LOCUS       NM_145206               4174 bp    mRNA    linear   PRI 29-OCT-2024
DEFINITION  Homo sapiens vesicle transport through interaction with t-SNAREs 1A
            (VTI1A), transcript variant 2, mRNA.
ACCESSION   NM_145206
VERSION     NM_145206.4
KEYWORDS    RefSeq; MANE Select.
SOURCE      Homo sapiens (human)
  ORGANISM  Homo sapiens
            Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi;
            Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini;
            Catarrhini; Hominidae; Homo.
REFERENCE   1  (bases 1 to 4174)
  AUTHORS   Bargagna,B., Staderini,T., Lang,S.H., Banci,L. and Camponeschi,F.
  TITLE     Defects in the Maturation of Mitochondrial Iron-Sulfur Proteins:
            Biophysical Investigation of the MMDS3 Causing Gly104Cys Variant of
            IBA57
  JOURNAL   Int J Mol Sci 25 (19), 10466 (2024)
   PUBMED   39408793
  REMARK    GeneRIF: Defects in the Maturation of Mitochondrial Iron-Sulfur
            Proteins: Biophysical Investigation of the MMDS3 Causing Gly104Cys
            Variant of IBA57.
            Publication Status: Online-Only
REFERENCE   2  (bases 1 to 4174)
  AUTHORS   Davidsen,J., Larsen,S., Coskun,M., Gogenur,I., Dahlgaard,K.,
            Bennett,E.P. and Troelsen,J.T.
  TITLE     The VTI1A-TCF4 colon cancer fusion protein is a dominant negative
            regulator of Wnt signaling and is transcriptionally regulated by
            intestinal homeodomain factor CDX2
  JOURNAL   PLoS One 13 (7), e0200215 (2018)
   PUBMED   29975781
  REMARK    GeneRIF: Transfection of LS174T cells showed that the VTI1A
            promoter is highly active compared to the TCF7L2 promoter, and that
            CDX2 activates transcription of VTI1A.
            Publication Status: Online-Only
REFERENCE   3  (bases 1 to 4174)
  AUTHORS   Wang,N., Deng,Z., Wang,M., Li,R., Xu,G. and Bao,G.
  TITLE     Additional evidence supports association of common genetic variants
            in VTI1A and ETFA with increased risk of glioma susceptibility
  JOURNAL   J Neurol Sci 375, 282-288 (2017)
   PUBMED   28320150
  REMARK    GeneRIF: our results indicate that genetic variants in VTI1A may
            modify individual susceptibility to non-GBM of glioma in the Han
            Chinese population and support the role of the VTI1A genes in the
            occurrence of glioma.
REFERENCE   4  (bases 1 to 4174)
  AUTHORS   Kinnersley,B., Labussiere,M., Holroyd,A., Di Stefano,A.L.,
            Broderick,P., Vijayakrishnan,J., Mokhtari,K., Delattre,J.Y.,
            Gousias,K., Schramm,J., Schoemaker,M.J., Fleming,S.J., Herms,S.,
            Heilmann,S., Schreiber,S., Wichmann,H.E., Nothen,M.M., Swerdlow,A.,
            Lathrop,M., Simon,M., Bondy,M., Sanson,M. and Houlston,R.S.
  TITLE     Genome-wide association study identifies multiple susceptibility
            loci for glioma
  JOURNAL   Nat Commun 6, 8559 (2015)
   PUBMED   26424050
  REMARK    Publication Status: Online-Only
REFERENCE   5  (bases 1 to 4174)
  AUTHORS   Bass,A.J., Lawrence,M.S., Brace,L.E., Ramos,A.H., Drier,Y.,
            Cibulskis,K., Sougnez,C., Voet,D., Saksena,G., Sivachenko,A.,
            Jing,R., Parkin,M., Pugh,T., Verhaak,R.G., Stransky,N.,
            Boutin,A.T., Barretina,J., Solit,D.B., Vakiani,E., Shao,W.,
            Mishina,Y., Warmuth,M., Jimenez,J., Chiang,D.Y., Signoretti,S.,
            Kaelin,W.G. Jr., Spardy,N., Hahn,W.C., Hoshida,Y., Ogino,S.,
            DePinho,R.A., Chin,L., Garraway,L.A., Fuchs,C.S., Baselga,J.,
            Tabernero,J., Gabriel,S., Lander,E.S., Getz,G. and Meyerson,M.
  TITLE     Genomic sequencing of colorectal adenocarcinomas identifies a
            recurrent VTI1A-TCF7L2 fusion
  JOURNAL   Nat Genet 43 (10), 964-968 (2011)
   PUBMED   21892161
  REMARK    GeneRIF: We found a colorectal carcinoma cell line harboring the
            fusion gene to be dependent on VTI1A-TCF7L2 for
            anchorage-independent growth using RNA interference-mediated
            knockdown.
            Publication Status: Online-Only
REFERENCE   6  (bases 1 to 4174)
  AUTHORS   Flowerdew,S.E. and Burgoyne,R.D.
  TITLE     A VAMP7/Vti1a SNARE complex distinguishes a non-conventional
            traffic route to the cell surface used by KChIP1 and Kv4 potassium
            channels
  JOURNAL   Biochem J 418 (3), 529-540 (2009)
   PUBMED   19138172
  REMARK    GeneRIF: The present results suggest that a SNARE complex
            containing VAMP7 and Vti1a defines a novel traffic pathway to the
            cell surface in both neuronal and non-neuronal cells.
REFERENCE   7  (bases 1 to 4174)
  AUTHORS   Kreykenbohm,V., Wenzel,D., Antonin,W., Atlachkine,V. and von
            Mollard,G.F.
  TITLE     The SNAREs vti1a and vti1b have distinct localization and SNARE
            complex partners
  JOURNAL   Eur J Cell Biol 81 (5), 273-280 (2002)
   PUBMED   12067063
REFERENCE   8  (bases 1 to 4174)
  AUTHORS   Mallard,F., Tang,B.L., Galli,T., Tenza,D., Saint-Pol,A., Yue,X.,
            Antony,C., Hong,W., Goud,B. and Johannes,L.
  TITLE     Early/recycling endosomes-to-TGN transport involves two SNARE
            complexes and a Rab6 isoform
  JOURNAL   J Cell Biol 156 (4), 653-664 (2002)
   PUBMED   11839770
REFERENCE   9  (bases 1 to 4174)
  AUTHORS   Antonin,W., Holroyd,C., Fasshauer,D., Pabst,S., Von Mollard,G.F.
            and Jahn,R.
  TITLE     A SNARE complex mediating fusion of late endosomes defines
            conserved properties of SNARE structure and function
  JOURNAL   EMBO J 19 (23), 6453-6464 (2000)
   PUBMED   11101518
REFERENCE   10 (bases 1 to 4174)
  AUTHORS   Fischer von Mollard,G. and Stevens,T.H.
  TITLE     A human homolog can functionally replace the yeast
            vesicle-associated SNARE Vti1p in two vesicle transport pathways
  JOURNAL   J Biol Chem 273 (5), 2624-2630 (1998)
   PUBMED   9446565
COMMENT     REVIEWED REFSEQ: This record has been curated by NCBI staff. The
            reference sequence was derived from AK095476.1, BC017052.1,
            AK303646.1, AL158212.15 and BQ447044.1.
            
            On Feb 27, 2020 this sequence version replaced NM_145206.3.
            
            Summary: The protein encoded by this gene is a member of the family
            of soluble N-ethylmaleimide-sensitive fusion protein-attachment
            protein receptors (SNAREs) that function in intracellular
            trafficking. This family member is involved in vesicular transport
            between endosomes and the trans-Golgi network. It is a
            vesicle-associated SNARE (v-SNARE) that interacts with target
            membrane SNAREs (t-SNAREs). Polymorphisms in this gene have been
            associated with binocular function, and also with susceptibility to
            colorectal and lung cancers. A recurrent rearrangement has been
            found between this gene and the transcription factor 7-like 2
            (TCF7L2) gene in colorectal cancers. Alternative splicing results
            in multiple transcript variants. [provided by RefSeq, Dec 2015].
            
            Transcript Variant: This variant (2) lacks an alternate in-frame
            exon in the central coding region, compared to variant 1, resulting
            in an isoform (b) that is shorter than isoform a.
            
            Sequence Note: This RefSeq record was created from transcript and
            genomic sequence data to make the sequence consistent with the
            reference genome assembly. The genomic coordinates used for the
            transcript record were based on transcript alignments.
            
            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 :: SRR11853565.4017.1,
                                           SRR11853558.3392.1 [ECO:0000332]
            RNAseq introns              :: single sample supports all introns
                                           SAMEA1965299, SAMEA1966682
                                           [ECO:0000348]
            ##Evidence-Data-END##
            
            ##RefSeq-Attributes-START##
            MANE Ensembl match     :: ENST00000393077.3/ ENSP00000376792.2
            RefSeq Select criteria :: based on conservation, expression
            ##RefSeq-Attributes-END##
            COMPLETENESS: complete on the 3' end.
PRIMARY     REFSEQ_SPAN         PRIMARY_IDENTIFIER PRIMARY_SPAN        COMP
            1-43                AK095476.1         219-261
            44-406              BC017052.1         1-363
            407-1520            AK303646.1         345-1458
            1521-3539           AL158212.15        7129-9147
            3540-4174           BQ447044.1         17-651              c
FEATURES             Location/Qualifiers
     source          1..4174
                     /organism="Homo sapiens"
                     /mol_type="mRNA"
                     /db_xref="taxon:9606"
                     /chromosome="10"
                     /map="10q25.2"
     gene            1..4174
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="vesicle transport through interaction with t-SNAREs
                     1A"
                     /db_xref="GeneID:143187"
                     /db_xref="HGNC:HGNC:17792"
                     /db_xref="MIM:614316"
     exon            1..253
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     CDS             160..813
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="isoform b is encoded by transcript variant 2; SNARE
                     Vti1a-beta protein; vesicle transport through interaction
                     with t-SNAREs homolog 1A; vesicle transport v-SNARE
                     protein Vti1-like 2"
                     /codon_start=1
                     /product="vesicle transport through interaction with
                     t-SNAREs homolog 1A isoform b"
                     /protein_id="NP_660207.2"
                     /db_xref="CCDS:CCDS7575.2"
                     /db_xref="GeneID:143187"
                     /db_xref="HGNC:HGNC:17792"
                     /db_xref="MIM:614316"
                     /translation="MSSDFEGYEQDFAVLTAEITSKIARVPRLPPDEKKQMVANVEKQ
                     LEEAKELLEQMDLEVREIPPQSRGMYSNRMRSYKQEMGKLETDFKRSRIAYSDEVRNE
                     LLGDDGNSSENQRAHLLDNTERLERSSRRLEAGYQIAVETEQIGQEMLENLSHDREKI
                     QRARERLRETDANLGKSSRILTGMLRRIIQNRILLVILGIIVVITILMAITFSVRRH"
     exon            254..312
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            313..423
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            424..501
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            502..586
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            587..657
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            658..719
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     exon            720..4174
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /inference="alignment:Splign:2.1.0"
     regulatory      3378..3383
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="hexamer: AATAAA"
     polyA_site      3398
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="major polyA site"
     regulatory      4152..4157
                     /regulatory_class="polyA_signal_sequence"
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="hexamer: ATTAAA"
     polyA_site      4174
                     /gene="VTI1A"
                     /gene_synonym="MMDS3; MVti1; Vti1-rp2; VTI1RP2"
                     /note="major polyA site"
ORIGIN      
        1 gaacaaccag gaagcggctg ggttgagagc tgtccccggt tctccgttct gctctcgggg
       61 gcaccttccg gggttcctaa gccgcggggc ccctcgctgc ccctcgaggc cctttccctg
      121 acctaggctt tggcctgggc tactcgttcc ggagccgcca tgtcgtccga cttcgaaggt
      181 tacgagcagg acttcgcggt gctcactgca gagatcacca gcaagattgc gagggtccca
      241 cgactcccgc ctgatgaaaa gaaacagatg gttgcaaatg tggagaaaca gcttgaagaa
      301 gcgaaagaac tgcttgaaca gatggatttg gaagtccgag agataccacc ccaaagtcga
      361 gggatgtaca gcaacagaat gagaagctac aaacaagaaa tgggaaaact cgaaacagat
      421 tttaaaaggt cacggatcgc ctacagtgac gaagtacgga atgagctcct gggggatgat
      481 gggaattcct cagagaacca gagggcacat ctgctcgata acacagagag gctggaaagg
      541 tcatctcgga gactagaggc tggataccaa atagcagtgg aaaccgagca aattggtcag
      601 gagatgttgg aaaaccttag tcatgacaga gaaaagatac agcgagcacg tgaaagactt
      661 cgggaaacag atgctaattt gggaaaaagc tccaggattc tgacagggat gttgcgaaga
      721 atcatccaga accgcatcct gctcgtcatc ctagggatca tcgtggtcat caccatcctg
      781 atggcgatca ctttttctgt cagaagacac tgatgtatct gctctccctt gataaacagc
      841 aacaacagct tgttctgagt aattaagaca aaatggtcac atgaatcatt ctgttgcgct
      901 gacaggcccc aggtgaccct ctctctccct caccgccgtt gggctgaagt gcaaagagtg
      961 taaaaatatt ttctattcct gtttgcatgt gggttggttt ccttttcgag gtttgtcttc
     1021 acccagattc gttttttaga ggggaaggtg aatgtttatt tacctttttg ctaatgtcat
     1081 caactagcca aaatagcccc agtgacactc ctagccctct ggacgtgtca agggccgtgg
     1141 tttgggagag gacatgatga gtcagtcacg agagcttctg tttgtcaccc gcctcttgtt
     1201 gctgaaaagc tcttctgtga tgtctgagga taaaaatgca gcaaaaagca ggggatggag
     1261 tcagtgaccc cgtccagcaa gccagccctg ttcctacaca ggcctcatga atatagtcat
     1321 caacctgcct gagtgctttc attgtaaagg tcggtattta atgtcggttg tacaggaaat
     1381 tgacttagca ctttccctgt ttttctattg cataattttt tttttaaccc aaagatattt
     1441 tttttgctga gcctgcccag tattcactgt tcacaacttt gattactggc tacaagaaat
     1501 attttcttgc cttccccaaa tcccatactc cccagaatct gctggcaaag tgagccctgg
     1561 tacaggattt aattgtgacc tcgtcttccc tgacctgtgt aagcatctct gtatcctttc
     1621 ggttttaata tctgcactgc caaaagcagt cctcatactt gcaaaaggtc tgacaaggtt
     1681 ctctccacat acattccagt atgtaaagag accatgaata tttcagtaag agcaagaaca
     1741 tgactccatc agtgtgaaat ttcaaatgtg attataaata tgggagagtc ctataggagg
     1801 gtccaccaga gataaacttc acggaaaacg ttccctaacc tcctttaaaa gaatagagga
     1861 tggcagattg ttccaaaagg aatggcttgg gtttttaact aacaaatgtt agcaagcctt
     1921 tcttgaattc actatgtatt caaacttcta atatgctttg tgattttttt ctttcatttc
     1981 tttctgtctg aggtaaccag gaattgcgtt caaaatgagc tcatttgtga tcaggcttaa
     2041 aagttgccca agctgaggtc gtttcccccc agtcacaaag cagaatgttt ttctcaagac
     2101 ttcataggca cttactggtc cgtactatct ttggaatata attagaagct ttgaatcctt
     2161 gaaaagcaaa cctgttctct tcatcaaaaa tgctaaccac ctgtgcccgt ggatcaatat
     2221 cacctggatg tagtgcttga tatttttccc aactcagaag aaaaccatta tggtttagag
     2281 aggaaatgca gaatggcaga atccaccaga gaaattgcac ttatcgaaac aggccaaggc
     2341 ctgcatgtgt tcggataaat catttagtat tgtgtaaata aagctgcagc ctttacttcg
     2401 gagggatggt gtgggatttt ggccgaggga agcaggacag agaaggagca ggaagctatg
     2461 ctaattttcc tgtcagctta agggatccgt ctcagcaaga atcttgtatt ctgataacgg
     2521 aatgctgtac gtgctgacca catctaagaa ccattaaaaa gcaaggaaac aaacaaacaa
     2581 cccttttctc attccgacac acgaatagtc atcgagtatt acaccagccc ctctggtggc
     2641 ttccttcaaa actgttgatc ttagctaaag tgtataacca gttaccagct gcacttcgca
     2701 cggccatccc gtccacaatg cagcagactc ttcccaaggc cacctagcaa gcaaggttga
     2761 tcggatcatc taaactggcc gcctcctgaa tatttcactg aatcctggcg ttcatgttga
     2821 agcagacaaa atgagaaagg aggagggcat tgctcacctc tcaatagctt ttttcgttca
     2881 agttctatgt ctttatcagc tcttgcctgt gattttaccc caattcaacc ttgggagtgg
     2941 gaagaatatg aacagataac ccttggccta acagctccat caaacctcct tgagagcaac
     3001 tacctaggcc aggctagtga gtgctttgtg aggaagctgg tcagaaggtt ccctcaactc
     3061 cttcctggtc ctcctggaca ctgcagaaaa gacttagggg atccccagca gaggccaatt
     3121 gctctccttc cttccctgcc ccaccaggaa aggaataacg tccacagact tgaagcagat
     3181 agtgaagtag atctgtgaga ggttctaggt acttagtgtg tagactttga cgaatatttc
     3241 tcaagttggg agcccttgtt aaaaatgatg tttaagggag tggttggggg gaagatgaag
     3301 gcatggagga ggaagaagag aaggaagccc ttgccatata aaattcatgc agactaaaca
     3361 gtttccctga cagaataaat aaagtggatg ctaccccact ccagaatcaa aagcaattta
     3421 attaaagtct cttaagttgt aaagagtttt aaatgatccg tgttgaaggc gaatgcctgc
     3481 aaatgcagtg ggtctgacgt cagctgccgg gcctgggctg ggaggccatt tgctattctg
     3541 tttaaggcag gctggattgt cttattttgg aaccagcttg gtggggggtt tgctttgcta
     3601 ctgcttctga gccctgagct tcaaaggctg aaattaatgg tgaacaaaat tgtgcggctc
     3661 tggccatccc atgcggggca agcccattga gggttatcat taagtaaaga aataaagagg
     3721 gggaaaaaag cctgcctgtt ccaaaaacct catcagataa tgacctcagt gattgggttt
     3781 tcattaccaa acagcatcca gagattatca acccatagaa gaagggaggg gaaaaaaaag
     3841 aaagaaagga aaagcaactg tctttctctc cctctctttc tccttttttt ttgcacatct
     3901 tttctttaaa actgtcagat catttcagta tttcaaatcc gaggaaaaca gcctgcctgc
     3961 tgctgtattt gaagttgtaa tggtgtcaaa aagtcacgac tgactgacag ccgtcagtcc
     4021 cagaggggct cattaaatca taaaaacttg acaaggaaat aattgcgcat tgccagcaac
     4081 ttggcgcctg tttagacgtt tttattttct ttcattatta gtccccacca ttacgttcat
     4141 taacaaattg cattaaacaa ctgttaaggg ctaa
//
