Sema4f (sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain) - Rat Genome Database
Submit Data |  Help |  Video Tutorials |  News |  Publications |  FTP Download |  REST API |  Citing RGD |  Contact   
Gene: Sema4f (sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain) Mus musculus
Analyze
Symbol: Sema4f
Name: sema domain, immunoglobulin domain (Ig), TM domain, and short cytoplasmic domain
RGD ID: 735858
MGI Page MGI
Description: Is expressed in brain; enteric nervous system; and genitourinary system. Orthologous to human SEMA4F (ssemaphorin 4F).
Type: protein-coding
RefSeq Status: REVIEWED
Also known as: Sema W; semaphorin-4F; semaphorin-W
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm38 - Mouse Genome Assembly GRCm38
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39682,888,865 - 82,916,750 (-)NCBIGRCm39mm39
GRCm39 Ensembl682,888,866 - 82,916,750 (-)Ensembl
GRCm38682,911,884 - 82,939,769 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl682,911,885 - 82,939,769 (-)EnsemblGRCm38mm10GRCm38
MGSCv37682,861,879 - 82,889,744 (-)NCBIGRCm37mm9NCBIm37
MGSCv36682,877,544 - 82,905,359 (-)NCBImm8
Celera684,888,677 - 84,916,520 (-)NCBICelera
Cytogenetic Map6C3NCBI
cM Map635.94NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:10349636   PMID:11042159   PMID:11076861   PMID:11217851   PMID:11483650   PMID:12435358   PMID:12477932   PMID:14681479   PMID:15051154   PMID:15782199   PMID:16141072   PMID:16141073  
PMID:16284245   PMID:16602821   PMID:17145500   PMID:17409257   PMID:18287559   PMID:20436479   PMID:20688153   PMID:21122816   PMID:21677750   PMID:21873635   PMID:21945643   PMID:22534286  
PMID:24572910   PMID:24952961   PMID:26633812   PMID:29031500  


Genomics

Comparative Map Data
Sema4f
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39682,888,865 - 82,916,750 (-)NCBIGRCm39mm39
GRCm39 Ensembl682,888,866 - 82,916,750 (-)Ensembl
GRCm38682,911,884 - 82,939,769 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl682,911,885 - 82,939,769 (-)EnsemblGRCm38mm10GRCm38
MGSCv37682,861,879 - 82,889,744 (-)NCBIGRCm37mm9NCBIm37
MGSCv36682,877,544 - 82,905,359 (-)NCBImm8
Celera684,888,677 - 84,916,520 (-)NCBICelera
Cytogenetic Map6C3NCBI
cM Map635.94NCBI
SEMA4F
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl274,654,228 - 74,683,853 (+)EnsemblGRCh38hg38GRCh38
GRCh38274,654,229 - 74,699,013 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh37274,881,374 - 74,910,968 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36274,734,901 - 74,762,693 (+)NCBINCBI36hg18NCBI36
Build 34274,793,047 - 74,820,840NCBI
Celera274,712,502 - 74,740,294 (+)NCBI
Cytogenetic Map2p13.1NCBI
HuRef274,618,813 - 74,648,432 (+)NCBIHuRef
CHM1_1274,810,748 - 74,840,372 (+)NCBICHM1_1
Sema4f
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24115,411,411 - 115,437,721 (-)NCBI
Rnor_6.0 Ensembl4113,738,226 - 113,764,532 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.04113,738,225 - 113,764,532 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.04178,414,271 - 178,440,640 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44117,104,658 - 117,130,965 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.14117,349,139 - 117,375,446 (-)NCBI
Celera4104,407,298 - 104,433,605 (-)NCBICelera
Cytogenetic Map4q34NCBI
Sema4f
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542411,123,263 - 11,152,907 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542411,123,326 - 11,152,909 (-)NCBIChiLan1.0ChiLan1.0
SEMA4F
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A76,226,330 - 76,253,890 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A76,226,330 - 76,253,890 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A74,720,714 - 74,777,154 (+)NCBIMhudiblu_PPA_v0panPan3
SEMA4F
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1748,479,659 - 48,506,660 (-)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11748,479,389 - 48,510,659 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Sema4f
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936556873,669 - 899,400 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SEMA4F
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl368,379,322 - 68,404,595 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1368,377,669 - 68,404,662 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2371,551,385 - 71,578,055 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SEMA4F
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11432,597,632 - 32,625,424 (-)NCBI
ChlSab1.1 Ensembl1432,596,829 - 32,625,211 (-)Ensembl
Sema4f
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474928,827,766 - 28,855,159 (-)NCBI

Position Markers
AB022316  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38682,912,295 - 82,912,402UniSTSGRCm38
MGSCv37682,862,289 - 82,862,396UniSTSGRCm37
Celera684,889,087 - 84,889,194UniSTS
Cytogenetic Map6C3UniSTS
cM Map635.0UniSTS
Whitehead/MRC_RH6850.27UniSTS
D6UmiJ23  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38682,912,428 - 82,912,559UniSTSGRCm38
MGSCv37682,862,422 - 82,862,553UniSTSGRCm37
Celera684,889,220 - 84,889,355UniSTS
Cytogenetic Map6C3UniSTS
cM Map634.66UniSTS
Sema4f  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm38682,937,118 - 82,937,425UniSTSGRCm38
MGSCv37682,887,112 - 82,887,419UniSTSGRCm37
Celera684,913,920 - 84,914,227UniSTS
Cytogenetic Map6C3UniSTS
cM Map635.0UniSTS


QTLs in Region (GRCm38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1301876Bits2_mbitterness sensitivity 2 (mouse)Not determined670425898104426034Mouse
10412195Efw_mepididymal fat weight (mouse)Not determined67554435694225955Mouse
1301813Skl3_mskeletal size (tail length) 3 (mouse)Not determined670425898104426034Mouse
1300954Fcsa1_mfemoral cross-sectional area 1 (mouse)Not determined671981024105981170Mouse
1558984Cplaq9_mcircadian period of locomotor activity 9 (mouse)Not determined63866962592607450Mouse
13824985Alh1_mamplitude of lateral head displacement 1 (mouse)67800000097000000Mouse
1301571Arrd1_mage-related retinal degeneration 1 (mouse)Not determined67554435692607450Mouse
25440480Moaq2_mmodifier of alien QTL 2 (mouse)61117500000Mouse
10043972Obq28_mobesity QTL 28 (mouse)Not determined65854043392540433Mouse
10412208Cypr4_mcytokine production 4 (mouse)Not determined675716503109716697Mouse
25314319Histh6_mhistamine hypersensitivity 6 (mouse)648720000125360000Mouse
4141990Etax6_methanol induced ataxia 6 (mouse)Not determined7132262186275719Mouse
4142361W10q11_mweight 10 weeks QTL 11 (mouse)Not determined450382396656149Mouse
13506930Recrq9_mrecombination rate in male meiosis QTL 9 (mouse)673500000134700000Mouse
4142271Egq8_mearly growth QTL 8 (mouse)Not determined450382396656149Mouse
1301369Im4_mimmunoregulatory 4 (mouse)Not determined66348473897484905Mouse
1300618Pgia19_mproteoglycan induced arthritis 19 (mouse)Not determined64531405987426034Mouse
1300650Bw18_mbody weight QTL 18 (mouse)Not determined666713869100714031Mouse
14697704Stsl4_mSalmonella typhimurium susceptibility locus 4 (mouse)67710000090000000Mouse
1302020Bbaa20_mB.burgdorferi-associated arthritis 20 (mouse)Not determined67132262193464093Mouse
1301740Bwq2_mbody weight QTL 2 (mouse)Not determined66005768094057799Mouse
15039373Adip28_madiposity 28 (mouse)65630821190308211Mouse
15039375Bw41_mbody weight QTL 41 (mouse)65630821190308211Mouse
1357683Igf1sl1_mIGF-1 serum levels 1 (mouse)Not determined652161713116155267Mouse
4142259Tabw2_mtally ho associated body weight 2 (mouse)Not determined46935985136423692Mouse
1301320Ots1_movarian teratoma susceptibility 1 (mouse)Not determined675447583104503555Mouse
4141028Mclr_mmethylcholanthrene lymphoma resistance (mouse)Not determined5437342788379171Mouse
1301034Egrm2_mearly growth rate (mouse)Not determined670425898104426034Mouse
1300869Stheal5_msoft tissue heal 5 (mouse)Not determined671575060105575178Mouse
4142232W6q4_mweight 6 weeks QTL 4 (mouse)Not determined450382396656149Mouse
1300674Nidd3n_mnon-insulin-dependent diabetes mellitus 3 in NSY (mouse)Not determined67554435694225955Mouse
4141376Dbm1_mdiabetes modifier 1 (mouse)Not determined678629504121115387Mouse
14696731Pairq1_mP. aeruginosa infection resistance QTL 1 (mouse)681500000102200000Mouse
26884414Bzwq12_mbi-zygomatic width QTL 12, 16 week (mouse)63400000139100000Mouse
10043901Pfat5_mpredicted fat percentage 5 (mouse)Not determined675607306109607450Mouse
1300556Cia6_mcollagen induced arthritis QTL 6 (mouse)Not determined6446488487426034Mouse
1558977Skmw10_mskeletal muscle weight 10 (mouse)Not determined65844758392447710Mouse
4142126W3q3_mweight 3 weeks QTL 3 (mouse)Not determined450382396656149Mouse
1301521Pas1c_mpulmonary adenoma susceptibility 1c (mouse)Not determined671981024105981170Mouse
25314320Histh5_mhistamine hypersensitivity 5 (mouse)648720000148450000Mouse
1301254Skts11_mskin tumor susceptibility 11 (mouse)Not determined65117915085179300Mouse
10412157Fl1n_mfatty liver 1 in NSY (mouse)Not determined645314059128835032Mouse
1301962Eila2_methanol induced locomotor activity 2 (mouse)Not determined648726556125356785Mouse
1357875Pfat2_mpredicted fat percentage 2 (mouse)Not determined676463949110464093Mouse

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2032
Count of miRNA genes:767
Interacting mature miRNAs:985
Transcripts:ENSMUST00000000641, ENSMUST00000113982, ENSMUST00000125579
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


Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001308374 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NM_011350 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011241264 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011241265 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB021291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AB022316 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC003061 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC007305 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AC158652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AF038652 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK035993 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK047067 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK143196 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK158292 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK190371 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK202829 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC057048 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC090625 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC094567 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC139232 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BY237710 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH466523 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSMUST00000000641   ⟹   ENSMUSP00000000641
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl682,911,885 - 82,939,769 (-)Ensembl
RefSeq Acc Id: ENSMUST00000125579
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl682,914,084 - 82,917,586 (-)Ensembl
RefSeq Acc Id: ENSMUST00000203271   ⟹   ENSMUSP00000144745
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl682,918,601 - 82,939,545 (-)Ensembl
RefSeq Acc Id: ENSMUST00000203911
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38.p6 Ensembl682,916,222 - 82,939,769 (-)Ensembl
RefSeq Acc Id: NM_001308374   ⟹   NP_001295303
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39682,888,866 - 82,916,750 (-)NCBI
GRCm38682,911,885 - 82,939,769 (-)NCBI
Sequence:
RefSeq Acc Id: NM_011350   ⟹   NP_035480
RefSeq Status: REVIEWED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39682,888,866 - 82,916,750 (-)NCBI
GRCm38682,911,885 - 82,939,769 (-)NCBI
MGSCv37682,861,879 - 82,889,744 (-)RGD
Celera684,888,677 - 84,916,520 (-)RGD
cM Map6 ENTREZGENE
Sequence:
RefSeq Acc Id: XM_011241264   ⟹   XP_011239566
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39682,888,865 - 82,916,741 (-)NCBI
GRCm38682,911,884 - 82,939,760 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011241265   ⟹   XP_011239567
RefSeq Status:
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39682,888,865 - 82,907,864 (-)NCBI
GRCm38682,911,884 - 82,930,884 (-)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_035480   ⟸   NM_011350
- Peptide Label: isoform a precursor
- UniProtKB: Q9Z123 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011239566   ⟸   XM_011241264
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_011239567   ⟸   XM_011241265
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: NP_001295303   ⟸   NM_001308374
- Peptide Label: isoform c
- Sequence:
RefSeq Acc Id: ENSMUSP00000144745   ⟸   ENSMUST00000203271
RefSeq Acc Id: ENSMUSP00000000641   ⟸   ENSMUST00000000641
Protein Domains
Ig-like C2-type   PSI   Sema

Promoters
RGD ID:6839970
Promoter ID:MM_KWN:46554
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain,   Lung
Transcripts:OTTMUST00000050184
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36682,867,434 - 82,867,934 (-)MPROMDB
RGD ID:6839969
Promoter ID:MM_KWN:46555
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Brain
Transcripts:OTTMUST00000050182,   UC009CLN.1,   UC009CLO.1
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv36682,889,446 - 82,889,946 (-)MPROMDB
RGD ID:6890100
Promoter ID:EPDNEW_M8500
Type:initiation region
Name:Sema4f_1
Description:Mus musculus sema domain, immunoglobulin domain , TM domain,and short cytoplasmic domain , transcript variant 1, mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm38682,939,715 - 82,939,775EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1340055 AgrOrtholog
Ensembl Genes ENSMUSG00000000627 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSMUSP00000000641 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUSP00000144745 UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000000641 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSMUST00000203271 UniProtKB/TrEMBL
Gene3D-CATH 2.130.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Plexin_repeat UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semap_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semaphorin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Semaphorin_4F UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WD40/YVTN_repeat-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:20355 UniProtKB/Swiss-Prot
MGD MGI:1340055 ENTREZGENE
NCBI Gene 20355 ENTREZGENE
PANTHER PTHR11036 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11036:SF72 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Sema4f PhenoGen
PROSITE SEMA UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PSI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Sema UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF101912 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0N4SUN0_MOUSE UniProtKB/TrEMBL
  Q810B2_MOUSE UniProtKB/TrEMBL
  Q9Z123 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary Q505G0 UniProtKB/Swiss-Prot
  Q9R1Y1 UniProtKB/Swiss-Prot