Sema4c (semaphorin 4C) - Rat Genome Database

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Gene: Sema4c (semaphorin 4C) Rattus norvegicus
Analyze
Symbol: Sema4c
Name: semaphorin 4C
RGD ID: 1562837
Description: Predicted to have chemorepellent activity and semaphorin receptor binding activity. Predicted to be involved in several processes, including nervous system development; neural crest cell migration; and positive regulation of stress-activated MAPK cascade. Predicted to localize to several cellular components, including extracellular space; postsynaptic density; and synaptic vesicle membrane. Orthologous to human SEMA4C (semaphorin 4C); INTERACTS WITH acetamide; bisphenol A; cefaloridine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: LOC301346; RGD1562837; sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C; semaphorin-4C; similar to Semaphorin 4C precursor (Semaphorin I); similar to Semaphorin 4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F)
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
mRatBN7.2938,791,668 - 38,802,171 (-)NCBI
Rnor_6.0 Ensembl943,129,415 - 43,139,870 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0943,129,413 - 43,140,442 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0942,783,319 - 42,793,776 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4935,492,647 - 35,503,102 (-)NCBIRGSC3.4rn4RGSC3.4
Celera936,558,044 - 36,568,492 (-)NCBICelera
Cytogenetic Map9q21NCBI
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
Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:11134026   PMID:15811348   PMID:17498836   PMID:19189244   PMID:21122816   PMID:22664934  


Genomics

Comparative Map Data
Sema4c
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2938,791,668 - 38,802,171 (-)NCBI
Rnor_6.0 Ensembl943,129,415 - 43,139,870 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0943,129,413 - 43,140,442 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0942,783,319 - 42,793,776 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4935,492,647 - 35,503,102 (-)NCBIRGSC3.4rn4RGSC3.4
Celera936,558,044 - 36,568,492 (-)NCBICelera
Cytogenetic Map9q21NCBI
SEMA4C
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl296,859,718 - 96,870,757 (-)EnsemblGRCh38hg38GRCh38
GRCh38296,859,718 - 96,870,943 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37297,525,455 - 97,535,817 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36296,889,200 - 96,899,462 (-)NCBINCBI36hg18NCBI36
Build 34296,947,352 - 96,957,582NCBI
Celera291,965,635 - 91,975,934 (-)NCBI
Cytogenetic Map2q11.2NCBI
HuRef291,485,571 - 91,495,645 (-)NCBIHuRef
CHM1_1297,530,409 - 97,540,671 (-)NCBICHM1_1
Sema4c
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39136,587,720 - 36,599,780 (-)NCBIGRCm39mm39
GRCm39 Ensembl136,587,720 - 36,597,430 (-)Ensembl
GRCm38136,548,639 - 36,560,699 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl136,548,639 - 36,558,349 (-)EnsemblGRCm38mm10GRCm38
MGSCv37136,605,487 - 36,615,226 (-)NCBIGRCm37mm9NCBIm37
MGSCv36136,493,186 - 36,504,590 (-)NCBImm8
Celera136,335,454 - 36,345,188 (-)NCBICelera
Cytogenetic Map1BNCBI
Sema4c
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554704,213,006 - 4,220,169 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554704,213,006 - 4,220,167 (-)NCBIChiLan1.0ChiLan1.0
SEMA4C
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A97,779,357 - 97,788,242 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A97,780,242 - 97,787,341 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A102,443,333 - 102,455,176 (+)NCBIMhudiblu_PPA_v0panPan3
SEMA4C
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11045,105,701 - 45,116,504 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1045,106,666 - 45,115,592 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1045,032,228 - 45,043,112 (+)NCBI
ROS_Cfam_1.01045,981,562 - 45,992,443 (+)NCBI
UMICH_Zoey_3.11045,693,071 - 45,703,955 (+)NCBI
UNSW_CanFamBas_1.01045,979,501 - 45,990,386 (+)NCBI
UU_Cfam_GSD_1.01046,162,896 - 46,173,783 (+)NCBI
Sema4c
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629283,541,170 - 83,551,897 (-)NCBI
SpeTri2.0NW_004936744794,127 - 804,618 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA4C
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl356,750,419 - 56,760,830 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1356,750,745 - 56,760,835 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2359,247,355 - 59,256,799 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA4C
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1141,189,547 - 1,199,906 (-)NCBI
ChlSab1.1 Ensembl141,189,495 - 1,199,446 (-)Ensembl
Vero_WHO_p1.0NW_023666041168,626,646 - 168,637,041 (-)NCBI
Sema4c
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247492,737,251 - 2,747,540 (-)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300124Cm4Cardiac mass QTL 43.55heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)9145029794Rat
10054125Srcrt7Stress Responsive Cort QTL 73.330.0011blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)9105522293442944Rat
1298088Edpm11Estrogen-dependent pituitary mass QTL 112.5pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)9235572247355722Rat
1641911Alcrsp13Alcohol response QTL 13response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)9235572247355722Rat
61425Cia15Collagen induced arthritis QTL 154.6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)9288097747375681Rat
631211Bw4Body weight QTL45.31retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)9288097747880977Rat
1354650Despr5Despair related QTL 54.010.0017locomotor behavior trait (VT:0001392)amount of time spent in voluntary immobility (CMO:0001043)9498609549986095Rat
2303559Gluco54Glucose level QTL 542blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)9498609549986095Rat
11353947Bp392Blood pressure QTL 392arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)91221677157216771Rat
9589133Insul26Insulin level QTL 2617.960.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)91242546357425463Rat
7411609Foco16Food consumption QTL 1625.60.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)91242546357425463Rat
1600365Mcs20Mammary carcinoma susceptibility QTL 203mammary gland integrity trait (VT:0010552)mammary tumor growth rate (CMO:0000344)91555490147249201Rat
724543Cm20Cardiac mass QTL 203.9heart mass (VT:0007028)calculated heart weight (CMO:0000073)91952048945029794Rat
631680Cm11Cardiac mass QTL 113.10.00089heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)92488509969885099Rat
70186Niddm26Non-insulin dependent diabetes mellitus QTL 263.87blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)92569234292741406Rat
631643Bp120Blood pressure QTL 12030.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)92569237370692373Rat
1598823Memor16Memory QTL 161.9exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)92575432054885226Rat
7207805Bmd88Bone mineral density QTL 884femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)92748603663264281Rat
1300180Bw14Body weight QTL 143.776body mass (VT:0001259)body weight (CMO:0000012)92748603666757620Rat
7207814Bmd91Bone mineral density QTL 913.5femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)92748615588333183Rat
70218Cm28Cardiac mass QTL 288.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)92907507983686404Rat
724544Uae9Urinary albumin excretion QTL 94.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)929075079122095297Rat
731164Uae25Urinary albumin excretion QTL 253.50.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)929466970107878528Rat
1641894Alcrsp12Alcohol response QTL 12response to alcohol trait (VT:0010489)brain neurotensin receptor 1 density (CMO:0002068)93238513377385133Rat
7411571Bw138Body weight QTL 13814.30.001body mass (VT:0001259)body weight gain (CMO:0000420)93764235182642351Rat
7411656Foco26Food consumption QTL 269.80.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)93764235182642351Rat
1598834Memor11Memory QTL 112.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)94126103490024806Rat
8662828Vetf6Vascular elastic tissue fragility QTL 63.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)94126103498606834Rat
2290450Scl57Serum cholesterol level QTL 574.15blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)941261034102531865Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:505
Count of miRNA genes:266
Interacting mature miRNAs:326
Transcripts:ENSRNOT00000021956
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 24 4 4 4 66 20 28 2
Low 3 19 52 36 19 36 8 11 8 15 13 9 8
Below cutoff 1 1 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000021956   ⟹   ENSRNOP00000021956
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl943,129,415 - 43,139,870 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000075882   ⟹   ENSRNOP00000068240
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl943,130,100 - 43,139,246 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076247
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl943,131,041 - 43,131,455 (-)Ensembl
RefSeq Acc Id: NM_001106902   ⟹   NP_001100372
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,670 - 38,802,128 (-)NCBI
Rnor_6.0943,129,415 - 43,139,870 (-)NCBI
Rnor_5.0942,783,319 - 42,793,776 (-)NCBI
RGSC_v3.4935,492,647 - 35,503,102 (-)RGD
Celera936,558,044 - 36,568,492 (-)RGD
Sequence:
RefSeq Acc Id: XM_006244758   ⟹   XP_006244820
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,799,549 (-)NCBI
Rnor_6.0943,129,413 - 43,137,824 (-)NCBI
Rnor_5.0942,783,319 - 42,793,776 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244759   ⟹   XP_006244821
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,801,428 (-)NCBI
Rnor_6.0943,129,413 - 43,139,478 (-)NCBI
Rnor_5.0942,783,319 - 42,793,776 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244760   ⟹   XP_006244822
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,799,947 (-)NCBI
Rnor_6.0943,129,413 - 43,137,824 (-)NCBI
Rnor_5.0942,783,319 - 42,793,776 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766995   ⟹   XP_008765217
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,801,537 (-)NCBI
Rnor_6.0943,129,413 - 43,139,478 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766996   ⟹   XP_008765218
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,802,171 (-)NCBI
Rnor_6.0943,129,413 - 43,140,442 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017596339   ⟹   XP_017451828
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,802,171 (-)NCBI
Rnor_6.0943,129,413 - 43,140,442 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039083220   ⟹   XP_038939148
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,799,947 (-)NCBI
RefSeq Acc Id: XM_039083221   ⟹   XP_038939149
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,799,947 (-)NCBI
RefSeq Acc Id: XM_039083222   ⟹   XP_038939150
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2938,791,668 - 38,797,388 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_001100372   ⟸   NM_001106902
- Peptide Label: precursor
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244821   ⟸   XM_006244759
- Peptide Label: isoform X2
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244822   ⟸   XM_006244760
- Peptide Label: isoform X2
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244820   ⟸   XM_006244758
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_008765218   ⟸   XM_008766996
- Peptide Label: isoform X2
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008765217   ⟸   XM_008766995
- Peptide Label: isoform X2
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017451828   ⟸   XM_017596339
- Peptide Label: isoform X2
- UniProtKB: D4A9J3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000021956   ⟸   ENSRNOT00000021956
RefSeq Acc Id: ENSRNOP00000068240   ⟸   ENSRNOT00000075882
RefSeq Acc Id: XP_038939149   ⟸   XM_039083221
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939148   ⟸   XM_039083220
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038939150   ⟸   XM_039083222
- Peptide Label: isoform X3
Protein Domains
Ig-like   Sema

Transcriptome

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

Promoters
RGD ID:13696618
Promoter ID:EPDNEW_R7131
Type:single initiation site
Name:Sema4c_1
Description:semaphorin 4C
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_6.0943,139,265 - 43,139,325EPDNEW

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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562837 AgrOrtholog
Ensembl Genes ENSRNOG00000016254 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000021956 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000068240 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000021956 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000075882 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/TrEMBL
  2.60.40.10 UniProtKB/TrEMBL
InterPro Ig-like UniProtKB/TrEMBL
  Ig-like_dom_sf UniProtKB/TrEMBL
  Ig-like_fold UniProtKB/TrEMBL
  Ig_sub UniProtKB/TrEMBL
  Plexin-like_fold UniProtKB/TrEMBL
  Plexin_repeat UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/TrEMBL
  Semaphorin UniProtKB/TrEMBL
  Semaphorin/CD100_Ag UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom UniProtKB/TrEMBL
KEGG Report rno:301346 UniProtKB/TrEMBL
NCBI Gene 301346 ENTREZGENE
PANTHER PTHR11036 UniProtKB/TrEMBL
Pfam PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
PhenoGen Sema4c PhenoGen
PROSITE IG_LIKE UniProtKB/TrEMBL
  SEMA UniProtKB/TrEMBL
SMART PSI UniProtKB/TrEMBL
  Sema UniProtKB/TrEMBL
  SM00409 UniProtKB/TrEMBL
Superfamily-SCOP Sema UniProtKB/TrEMBL
  SSF48726 UniProtKB/TrEMBL
UniProt D4A9J3 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-21 Sema4c  semaphorin 4C  Sema4c  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Sema4c  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C   Sema4c_predicted  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Sema4c_predicted  sema domain, immunoglobulin domain (Ig), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 4C (predicted)  RGD1562837_predicted  similar to Semaphorin 4C precursor (Semaphorin I) (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-10 RGD1562837_predicted  similar to Semaphorin 4C precursor (Semaphorin I) (predicted)    similar to Semaphorin 4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F) (predicted)  Name updated 1299863 APPROVED
2006-03-07 RGD1562837_predicted  similar to Semaphorin 4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F) (predicted)  LOC301346  similar to Semaphorin 4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F)  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC301346  similar to Semaphorin 4C precursor (Semaphorin I) (Sema I) (Semaphorin C-like 1) (M-Sema F)      Symbol and Name status set to provisional 70820 PROVISIONAL