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Previous release (v1)
2024-07-01 23:13:05, GGRNA.v2 : RefSeq release 224 (May, 2024)
LOCUS NM_199239 5629 bp mRNA linear ROD 03-APR-2024
DEFINITION Mus musculus sema domain, transmembrane domain (TM), and
cytoplasmic domain, (semaphorin) 6D (Sema6d), transcript variant 5,
mRNA.
ACCESSION NM_199239
VERSION NM_199239.4
KEYWORDS RefSeq.
SOURCE Mus musculus (house mouse)
ORGANISM Mus musculus
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha;
Muroidea; Muridae; Murinae; Mus; Mus.
REFERENCE 1 (bases 1 to 5629)
AUTHORS Hirai,T., Naito,Y., Koyama,S., Nakanishi,Y., Masuhiro,K., Izumi,M.,
Kuge,T., Naito,M., Mizuno,Y., Yamaguchi,Y., Kang,S., Yaga,M.,
Futami,Y., Nojima,S., Nishide,M., Morita,T., Kato,Y., Tsuda,T.,
Takemoto,N., Kinugasa-Katayama,Y., Aoshi,T., Villa,J.K.,
Yamashita,K., Enokida,T., Hoshi,Y., Matsuura,K., Tahara,M.,
Takamatsu,H., Takeda,Y., Inohara,H. and Kumanogoh,A.
TITLE Sema6D forward signaling impairs T cell activation and
proliferation in head and neck cancer
JOURNAL JCI Insight 9 (3), e166349 (2024)
PUBMED 38329122
REMARK GeneRIF: Sema6D forward signaling impairs T cell activation and
proliferation in head and neck cancer.
Publication Status: Online-Only
REFERENCE 2 (bases 1 to 5629)
AUTHORS Prieur,D.S., Francius,C., Gaspar,P., Mason,C.A. and Rebsam,A.
TITLE Semaphorin-6D and Plexin-A1 Act in a Non-Cell-Autonomous Manner to
Position and Target Retinal Ganglion Cell Axons
JOURNAL J Neurosci 43 (32), 5769-5778 (2023)
PUBMED 37344233
REMARK GeneRIF: Semaphorin-6D and Plexin-A1 Act in a Non-Cell-Autonomous
Manner to Position and Target Retinal Ganglion Cell Axons.
REFERENCE 3 (bases 1 to 5629)
AUTHORS Sun,T., Zeng,H., Fan,L., Fei,J. and Chen,G.
TITLE Semaphorin 6D regulate corralling, hematoma compaction and white
matter injury in mice after intracerebral hemorrhage
JOURNAL J Stroke Cerebrovasc Dis 31 (11), 106803 (2022)
PUBMED 36174325
REMARK GeneRIF: Semaphorin 6D regulate corralling, hematoma compaction and
white matter injury in mice after intracerebral hemorrhage.
REFERENCE 4 (bases 1 to 5629)
AUTHORS Jidigam,V.K., Sawant,O.B., Fuller,R.D., Wilcots,K., Singh,R.,
Lang,R.A. and Rao,S.
TITLE Neuronal Bmal1 regulates retinal angiogenesis and
neovascularization in mice
JOURNAL Commun Biol 5 (1), 792 (2022)
PUBMED 35933488
REMARK Publication Status: Online-Only
REFERENCE 5 (bases 1 to 5629)
AUTHORS Moulis,M., Runser,S.V.M., Glorieux,L., Dauguet,N., Vanderaa,C.,
Gatto,L., Tyteca,D., Henriet,P., Spagnoli,F.M., Iber,D. and
Pierreux,C.E.
TITLE Identification and implication of tissue-enriched ligands in
epithelial-endothelial crosstalk during pancreas development
JOURNAL Sci Rep 12 (1), 12498 (2022)
PUBMED 35864120
REMARK Publication Status: Online-Only
REFERENCE 6 (bases 1 to 5629)
AUTHORS Chen,B., Schaevitz,L.R. and McConnell,S.K.
TITLE Fezl regulates the differentiation and axon targeting of layer 5
subcortical projection neurons in cerebral cortex
JOURNAL Proc Natl Acad Sci U S A 102 (47), 17184-17189 (2005)
PUBMED 16284245
REFERENCE 7 (bases 1 to 5629)
AUTHORS Toyofuku,T., Zhang,H., Kumanogoh,A., Takegahara,N., Yabuki,M.,
Harada,K., Hori,M. and Kikutani,H.
TITLE Guidance of myocardial patterning in cardiac development by Sema6D
reverse signalling
JOURNAL Nat Cell Biol 6 (12), 1204-1211 (2004)
PUBMED 15543137
REMARK GeneRIF: Sema6D coordinates both compact-layer expansion and
trabeculation, functioning as both a ligand and a receptor for
Plexin-A1.
REFERENCE 8 (bases 1 to 5629)
AUTHORS Toyofuku,T., Zhang,H., Kumanogoh,A., Takegahara,N., Suto,F.,
Kamei,J., Aoki,K., Yabuki,M., Hori,M., Fujisawa,H. and Kikutani,H.
TITLE Dual roles of Sema6D in cardiac morphogenesis through
region-specific association of its receptor, Plexin-A1, with
off-track and vascular endothelial growth factor receptor type 2
JOURNAL Genes Dev 18 (4), 435-447 (2004)
PUBMED 14977921
REMARK GeneRIF: Plexin-S1, with Sema6D, exerts distinct biological
activities at adjacent regions, crucial for complex cardiac
morphogenesis.
REFERENCE 9 (bases 1 to 5629)
AUTHORS Taniguchi,M. and Shimizu,T.
TITLE Characterization of a novel member of murine semaphorin family
JOURNAL Biochem Biophys Res Commun 314 (1), 242-248 (2004)
PUBMED 14715272
REFERENCE 10 (bases 1 to 5629)
AUTHORS Qu,X., Wei,H., Zhai,Y., Que,H., Chen,Q., Tang,F., Wu,Y., Xing,G.,
Zhu,Y., Liu,S., Fan,M. and He,F.
TITLE Identification, characterization, and functional study of the two
novel human members of the semaphorin gene family
JOURNAL J Biol Chem 277 (38), 35574-35585 (2002)
PUBMED 12110693
COMMENT VALIDATED REFSEQ: This record has undergone validation or
preliminary review. The reference sequence was derived from
AL935323.6.
On May 27, 2022 this sequence version replaced NM_199239.3.
Transcript Variant: This variant (5) contains an additional
in-frame exon in the central coding region, compared to variant 1,
resulting in an isoform (Sema6D-5) that is longer than isoform
Sema6D-1. The 5' UTR is incomplete because the evidence for this
variant is for the CDS only, and multiple possible 5' UTR exon
combinations exist.
Publication Note: This RefSeq record includes a subset of the
publications that are available for this gene. Please see the Gene
record to access additional publications.
##Evidence-Data-START##
Transcript exon combination :: AB091534.1 [ECO:0000332]
RNAseq introns :: single sample supports all introns
SAMN00849374, SAMN00849375
[ECO:0000348]
##Evidence-Data-END##
COMPLETENESS: complete on the 3' end.
PRIMARY REFSEQ_SPAN PRIMARY_IDENTIFIER PRIMARY_SPAN COMP
1-163 AL935323.6 40229-40391
164-275 AL935323.6 40795-40906
276-336 AL935323.6 41444-41504
337-399 AL935323.6 41626-41688
400-501 AL935323.6 41801-41902
502-592 AL935323.6 42134-42224
593-712 AL935323.6 42658-42777
713-801 AL935323.6 43478-43566
802-1019 AL935323.6 44292-44509
1020-1151 AL935323.6 44619-44750
1152-1307 AL935323.6 45058-45213
1308-1481 AL935323.6 45294-45467
1482-1622 AL935323.6 46216-46356
1623-1700 AL935323.6 46455-46532
1701-1801 AL935323.6 46892-46992
1802-1858 AL935323.6 47353-47409
1859-5629 AL935323.6 50669-54439
FEATURES Location/Qualifiers
source 1..5629
/organism="Mus musculus"
/mol_type="mRNA"
/strain="C57BL/6"
/db_xref="taxon:10090"
/chromosome="2"
/map="2 60.69 cM"
gene 1..5629
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="sema domain, transmembrane domain (TM), and
cytoplasmic domain, (semaphorin) 6D"
/db_xref="GeneID:214968"
/db_xref="MGI:MGI:2387661"
exon 1..163
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
misc_feature 19..21
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="upstream in-frame stop codon"
CDS 55..3147
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="isoform Sema6D-5 precursor is encoded by transcript
variant 5; semaphorin-6D"
/codon_start=1
/product="semaphorin-6D isoform Sema6D-5 precursor"
/protein_id="NP_954709.1"
/db_xref="CCDS:CCDS38225.1"
/db_xref="GeneID:214968"
/db_xref="MGI:MGI:2387661"
/translation="
MGFLLLWFCVLFLLVSRLRAVSFPEDDEPLNTVDYHYSRQYPVFRGRPSGNESQHRLDFQLMLKIRDTLYIAGRDQVYTVNLNEIPQTEVIPSKKLTWRSRQQDRENCAMKGKHKDECHNFIKVFVPRNDEMVFVCGTNAFNPMCRYYRLRTLEYDGEEISGLARCPFDARQTNVALFADGKLYSATVADFLASDAVIYRSMGDGSALRTIKYDSKWIKEPHFLHAIEYGNYVYFFFREIAVEHNNLGKAVYSRVARICKNDMGGSQRVLEKHWTSFLKARLNCSVPGDSFFYFDVLQSITDIIQINGIPTVVGVFTTQLNSIPGSAVCAFSMDDIEKVFKGRFKEQKTPDSVWTAVPEDKVPKPRPGCCAKHGLAEAYKTSIDFPDDTLAFIKSHPLMDSAVPPIADEPWFTKTRVRYRLTAIEVDRSAGPYQNYTVIFVGSEAGVVLKVLAKTSPFSLNDSVLLEEIEAYNPAKCSAESEEDRKVVSLQLDKDHHALYVAFSSCVVRIPLSRCERYGSCKKSCIASRDPYCGWLSQGVCERVTLGMLLLTEDFFAFHNHSPGGYEQDTEYGNTAHLGDCHESLPPSTTPDYKIFGGPTSGVRWEVQSGESNQMVHMNVLITCVFAAFVLGAFIAGVAVYCYRDMFVRKNRKIHKDAESAQSCTDSSGSFAKLNGLFDSPVKEYQQNIDSPKLYSNLLTSRKELPPNTDTKSMAVDHRGQPPELAALPTPESTPVLHQKTLQAMKSHSEKAHSHGASRKEHPQFFPSSPPPHSPLSHGHIPSAIVLPNATHDYNTSFSNSNAHKAEKKLQSMDHPLTKSSSKREHRRSVDSRNTLNDLLKHLNDPNSNPKAILGEIHMAHQTLMLDPVGPMAEVPPKVPNREASLYSPPSTLPRNSPTKRVDVPTTPGVPMTSLERQRGYHKNSSQRHSISAVPKNLNSPNGVLLSRQPSMNRGGYMPTPTGAKVDYIQGTPVSVHLQPSLSRQSSYTSNGTLPRTGLKRTPSLKPDVPPKPSFVPQTTSVRPLNKYTY"
sig_peptide 55..114
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="COORDINATES: ab initio prediction:SignalP:6.0"
misc_feature 199..1593
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="The Sema domain, a protein interacting module, of
semaphorins and plexins; Region: Sema; cl15693"
/db_xref="CDD:472829"
misc_feature 1594..>1683
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="Plexin repeat; Region: PSI; pfam01437"
/db_xref="CDD:396154"
misc_feature <2650..3093
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/note="large tegument protein UL36; Provisional; Region:
PHA03247"
/db_xref="CDD:223021"
exon 164..275
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 276..336
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 337..399
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 400..501
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 502..592
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 593..712
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 713..801
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 802..1019
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1020..1151
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1152..1307
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1308..1481
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1482..1622
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1623..1700
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1701..1801
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1802..1858
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
exon 1859..5629
/gene="Sema6d"
/gene_synonym="1110067B02Rik; D330011G23; mKIAA1479"
/inference="alignment:Splign:2.1.0"
ORIGIN
gtagctaagtgggacttctgaggagggggagctcagatttcttcttggccaaccatggggttccttctgctttggttctgcgtgctgttccttctggtctccaggttacgggcggtcagcttcccagaagacgatgagcccctcaacacggttgactatcactattcaaggcaatatccggtttttagaggacgcccttcaggcaacgaatcgcagcacaggctggactttcagctgatgttgaaaattcgagacacactttatattgctggcagggatcaagtctatacagtgaacttaaatgaaatcccccaaacagaggtgataccaagcaagaagctgacgtggaggtccagacagcaggatcgagaaaattgtgctatgaaaggcaagcataaagatgaatgccacaacttcatcaaagtctttgtcccaagaaatgatgagatggtttttgtctgtggtaccaatgctttcaacccgatgtgcagatactataggttgagaacgttagagtatgatggggaagaaattagtggcctggcacgatgcccgtttgatgcccgacaaaccaatgtcgccctctttgctgatggaaaactctattctgccacagtggctgatttcctggccagtgatgctgtcatttacagaagcatgggagatggatctgcccttcgcacaataaaatacgattccaagtggatcaaagaaccacacttccttcatgccatagaatatggaaactatgtctatttcttcttcagagaaatcgccgtggaacataataacttaggcaaggctgtgtattcccgcgtggctcgcatttgtaaaaacgacatgggtggctcacagcgggtcctggagaaacactggacttccttccttaaggctcggctgaactgctccgttcctggagattcctttttctacttcgacgtcctgcagtctataacagacataatccaaatcaatggcatccccactgtggttggggtcttcaccacacagctcaacagcattcctggttctgcagtctgtgcctttagcatggacgacattgagaaagtgttcaaagggcggttcaaagagcagaaaaccccagactctgtttggacagcagttcccgaagacaaagtaccaaaaccaaggcctggctgttgtgccaaacacggcctcgcagaagcttacaagacctccatcgactttccagatgacaccctggctttcatcaagtcccacccgctgatggactctgccgtcccacccattgccgatgagccctggttcacaaagacacgggtcaggtacaggttgacagccatcgaagtggaccgttcagcagggccataccaaaactacacagtcatctttgttggctctgaagctggcgtggtacttaaagttttggcaaagaccagtcctttctctctgaatgacagtgtattactcgaagagattgaagcttataacccagccaagtgcagcgccgagagtgaggaggacagaaaggtggtctcattacagctggacaaggatcaccatgctttatacgtggccttctctagctgcgtggtccgcatccccctcagccgctgtgagcgctacggatcgtgtaaaaagtcttgcattgcatcacgtgacccgtactgtggttggttaagccagggagtttgtgagagagtgaccctagggatgctgctgttaaccgaagacttctttgctttccataaccacagccctggaggatatgagcaggacacggagtacggcaacacagcccacctaggggactgccacgaaagtttgcctccttcaactacaccagattacaaaatatttggcggtccaacatctggtgtacggtgggaagtccagtctggagaatccaatcagatggtccacatgaatgtcctcatcacctgcgtgtttgccgcttttgtcttgggcgcgttcatcgcaggagtggccgtgtactgctaccgtgacatgttcgttcggaagaacagaaagatccataaagacgcagaatccgcccagtcgtgcacagactccagcggaagcttcgccaagctgaacggcctctttgacagccccgtcaaggaataccagcagaacattgattctcccaaactctacagcaacctgctgaccagtcggaaggaactgccaccaaacacggatacaaagtccatggccgtggaccacagaggccagcctcccgagctggctgctctccccacgccggaatccacacctgtcctccaccagaagaccctgcaggccatgaagagccactctgagaaggcccacagccacggtgcttcaaggaaagaacacccccagttttttccttctagtcctccaccccattccccattgagtcacgggcatatccccagtgccatcgttcttccaaacgccactcacgactacaatacatccttctccaactcgaatgcccacaaagccgaaaagaagcttcagagcatggatcaccctcttacgaagtcatccagtaagcgggagcaccggcggtctgtggattccaggaatactctcaatgatctcctgaagcatctaaatgacccaaacagtaaccccaaagccatcctgggagagatccatatggctcatcaaaccctcatgctggacccggtgggaccaatggctgaggtcccacccaaggtccctaaccgggaggcatctctatactcccctccctccacactccccagaaatagtccaaccaagagagtagatgtccccaccactcctggggtgccaatgacttctctggaaagacaaaggggttatcacaaaaattcctcccagaggcactctatatctgccgtgcctaaaaacttaaactcaccaaatggtgttttgttatctagacagccgagtatgaaccgtggaggctatatgcccaccccaacaggggcgaaggtggactatattcaggggacaccggtgagtgttcatctgcagccctccctctccagacagagcagctataccagtaatggcaccctccccaggacgggactaaagaggacaccatccttaaaacctgatgtgccaccaaagccttcctttgttccgcaaaccacatctgtcagaccactgaacaagtacacgtactaggcctcaagtatgctattcccgtgtggctttatcctgtccctgctgttgcgaggaagctgtgagggtaccttcagatgagatacctgcttgtattttaagagaaacaagtagccaaagaaactctgtcactttggtaacaccagaacttgccacatgtagctactacagcaaggcttctgtgtacttgccggaaacgaagggaggtcctgctcactccatttctttcgtttgaagcagaagggatgtgtagccagggaaggctcccttcaccagtgtaaagagctgatacagtactcagaagactgaacaaatacttgaaaatgggttcaatgtagactgccattctgtgtggtcttcccattaaatgtgaacattttaatatgtatgcattcaccttgcctcttgcacaaatgtcaaaatggaaagatgggaatgtctcaaaacaaaatgagcttggagattaccaagcagtttgctgaaaattcaatctttgacccaaactgtagcaatttttattttctgagtgtggcactgttttgttttatttttttgttttgttttgtttttcaatgccaccaacaaactatgttaagagaggggcgagtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgagagagagagagagagagagagagagagagagagagagagatctacccattagaattgatttaggtgcccattgcatcttttgtactatggagttgtttacagtaagcatgactgaacaagcactaacatcctcctacaccggtccatcgtgttcggctctgatcaggaatagacaaggcttctttgactgtcaagtgattaacatatggtacccggtgtcagaacatttaagcgttctaaataattttgtgctgctatccatcagaacgtctattccagccttgccagcttaagaacttagagaaattaagaggtatctttgatgtatctaccagtattcaatagtaacatttacctgtccactgtgaatcaaagcctggggcacgctactcaaccttagacacacttacaggcttttattttgattgtgttattttattttccatacagtaaaaaatgtcctctcttaactcctctcacccccaactcccaaggcaaaagagaaaccaaaagtaggacaaaagaaagagacagacagacagacagacagaacaggaattacagttggcttagcagggaggatctgtagagctctcgatgatccttcctccatgtgtgtcctgtgaggattttgctcatgagtcatgcaggcagtgacagtgaactgtaaataccacatgtgagtttacctggatctgtgcattttgtgccttattcactcgagtggtagaagttccgcggtatgttgagtgtttccactacagagcatcatttcccatgtgccacttgtaaatgttttgcagccagcacctgaggacttcttatacagtcataaagccacctagagcgatttgttgttgagcaacgccgccccttccctccaggatcagaagcagcacccacccttgccatgataaacattccatcccctgctgttctgataatgtgaagtcagatgagggttcccaggttatgtggcacctgcggaaaccatgtctagagtcgtttctatgtagcttggcagagcccactgatggctgcaggtgtgtagcctactgacagctttggttaacccactgcacatcacccagtcatttacccaacttactctagaaatgtccacagctaaggaaggctcctgagccagtcaggcggagttcaagtgatatcttgggacagtgaccatggtctgcattacttgggggaggatggggtacaagacaccagatcatttttatacaggatgtagagtactgatgcggttgatcttttccttcaagaacattcttttctatagaaaaatgattccctgtgatcttctggaagctccaaagctgaaacccttcagctttgcaactaaaaatattacagtttaataatcaattaaaccaaccaacaataagcactacacatctgccaccaacaatgttgtttgcatttaccttaccaatattaatcccagcgtggtaactctgtgtgaccccgataacattttgtaacattgtgctgccttagagtttgtactgtgagttctatcagtatttatgttgaaatttctaacatggattctagtctctattctgttaatttaattttaaatgctttatccatttgtgcaaaggtaaacacagattgtatcttttttaatggtacggcataaaaaaataaccctaaagtgaagtggctctatactgttttatagagtactttaacgtgtatagatatcttgtaaacttgtattgtggatgtgtaaataatatgtactttgggtttttaacaccgcatgtaaagtcaaaataaaatatccaagtcattacatcctgccttttgatgttaa
//
by
@meso_cacase at
DBCLS
This page is licensed under a
Creative Commons Attribution 4.0 International License (CC BY 4.0).
If you use GGRNA in your work, please cite:
Naito Y, Bono H. (2012)
GGRNA: an ultrafast, transcript-oriented search engine for genes and transcripts.
Nucleic Acids Res., 40, W592-W596.
[Full Text]