138 - 27,808,811 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_071638 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAG28411 (Get FASTA)   NCBI Sequence Viewer  
  EDL98472 (Get FASTA)   NCBI Sequence Viewer  
  EDL98473 (Get FASTA)   NCBI Sequence Viewer  
  Q9ESB5 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_071638   ⟸   NM_022302
- UniProtKB: Q9ESB5 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000009718   ⟸   ENSRNOT00000009718
Protein Domains
ABM   EF-hand

Transcriptome

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


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)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:708548 AgrOrtholog
Ensembl Genes ENSRNOG00000007256 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000009718 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000009718 ENTREZGENE, UniProtKB/Swiss-Prot
InterPro ABM_dom UniProtKB/Swiss-Prot
  Dimeric_a/b-barrel UniProtKB/Swiss-Prot
  EF-hand-dom_pair UniProtKB/Swiss-Prot
  EF_Hand_1_Ca_BS UniProtKB/Swiss-Prot
  EF_hand_dom UniProtKB/Swiss-Prot
  NECAB1/2/3 UniProtKB/Swiss-Prot
KEGG Report rno:64169 UniProtKB/Swiss-Prot
NCBI Gene 64169 ENTREZGENE
PANTHER PTHR12178 UniProtKB/Swiss-Prot
Pfam ABM UniProtKB/Swiss-Prot
  EF-hand_8 UniProtKB/Swiss-Prot
PhenoGen Necab1 PhenoGen
PROSITE ABM UniProtKB/Swiss-Prot
  EF_HAND_1 UniProtKB/Swiss-Prot
  EF_HAND_2 UniProtKB/Swiss-Prot
SMART EFh UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47473 UniProtKB/Swiss-Prot
  SSF54909 UniProtKB/Swiss-Prot
UniProt NECA1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-25 Necab1  N-terminal EF-hand calcium binding protein 1  Efcbp1  EF hand calcium binding protein 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Efcbp1  EF hand calcium binding protein 1      Symbol and Name status set to approved 1299863 APPROVED