SEM6D_MOUSE
ID SEM6D_MOUSE Reviewed; 1073 AA.
AC Q76KF0; A2AW72; Q76KF1; Q76KF2; Q76KF3; Q76KF4; Q80TD0;
DT 20-DEC-2005, integrated into UniProtKB/Swiss-Prot.
DT 05-JUL-2004, sequence version 1.
DT 03-AUG-2022, entry version 131.
DE RecName: Full=Semaphorin-6D;
DE Flags: Precursor;
GN Name=Sema6d; Synonyms=Kiaa1479;
OS Mus musculus (Mouse).
OC Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia;
OC Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae;
OC Murinae; Mus; Mus.
OX NCBI_TaxID=10090;
RN [1]
RP NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 1; 2; 4; 5 AND 6), AND TISSUE
RP SPECIFICITY.
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=14715272; DOI=10.1016/j.bbrc.2003.12.083;
RA Taniguchi M., Shimizu T.;
RT "Characterization of a novel member of murine semaphorin family.";
RL Biochem. Biophys. Res. Commun. 314:242-248(2004).
RN [2]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC TISSUE=Brain;
RX PubMed=12693553; DOI=10.1093/dnares/10.1.35;
RA Okazaki N., Kikuno R., Ohara R., Inamoto S., Aizawa H., Yuasa S.,
RA Nakajima D., Nagase T., Ohara O., Koga H.;
RT "Prediction of the coding sequences of mouse homologues of KIAA gene: II.
RT The complete nucleotide sequences of 400 mouse KIAA-homologous cDNAs
RT identified by screening of terminal sequences of cDNA clones randomly
RT sampled from size-fractionated libraries.";
RL DNA Res. 10:35-48(2003).
RN [3]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=C57BL/6J;
RX PubMed=19468303; DOI=10.1371/journal.pbio.1000112;
RA Church D.M., Goodstadt L., Hillier L.W., Zody M.C., Goldstein S., She X.,
RA Bult C.J., Agarwala R., Cherry J.L., DiCuccio M., Hlavina W., Kapustin Y.,
RA Meric P., Maglott D., Birtle Z., Marques A.C., Graves T., Zhou S.,
RA Teague B., Potamousis K., Churas C., Place M., Herschleb J., Runnheim R.,
RA Forrest D., Amos-Landgraf J., Schwartz D.C., Cheng Z., Lindblad-Toh K.,
RA Eichler E.E., Ponting C.P.;
RT "Lineage-specific biology revealed by a finished genome assembly of the
RT mouse.";
RL PLoS Biol. 7:E1000112-E1000112(2009).
RN [4]
RP NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORM 2).
RC STRAIN=C57BL/6J; TISSUE=Brain;
RX PubMed=15489334; DOI=10.1101/gr.2596504;
RG The MGC Project Team;
RT "The status, quality, and expansion of the NIH full-length cDNA project:
RT the Mammalian Gene Collection (MGC).";
RL Genome Res. 14:2121-2127(2004).
RN [5]
RP PHOSPHORYLATION [LARGE SCALE ANALYSIS] AT SER-723 AND SER-734, AND
RP IDENTIFICATION BY MASS SPECTROMETRY [LARGE SCALE ANALYSIS].
RC TISSUE=Brain;
RX PubMed=21183079; DOI=10.1016/j.cell.2010.12.001;
RA Huttlin E.L., Jedrychowski M.P., Elias J.E., Goswami T., Rad R.,
RA Beausoleil S.A., Villen J., Haas W., Sowa M.E., Gygi S.P.;
RT "A tissue-specific atlas of mouse protein phosphorylation and expression.";
RL Cell 143:1174-1189(2010).
CC -!- FUNCTION: Shows growth cone collapsing activity on dorsal root ganglion
CC (DRG) neurons in vitro. May be a stop signal for the DRG neurons in
CC their target areas, and possibly also for other neurons. May also be
CC involved in the maintenance and remodeling of neuronal connections (By
CC similarity). {ECO:0000250}.
CC -!- SUBCELLULAR LOCATION: Cell membrane {ECO:0000250}; Single-pass type I
CC membrane protein {ECO:0000250}.
CC -!- ALTERNATIVE PRODUCTS:
CC Event=Alternative splicing; Named isoforms=6;
CC Name=4;
CC IsoId=Q76KF0-1; Sequence=Displayed;
CC Name=1;
CC IsoId=Q76KF0-2; Sequence=VSP_016568, VSP_016569;
CC Name=2;
CC IsoId=Q76KF0-3; Sequence=VSP_016569;
CC Name=3;
CC IsoId=Q76KF0-4; Sequence=VSP_016571;
CC Name=5;
CC IsoId=Q76KF0-5; Sequence=VSP_016568, VSP_016571;
CC Name=6;
CC IsoId=Q76KF0-6; Sequence=VSP_016570;
CC -!- TISSUE SPECIFICITY: Expressed in brain and lung.
CC {ECO:0000269|PubMed:14715272}.
CC -!- SIMILARITY: Belongs to the semaphorin family. {ECO:0000305}.
CC -!- SEQUENCE CAUTION:
CC Sequence=BAC65797.1; Type=Erroneous initiation; Evidence={ECO:0000305};
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DR EMBL; AB091532; BAD05168.1; -; mRNA.
DR EMBL; AB091533; BAD05169.1; -; mRNA.
DR EMBL; AB091534; BAD05170.1; -; mRNA.
DR EMBL; AB091535; BAD05171.1; -; mRNA.
DR EMBL; AB091536; BAD05172.1; -; mRNA.
DR EMBL; AK122515; BAC65797.1; ALT_INIT; mRNA.
DR EMBL; AL935323; -; NOT_ANNOTATED_CDS; Genomic_DNA.
DR EMBL; BC060680; AAH60680.1; -; mRNA.
DR CCDS; CCDS16670.1; -. [Q76KF0-2]
DR CCDS; CCDS16671.1; -. [Q76KF0-3]
DR CCDS; CCDS16672.1; -. [Q76KF0-6]
DR CCDS; CCDS16673.1; -. [Q76KF0-1]
DR CCDS; CCDS38225.1; -. [Q76KF0-5]
DR RefSeq; NP_001277926.1; NM_001290997.1. [Q76KF0-3]
DR RefSeq; NP_001277929.1; NM_001291000.1.
DR RefSeq; NP_766125.2; NM_172537.4. [Q76KF0-2]
DR RefSeq; NP_954708.1; NM_199238.3. [Q76KF0-3]
DR RefSeq; NP_954709.1; NM_199239.3. [Q76KF0-5]
DR RefSeq; NP_954710.1; NM_199240.3. [Q76KF0-6]
DR RefSeq; NP_954711.1; NM_199241.3. [Q76KF0-1]
DR RefSeq; XP_011237729.1; XM_011239427.2. [Q76KF0-6]
DR RefSeq; XP_017172490.1; XM_017317001.1. [Q76KF0-1]
DR RefSeq; XP_017172501.1; XM_017317012.1. [Q76KF0-6]
DR RefSeq; XP_017172508.1; XM_017317019.1. [Q76KF0-5]
DR RefSeq; XP_017172510.1; XM_017317021.1. [Q76KF0-4]
DR AlphaFoldDB; Q76KF0; -.
DR SMR; Q76KF0; -.
DR BioGRID; 229581; 8.
DR STRING; 10090.ENSMUSP00000099529; -.
DR GlyGen; Q76KF0; 5 sites.
DR iPTMnet; Q76KF0; -.
DR PhosphoSitePlus; Q76KF0; -.
DR MaxQB; Q76KF0; -.
DR PaxDb; Q76KF0; -.
DR PRIDE; Q76KF0; -.
DR ProteomicsDB; 256949; -. [Q76KF0-1]
DR ProteomicsDB; 256950; -. [Q76KF0-2]
DR ProteomicsDB; 256951; -. [Q76KF0-3]
DR ProteomicsDB; 256952; -. [Q76KF0-4]
DR ProteomicsDB; 256953; -. [Q76KF0-5]
DR ProteomicsDB; 256954; -. [Q76KF0-6]
DR Antibodypedia; 24461; 186 antibodies from 27 providers.
DR DNASU; 214968; -.
DR Ensembl; ENSMUST00000051419; ENSMUSP00000061123; ENSMUSG00000027200. [Q76KF0-2]
DR Ensembl; ENSMUST00000076335; ENSMUSP00000075674; ENSMUSG00000027200. [Q76KF0-3]
DR Ensembl; ENSMUST00000077847; ENSMUSP00000077014; ENSMUSG00000027200. [Q76KF0-6]
DR Ensembl; ENSMUST00000078621; ENSMUSP00000077691; ENSMUSG00000027200. [Q76KF0-5]
DR Ensembl; ENSMUST00000103238; ENSMUSP00000099528; ENSMUSG00000027200. [Q76KF0-6]
DR Ensembl; ENSMUST00000103239; ENSMUSP00000099529; ENSMUSG00000027200. [Q76KF0-1]
DR Ensembl; ENSMUST00000103241; ENSMUSP00000099531; ENSMUSG00000027200. [Q76KF0-3]
DR GeneID; 214968; -.
DR KEGG; mmu:214968; -.
DR UCSC; uc008mbk.2; mouse. [Q76KF0-3]
DR UCSC; uc008mbo.2; mouse. [Q76KF0-2]
DR UCSC; uc056zpa.1; mouse. [Q76KF0-5]
DR UCSC; uc056zpb.1; mouse. [Q76KF0-1]
DR UCSC; uc056zpc.1; mouse. [Q76KF0-6]
DR CTD; 80031; -.
DR MGI; MGI:2387661; Sema6d.
DR VEuPathDB; HostDB:ENSMUSG00000027200; -.
DR eggNOG; KOG3611; Eukaryota.
DR GeneTree; ENSGT00940000159303; -.
DR HOGENOM; CLU_009051_2_0_1; -.
DR InParanoid; Q76KF0; -.
DR OMA; IAEEPWF; -.
DR PhylomeDB; Q76KF0; -.
DR TreeFam; TF316102; -.
DR Reactome; R-MMU-416700; Other semaphorin interactions.
DR BioGRID-ORCS; 214968; 1 hit in 74 CRISPR screens.
DR ChiTaRS; Sema6d; mouse.
DR PRO; PR:Q76KF0; -.
DR Proteomes; UP000000589; Chromosome 2.
DR RNAct; Q76KF0; protein.
DR Bgee; ENSMUSG00000027200; Expressed in ventral tegmental area and 241 other tissues.
DR ExpressionAtlas; Q76KF0; baseline and differential.
DR Genevisible; Q76KF0; MM.
DR GO; GO:0009986; C:cell surface; ISO:MGI.
DR GO; GO:0062023; C:collagen-containing extracellular matrix; HDA:BHF-UCL.
DR GO; GO:0005737; C:cytoplasm; ISO:MGI.
DR GO; GO:0005615; C:extracellular space; IBA:GO_Central.
DR GO; GO:0005794; C:Golgi apparatus; ISO:MGI.
DR GO; GO:0005887; C:integral component of plasma membrane; IBA:GO_Central.
DR GO; GO:0005886; C:plasma membrane; ISO:MGI.
DR GO; GO:0045499; F:chemorepellent activity; IBA:GO_Central.
DR GO; GO:0030215; F:semaphorin receptor binding; IPI:MGI.
DR GO; GO:0007411; P:axon guidance; IBA:GO_Central.
DR GO; GO:0050919; P:negative chemotaxis; IBA:GO_Central.
DR GO; GO:0030517; P:negative regulation of axon extension; ISO:MGI.
DR GO; GO:0048843; P:negative regulation of axon extension involved in axon guidance; IBA:GO_Central.
DR GO; GO:0014912; P:negative regulation of smooth muscle cell migration; IDA:MGI.
DR GO; GO:0001755; P:neural crest cell migration; IBA:GO_Central.
DR GO; GO:0030335; P:positive regulation of cell migration; IBA:GO_Central.
DR GO; GO:0014911; P:positive regulation of smooth muscle cell migration; IDA:MGI.
DR GO; GO:0071526; P:semaphorin-plexin signaling pathway; IBA:GO_Central.
DR GO; GO:0014909; P:smooth muscle cell migration; IDA:MGI.
DR GO; GO:0021591; P:ventricular system development; IDA:MGI.
DR Gene3D; 2.130.10.10; -; 1.
DR InterPro; IPR002165; Plexin_repeat.
DR InterPro; IPR001627; Semap_dom.
DR InterPro; IPR036352; Semap_dom_sf.
DR InterPro; IPR027231; Semaphorin.
DR InterPro; IPR015943; WD40/YVTN_repeat-like_dom_sf.
DR PANTHER; PTHR11036; PTHR11036; 1.
DR Pfam; PF01437; PSI; 1.
DR Pfam; PF01403; Sema; 1.
DR SMART; SM00630; Sema; 1.
DR SUPFAM; SSF101912; SSF101912; 1.
DR PROSITE; PS51004; SEMA; 1.
PE 1: Evidence at protein level;
KW Alternative splicing; Cell membrane; Developmental protein;
KW Differentiation; Disulfide bond; Glycoprotein; Membrane; Neurogenesis;
KW Phosphoprotein; Reference proteome; Signal; Transmembrane;
KW Transmembrane helix.
FT SIGNAL 1..20
FT /evidence="ECO:0000255"
FT CHAIN 21..1073
FT /note="Semaphorin-6D"
FT /id="PRO_0000044616"
FT TOPO_DOM 21..662
FT /note="Extracellular"
FT /evidence="ECO:0000255"
FT TRANSMEM 663..683
FT /note="Helical"
FT /evidence="ECO:0000255"
FT TOPO_DOM 684..1073
FT /note="Cytoplasmic"
FT /evidence="ECO:0000255"
FT DOMAIN 27..512
FT /note="Sema"
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DOMAIN 514..569
FT /note="PSI"
FT REGION 745..825
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 839..876
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 919..986
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT REGION 1021..1073
FT /note="Disordered"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 787..803
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 850..876
FT /note="Basic and acidic residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 928..946
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 968..986
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1021..1041
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT COMPBIAS 1058..1073
FT /note="Polar residues"
FT /evidence="ECO:0000256|SAM:MobiDB-lite"
FT MOD_RES 723
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 734
FT /note="Phosphoserine"
FT /evidence="ECO:0007744|PubMed:21183079"
FT MOD_RES 744
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8NFY4"
FT MOD_RES 773
FT /note="Phosphothreonine"
FT /evidence="ECO:0000250|UniProtKB:Q8NFY4"
FT MOD_RES 931
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8NFY4"
FT MOD_RES 957
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8NFY4"
FT MOD_RES 983
FT /note="Phosphoserine"
FT /evidence="ECO:0000250|UniProtKB:Q8NFY4"
FT CARBOHYD 51
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 283
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 435
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 461
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT CARBOHYD 631
FT /note="N-linked (GlcNAc...) asparagine"
FT /evidence="ECO:0000255"
FT DISULFID 108..118
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 136..145
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 259..370
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 284..329
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 477..506
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 515..533
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 521..568
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT DISULFID 525..541
FT /evidence="ECO:0000255|PROSITE-ProRule:PRU00352"
FT VAR_SEQ 549
FT /note="L -> LLLTEDFFAFHNHS (in isoform 1 and isoform 5)"
FT /evidence="ECO:0000303|PubMed:14715272"
FT /id="VSP_016568"
FT VAR_SEQ 570..644
FT /note="Missing (in isoform 1 and isoform 2)"
FT /evidence="ECO:0000303|PubMed:12693553,
FT ECO:0000303|PubMed:14715272, ECO:0000303|PubMed:15489334"
FT /id="VSP_016569"
FT VAR_SEQ 570..588
FT /note="Missing (in isoform 6)"
FT /evidence="ECO:0000303|PubMed:14715272"
FT /id="VSP_016570"
FT VAR_SEQ 589..644
FT /note="Missing (in isoform 3 and isoform 5)"
FT /evidence="ECO:0000303|PubMed:14715272"
FT /id="VSP_016571"
SQ SEQUENCE 1073 AA; 119815 MW; D985053A2D37DA2A CRC64;
MGFLLLWFCV LFLLVSRLRA VSFPEDDEPL NTVDYHYSRQ YPVFRGRPSG NESQHRLDFQ
LMLKIRDTLY IAGRDQVYTV NLNEIPQTEV IPSKKLTWRS RQQDRENCAM KGKHKDECHN
FIKVFVPRND EMVFVCGTNA FNPMCRYYRL RTLEYDGEEI SGLARCPFDA RQTNVALFAD
GKLYSATVAD FLASDAVIYR SMGDGSALRT IKYDSKWIKE PHFLHAIEYG NYVYFFFREI
AVEHNNLGKA VYSRVARICK NDMGGSQRVL EKHWTSFLKA RLNCSVPGDS FFYFDVLQSI
TDIIQINGIP TVVGVFTTQL NSIPGSAVCA FSMDDIEKVF KGRFKEQKTP DSVWTAVPED
KVPKPRPGCC AKHGLAEAYK TSIDFPDDTL AFIKSHPLMD SAVPPIADEP WFTKTRVRYR
LTAIEVDRSA GPYQNYTVIF VGSEAGVVLK VLAKTSPFSL NDSVLLEEIE AYNPAKCSAE
SEEDRKVVSL QLDKDHHALY VAFSSCVVRI PLSRCERYGS CKKSCIASRD PYCGWLSQGV
CERVTLGMLP GGYEQDTEYG NTAHLGDCHE SLPPSTTPDY KIFGGPTSDM EVSSSSVTTV
ASSPEITSKV IDTWRPKLTS SRKFVVQDDP NTSDFTDTIS GIPKGVRWEV QSGESNQMVH
MNVLITCVFA AFVLGAFIAG VAVYCYRDMF VRKNRKIHKD AESAQSCTDS SGSFAKLNGL
FDSPVKEYQQ NIDSPKLYSN LLTSRKELPP NTDTKSMAVD HRGQPPELAA LPTPESTPVL
HQKTLQAMKS HSEKAHSHGA SRKEHPQFFP SSPPPHSPLS HGHIPSAIVL PNATHDYNTS
FSNSNAHKAE KKLQSMDHPL TKSSSKREHR RSVDSRNTLN DLLKHLNDPN SNPKAILGEI
HMAHQTLMLD PVGPMAEVPP KVPNREASLY SPPSTLPRNS PTKRVDVPTT PGVPMTSLER
QRGYHKNSSQ RHSISAVPKN LNSPNGVLLS RQPSMNRGGY MPTPTGAKVD YIQGTPVSVH
LQPSLSRQSS YTSNGTLPRT GLKRTPSLKP DVPPKPSFVP QTTSVRPLNK YTY
