Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicle-associated membrane protein 7.

Parent gene

Gene structure

  • The exon-intron structure of all isoforms are indicated below. CDS regions are colored in green. TSS and TTs that were predicted with CTR-Seq data are indicated in solid circle and squares, respectively. More specific data are shown in the table below.

Chromosome Gene Transcript Category ID Start End
chr_1 g12411 g12411.t5 isoform g12411.t5 23431665 23433523
chr_1 g12411 g12411.t5 exon g12411.t5.exon1 23431665 23432278
chr_1 g12411 g12411.t5 cds g12411.t5.CDS1 23432129 23432278
chr_1 g12411 g12411.t5 exon g12411.t5.exon2 23432336 23432709
chr_1 g12411 g12411.t5 cds g12411.t5.CDS2 23432336 23432709
chr_1 g12411 g12411.t5 exon g12411.t5.exon3 23432767 23432921
chr_1 g12411 g12411.t5 cds g12411.t5.CDS3 23432767 23432893
chr_1 g12411 g12411.t5 exon g12411.t5.exon4 23433378 23433523
chr_1 g12411 g12411.t5 TSS g12411.t5 23433461 23433461
chr_1 g12411 g12411.t5 TTS g12411.t5 NA NA

Sequences

>g12411.t5 Gene=g12411 Length=1289
AAAGTTTCTCGATTTTTAATTTTTCCACGAATTTCTTTCTTTTAATGTTAAGAAAGCAAA
GAAACAAGATAATAACTGTTTAAAGTTCTTATTTATCGTGAAGTTATAATTTTAAAGAAT
TCTGTGAAACTCAATAAGTATTGTTGACAGCAGGTTATCAACATCAACAACAAGATGCCT
CTTCTATATGCAGTTATCACAAGAGGAAATACTGTATTGTGTAAATATGCCGACTGCGTT
GGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGACAAACCATAAA
ATGACATACACACATGGCCAATACCTTTTCCATTATATTTGTGCTGATAAAATAATTTAC
ATGACCATAAGTGATGATGAGTTTCCACGACAGCGTGCCTTTCTATATCTCTCAGAAATA
AAACAGAAATTTTTAGCAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGCAATG
AATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGGCGAG
TATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAAGATATTATGGTTAAA
AATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATCAGAA
AGTTTACGAAATAATGCTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACACTA
TTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATACTTTTCATAATATAC
ATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAAAGTGTTAAAACATAA
TTTATATTTTAAGCAAAACAATAATATGATGGTAAGAGACTATGTGATTGTTAAATGTCT
CTCGAAAAAAAATTGTTTATTTCAACCACATAGATTCTCAGTTATGAATTTATCAATATT
TTATACATTATTATTTCTAATGAGGGTAAGTGTTGAAATAAATGTGAAAGGAAGTCAATT
TTAACTTCTAACAATCTTATCAGTAGTTGATCAAAATTATATATGAGTGAAAAAATCTAA
TTAATCTTCTTCTCATCAACACATGACCCTCATTCTTACATATACAAAAAAATTTATGTA
TCAACCACAATAAATATGATAAAAATAATTTTATTATTATTTGACTACTGCACCAAAAAA
ACTCCGTTTTTATTAAAATATTGAATGTAATCAAAACTAAGAAGCGAGAAAAATAAATGA
AAAATTTCTTAATGCAAAATAAAACTTTT

>g12411.t5 Gene=g12411 Length=216
MPLLYAVITRGNTVLCKYADCVGNFSEVTENLISKIQLTNHKMTYTHGQYLFHYICADKI
IYMTISDDEFPRQRAFLYLSEIKQKFLATYGLTAATALPYAMNTEFSRVMSAEMKKCNES
GEYDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKSESLRNNAVSFRQTSRTIAR
TLFWRNVKMYILLGLLILFIIYIIVAMFCGFALKCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12411.t5 CDD cd14824 Longin 4 117 1.36991E-34
11 g12411.t5 Gene3D G3DSA:3.30.450.50 - 1 122 1.7E-43
10 g12411.t5 Gene3D G3DSA:1.20.5.110 - 123 209 9.7E-26
3 g12411.t5 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 209 2.6E-93
4 g12411.t5 PANTHER PTHR21136 SNARE PROTEINS 1 209 2.6E-93
7 g12411.t5 PRINTS PR00219 Synaptobrevin signature 130 149 1.2E-15
6 g12411.t5 PRINTS PR00219 Synaptobrevin signature 150 169 1.2E-15
5 g12411.t5 PRINTS PR00219 Synaptobrevin signature 186 205 1.2E-15
1 g12411.t5 Pfam PF13774 Regulated-SNARE-like domain 31 107 1.1E-24
2 g12411.t5 Pfam PF00957 Synaptobrevin 124 210 4.0E-30
12 g12411.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 189 -
14 g12411.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 190 213 -
13 g12411.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 214 216 -
19 g12411.t5 ProSiteProfiles PS50859 Longin domain profile. 7 110 28.758
18 g12411.t5 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 125 185 16.74
17 g12411.t5 SMART SM01270 Longin_2 28 109 3.5E-30
8 g12411.t5 SUPERFAMILY SSF64356 SNARE-like 3 117 3.62E-29
9 g12411.t5 SUPERFAMILY SSF58038 SNARE fusion complex 121 186 6.8E-18
16 g12411.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 190 212 -

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016021 integral component of membrane CC
GO:0016192 vesicle-mediated transport BP

KEGG

Orthology

Pathway

  • This transcript belongs to the following pathways

Expression

Transcript expression in Pv11 cells

TPM values are indicated as average +/- STDEV.

Differential expression

Differentially expressed genes were identified with DESeq2 using the ‘run_DE_analysis.pl’ script from Trinity. Transcripts were determined as differentially expressed when (1) FDR < 0.05 (2) fold change > 2 (TPM calculated by RSEM). DE information and fold change between conditions are indicated in the plot below.

Raw TPM values