Specc1l (sperm antigen with calponin homology and coiled-coil domains 1-like) - Rat Genome Database

Send us a Message



Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Gene: Specc1l (sperm antigen with calponin homology and coiled-coil domains 1-like) Rattus norvegicus
Analyze
Symbol: Specc1l
Name: sperm antigen with calponin homology and coiled-coil domains 1-like
RGD ID: 1309570
Description: Predicted to have beta-catenin binding activity. Predicted to be involved in several processes, including anterior neural tube closure; negative regulation of protein depolymerization; and positive regulation of protein kinase B signaling. Predicted to localize to cell-cell junction; cytoplasm; and cytoskeleton. Human ortholog(s) of this gene implicated in Opitz GBBB syndrome type II and oblique facial clefting 1. Orthologous to human SPECC1L (sperm antigen with calponin homology and coiled-coil domains 1 like); INTERACTS WITH bisphenol A; cadmium dichloride; chlorpyrifos.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: 28S ribosomal protein S7, mitochondrial-like; cytospin A; cytospin-A; Cytsa; LOC102546441; LOC361828; RGD1309570; similar to mKIAA0376 protein; SPECC1-like
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
mRatBN7.22013,337,983 - 13,443,665 (-)NCBI
Rnor_6.0 Ensembl2014,287,457 - 14,393,793 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02014,287,470 - 14,393,879 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02016,470,744 - 16,577,173 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42013,840,439 - 13,945,178 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12013,838,941 - 13,945,405 (-)NCBI
Celera2014,825,150 - 14,929,010 (-)NCBICelera
Cytogenetic Map20p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:21703590   PMID:26787558  


Genomics

Comparative Map Data
Specc1l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.22013,337,983 - 13,443,665 (-)NCBI
Rnor_6.0 Ensembl2014,287,457 - 14,393,793 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.02014,287,470 - 14,393,879 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.02016,470,744 - 16,577,173 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42013,840,439 - 13,945,178 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.12013,838,941 - 13,945,405 (-)NCBI
Celera2014,825,150 - 14,929,010 (-)NCBICelera
Cytogenetic Map20p12NCBI
SPECC1L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2224,270,817 - 24,417,739 (+)EnsemblGRCh38hg38GRCh38
GRCh382224,270,831 - 24,417,738 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh372224,666,799 - 24,813,706 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362222,996,866 - 23,143,221 (+)NCBINCBI36hg18NCBI36
Celera228,467,175 - 8,613,432 (+)NCBI
Cytogenetic Map22q11.23NCBI
HuRef227,616,847 - 7,763,724 (+)NCBIHuRef
CHM1_12224,625,424 - 24,772,401 (+)NCBICHM1_1
Specc1l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391075,047,872 - 75,148,234 (+)NCBIGRCm39mm39
GRCm39 Ensembl1075,047,905 - 75,148,577 (+)Ensembl
GRCm381075,212,037 - 75,312,400 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1075,212,073 - 75,312,743 (+)EnsemblGRCm38mm10GRCm38
MGSCv371074,674,818 - 74,775,145 (+)NCBIGRCm37mm9NCBIm37
MGSCv361074,674,412 - 74,756,109 (+)NCBImm8
Celera1076,258,909 - 76,359,489 (+)NCBICelera
Cytogenetic Map10C1NCBI
Specc1l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554557,739,105 - 7,879,489 (+)NCBIChiLan1.0ChiLan1.0
SPECC1L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12221,943,630 - 22,089,686 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2221,943,630 - 22,089,686 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0225,078,435 - 5,224,090 (+)NCBIMhudiblu_PPA_v0panPan3
SPECC1L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12627,994,278 - 28,127,383 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2628,025,987 - 28,125,695 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2627,101,372 - 27,201,064 (+)NCBI
ROS_Cfam_1.02629,398,465 - 29,531,216 (+)NCBI
UMICH_Zoey_3.12627,513,613 - 27,612,876 (+)NCBI
UNSW_CanFamBas_1.02627,130,906 - 27,230,482 (+)NCBI
UU_Cfam_GSD_1.02628,119,986 - 28,219,566 (+)NCBI
Specc1l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118142,161,078 - 142,305,767 (-)NCBI
SpeTri2.0NW_004936619448,304 - 592,981 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SPECC1L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.11449,332,937 - 49,463,965 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21452,782,692 - 52,909,765 (+)NCBISscrofa10.2Sscrofa10.2susScr3
SPECC1L
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1197,488,821 - 7,539,961 (+)NCBI
Vero_WHO_p1.0NW_0236660854,919,762 - 5,063,070 (-)NCBI
Specc1l
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247479,687,369 - 9,837,344 (+)NCBI

Position Markers
RH132515  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22013,339,950 - 13,340,167 (+)MAPPER
Rnor_6.02014,289,438 - 14,289,654NCBIRnor6.0
Rnor_5.02016,472,712 - 16,472,928UniSTSRnor5.0
RGSC_v3.42013,840,696 - 13,840,912UniSTSRGSC3.4
Celera2014,825,407 - 14,825,623UniSTS
RH 3.4 Map20154.39UniSTS
Cytogenetic Map20p12UniSTS
RH125059  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.22013,345,259 - 13,346,323 (+)MAPPER
mRatBN7.2837,172,781 - 37,173,497 (+)MAPPER
Rnor_6.0839,932,102 - 39,932,817NCBIRnor6.0
Rnor_6.02014,294,748 - 14,295,811NCBIRnor6.0
Rnor_5.02016,478,022 - 16,479,085UniSTSRnor5.0
Rnor_5.0839,932,926 - 39,933,641UniSTSRnor5.0
RGSC_v3.4838,707,724 - 38,708,439UniSTSRGSC3.4
RGSC_v3.42013,846,006 - 13,847,069UniSTSRGSC3.4
Celera2014,830,717 - 14,831,780UniSTS
Celera837,281,381 - 37,282,096UniSTS
Cytogenetic Map20p12UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354642Despr15Despair related QTL 150.0027locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)20124652101Rat
1600382Edcs3Endometrial carcinoma susceptibility QTL33.50.003uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)20125653396Rat
1641893Alcrsp7Alcohol response QTL 7response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
2317851Alcrsp22Alcohol response QTL 223.20.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)20126305996Rat
7387283Uae44Urinary albumin excretion QTL 440.1712urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)20127357423Rat
9590275Scort15Serum corticosterone level QTL 153.480.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20128375393Rat
9589155Insul32Insulin level QTL 326.380.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20128375393Rat
9590109Sffal8Serum free fatty acids level QTL 85.320.01blood free fatty acid amount (VT:0001553)plasma free fatty acids level (CMO:0000546)20128375393Rat
7411650Foco23Food consumption QTL 2320.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20128375393Rat
8694189Bw153Body weight QTL 1533.130.001body mass (VT:0001259)body weight gain (CMO:0000420)20128375393Rat
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20133300419Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20137550487Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20137550487Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20201865447018654Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20299970747999707Rat
2317057Aia27Adjuvant induced arthritis QTL 272.83joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)20340211127968216Rat
1558640Prcs2Prostate cancer susceptibility QTL 23.3prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)20403911318872273Rat
4889857Pur27Proteinuria QTL 2712.20.001total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20403911318872273Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)20410895649108956Rat
61432Cia1Collagen induced arthritis QTL 1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)20485547515050565Rat
70154Insul2Insulin level QTL 23.75blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)20587544818739210Rat
1581577Pur15Proteinuria QTL 154.380.0002total urine protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)20865434118872273Rat
4889870Pur30Proteinuria QTL 30190.005total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)20865434130991290Rat
631265Iresp1Immunoglobin response QTL18.3blood anti-double stranded DNA antibody amount (VT:0004762)serum anti-DNA antibody level (CMO:0001533)20965564214411641Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201383430956205956Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201383430956205956Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:119
Count of miRNA genes:88
Interacting mature miRNAs:101
Transcripts:ENSRNOT00000001764
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


Expression


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 42 23 7 19 7 8 11 74 35 36 11 8
Low 1 34 34 34 5
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000001764   ⟹   ENSRNOP00000001764
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2014,287,457 - 14,393,793 (-)Ensembl
RefSeq Acc Id: NM_001039455   ⟹   NP_001034544
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,339,694 - 13,443,665 (-)NCBI
Rnor_6.02014,289,181 - 14,393,872 (-)NCBI
Rnor_5.02016,470,744 - 16,577,173 (-)NCBI
RGSC_v3.42013,840,439 - 13,945,178 (-)RGD
Celera2014,825,150 - 14,929,010 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256339   ⟹   XP_006256401
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,337,983 - 13,443,382 (-)NCBI
Rnor_6.02014,287,470 - 14,393,576 (-)NCBI
Rnor_5.02016,470,744 - 16,577,173 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039098826   ⟹   XP_038954754
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.22013,337,983 - 13,425,173 (-)NCBI
RefSeq Acc Id: XR_597355
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.02014,319,188 - 14,393,879 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001034544 (Get FASTA)   NCBI Sequence Viewer  
  XP_006256401 (Get FASTA)   NCBI Sequence Viewer  
  XP_038954754 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAX84187 (Get FASTA)   NCBI Sequence Viewer  
  EDL97232 (Get FASTA)   NCBI Sequence Viewer  
  Q2KN99 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001034544   ⟸   NM_001039455
- UniProtKB: Q2KN99 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256401   ⟸   XM_006256339
- Peptide Label: isoform X1
- UniProtKB: Q2KN99 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000001764   ⟸   ENSRNOT00000001764
RefSeq Acc Id: XP_038954754   ⟸   XM_039098826
- Peptide Label: isoform X2
Protein Domains
Calponin-homology (CH)

Transcriptome

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

Promoters
RGD ID:13701544
Promoter ID:EPDNEW_R12068
Type:initiation region
Name:Specc1l_1
Description:sperm antigen with calponin homology and coiled-coil domains1-like
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_6.02014,393,804 - 14,393,864EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1309570 AgrOrtholog
Ensembl Genes ENSRNOG00000001303 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000001764 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000001764 ENTREZGENE, UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.418.10 UniProtKB/Swiss-Prot
InterPro CH-domain UniProtKB/Swiss-Prot
  CH_dom_sf UniProtKB/Swiss-Prot
  CYTSA UniProtKB/Swiss-Prot
KEGG Report rno:361828 UniProtKB/Swiss-Prot
NCBI Gene 361828 ENTREZGENE
PANTHER PTHR23167:SF18 UniProtKB/Swiss-Prot
Pfam PF00307 UniProtKB/Swiss-Prot
PhenoGen Specc1l PhenoGen
PROSITE PS50021 UniProtKB/Swiss-Prot
SMART SM00033 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47576 UniProtKB/Swiss-Prot
UniProt CYTSA_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Specc1l  sperm antigen with calponin homology and coiled-coil domains 1-like  LOC102546441  28S ribosomal protein S7, mitochondrial-like  Data Merged 737654 PROVISIONAL
2013-12-18 LOC102546441  28S ribosomal protein S7, mitochondrial-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2011-08-02 Specc1l  sperm antigen with calponin homology and coiled-coil domains 1-like  Cytsa  cytospin A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2010-05-05 Cytsa  cytospin A  Specc1l  SPECC1-like  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Specc1l  SPECC1-like  RGD1309570  similar to mKIAA0376 protein  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-07 RGD1309570  similar to mKIAA0376 protein  RGD1309570_predicted  similar to mKIAA0376 protein (predicted)  Symbol and Name status set to approved 1299863 APPROVED
2005-01-20 RGD1309570_predicted  similar to mKIAA0376 protein (predicted)  LOC361828_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361828_predicted  similar to mKIAA0376 protein (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL