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.t7 isoform g12411.t7 23431665 23433523
chr_1 g12411 g12411.t7 exon g12411.t7.exon1 23431665 23432278
chr_1 g12411 g12411.t7 cds g12411.t7.CDS1 23432129 23432278
chr_1 g12411 g12411.t7 exon g12411.t7.exon2 23432336 23432617
chr_1 g12411 g12411.t7 cds g12411.t7.CDS2 23432336 23432617
chr_1 g12411 g12411.t7 exon g12411.t7.exon3 23432780 23432921
chr_1 g12411 g12411.t7 cds g12411.t7.CDS3 23432780 23432893
chr_1 g12411 g12411.t7 exon g12411.t7.exon4 23433378 23433523
chr_1 g12411 g12411.t7 TSS g12411.t7 23433461 23433461
chr_1 g12411 g12411.t7 TTS g12411.t7 NA NA

Sequences

>g12411.t7 Gene=g12411 Length=1184
AAAGTTTCTCGATTTTTAATTTTTCCACGAATTTCTTTCTTTTAATGTTAAGAAAGCAAA
GAAACAAGATAATAACTGTTTAAAGTTCTTATTTATCGTGAAGTTATAATTTTAAAGAAT
TCTGTGAAACTCAATAAGTATTGTTGACAGCAGGTTATCAACATCAACAACAAGATGCCT
CTTCTATATGCAGTTATCACAAGAGGAAATACTGTATTGTGTAAATATGCCGACTGCGTT
GGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGCGTGCCTTTCTA
TATCTCTCAGAAATAAAACAGAAATTTTTAGCAACTTATGGTTTGACAGCAGCAACAGCT
CTTCCTTATGCAATGAATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGC
AATGAAAGTGGCGAGTATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAA
GATATTATGGTTAAAAATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTG
GTTAATAAATCAGAAAGTTTACGAAATAATGCTGTTTCATTCAGACAAACAAGTAGAACA
ATAGCAAGAACACTATTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATA
CTTTTCATAATATACATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAA
AGTGTTAAAACATAATTTATATTTTAAGCAAAACAATAATATGATGGTAAGAGACTATGT
GATTGTTAAATGTCTCTCGAAAAAAAATTGTTTATTTCAACCACATAGATTCTCAGTTAT
GAATTTATCAATATTTTATACATTATTATTTCTAATGAGGGTAAGTGTTGAAATAAATGT
GAAAGGAAGTCAATTTTAACTTCTAACAATCTTATCAGTAGTTGATCAAAATTATATATG
AGTGAAAAAATCTAATTAATCTTCTTCTCATCAACACATGACCCTCATTCTTACATATAC
AAAAAAATTTATGTATCAACCACAATAAATATGATAAAAATAATTTTATTATTATTTGAC
TACTGCACCAAAAAAACTCCGTTTTTATTAAAATATTGAATGTAATCAAAACTAAGAAGC
GAGAAAAATAAATGAAAAATTTCTTAATGCAAAATAAAACTTTT

>g12411.t7 Gene=g12411 Length=181
MPLLYAVITRGNTVLCKYADCVGNFSEVTENLISKIQLRAFLYLSEIKQKFLATYGLTAA
TALPYAMNTEFSRVMSAEMKKCNESGEYDSIQRVHGQIDELKDIMVKNIENITTRGERLE
LLVNKSESLRNNAVSFRQTSRTIARTLFWRNVKMYILLGLLILFIIYIIVAMFCGFALKC
R

Protein features from InterProScan

Transcript Database ID Name Start End E.value
18 g12411.t7 CDD cd14824 Longin 4 82 9.22619E-10
14 g12411.t7 Gene3D G3DSA:3.30.450.50 - 1 38 8.6E-8
13 g12411.t7 Gene3D G3DSA:3.30.450.50 - 39 89 3.0E-11
12 g12411.t7 Gene3D G3DSA:1.20.5.110 - 90 152 1.6E-22
3 g12411.t7 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 37 6.7E-68
5 g12411.t7 PANTHER PTHR21136 SNARE PROTEINS 1 37 6.7E-68
4 g12411.t7 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 39 174 6.7E-68
6 g12411.t7 PANTHER PTHR21136 SNARE PROTEINS 39 174 6.7E-68
8 g12411.t7 PRINTS PR00219 Synaptobrevin signature 95 114 8.3E-16
9 g12411.t7 PRINTS PR00219 Synaptobrevin signature 115 134 8.3E-16
7 g12411.t7 PRINTS PR00219 Synaptobrevin signature 151 170 8.3E-16
1 g12411.t7 Pfam PF13774 Regulated-SNARE-like domain 40 72 2.8E-6
2 g12411.t7 Pfam PF00957 Synaptobrevin 89 175 2.6E-30
15 g12411.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 154 -
17 g12411.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 155 178 -
16 g12411.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 179 181 -
21 g12411.t7 ProSiteProfiles PS50859 Longin domain profile. 40 75 11.19
20 g12411.t7 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 90 150 16.74
10 g12411.t7 SUPERFAMILY SSF64356 SNARE-like 3 82 1.01E-10
11 g12411.t7 SUPERFAMILY SSF58038 SNARE fusion complex 86 151 4.55E-18
19 g12411.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 155 177 -

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

This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).

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. There were no conditions that were differentially expressed