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.t3 isoform g12411.t3 23431665 23432893
chr_1 g12411 g12411.t3 exon g12411.t3.exon1 23431665 23432278
chr_1 g12411 g12411.t3 cds g12411.t3.CDS1 23432129 23432278
chr_1 g12411 g12411.t3 exon g12411.t3.exon2 23432336 23432893
chr_1 g12411 g12411.t3 cds g12411.t3.CDS2 23432336 23432650
chr_1 g12411 g12411.t3 TSS g12411.t3 23433461 23433461
chr_1 g12411 g12411.t3 TTS g12411.t3 NA NA

Sequences

>g12411.t3 Gene=g12411 Length=1172
ATGCCTCTTCTATATGCAGTTATCACAAGAGGAAATACTGTATTGTGTAAATATGCCGAC
TGCGTTGGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGACAAAC
CATAAAAGTAAAATTCTTTTAATCTTAATTTTATTCAATGATTAATTTCTTAATATATTT
TTAGTGACATACACACATGGCCAATACCTTTTCCATTATATTTGTGCTGATAAAATAATT
TACATGACCATAAGTGATGATGAGTTTCCACGACAGCGTGCCTTTCTATATCTCTCAGAA
ATAAAACAGAAATTTTTAGCAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGCA
ATGAATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGGC
GAGTATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAAGATATTATGGTT
AAAAATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATCA
GAAAGTTTACGAAATAATGCTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACA
CTATTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATACTTTTCATAATA
TACATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAAAGTGTTAAAACA
TAATTTATATTTTAAGCAAAACAATAATATGATGGTAAGAGACTATGTGATTGTTAAATG
TCTCTCGAAAAAAAATTGTTTATTTCAACCACATAGATTCTCAGTTATGAATTTATCAAT
ATTTTATACATTATTATTTCTAATGAGGGTAAGTGTTGAAATAAATGTGAAAGGAAGTCA
ATTTTAACTTCTAACAATCTTATCAGTAGTTGATCAAAATTATATATGAGTGAAAAAATC
TAATTAATCTTCTTCTCATCAACACATGACCCTCATTCTTACATATACAAAAAAATTTAT
GTATCAACCACAATAAATATGATAAAAATAATTTTATTATTATTTGACTACTGCACCAAA
AAAACTCCGTTTTTATTAAAATATTGAATGTAATCAAAACTAAGAAGCGAGAAAAATAAA
TGAAAAATTTCTTAATGCAAAATAAAACTTTT

>g12411.t3 Gene=g12411 Length=154
MTISDDEFPRQRAFLYLSEIKQKFLATYGLTAATALPYAMNTEFSRVMSAEMKKCNESGE
YDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKSESLRNNAVSFRQTSRTIARTL
FWRNVKMYILLGLLILFIIYIIVAMFCGFALKCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12411.t3 CDD cd14824 Longin 1 55 1.93732E-14
11 g12411.t3 Gene3D G3DSA:3.30.450.50 - 1 60 1.4E-15
10 g12411.t3 Gene3D G3DSA:1.20.5.110 - 61 147 7.8E-26
3 g12411.t3 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 147 8.2E-59
4 g12411.t3 PANTHER PTHR21136 SNARE PROTEINS 1 147 8.2E-59
7 g12411.t3 PRINTS PR00219 Synaptobrevin signature 68 87 5.9E-16
6 g12411.t3 PRINTS PR00219 Synaptobrevin signature 88 107 5.9E-16
5 g12411.t3 PRINTS PR00219 Synaptobrevin signature 124 143 5.9E-16
1 g12411.t3 Pfam PF13774 Regulated-SNARE-like domain 1 45 3.6E-11
2 g12411.t3 Pfam PF00957 Synaptobrevin 62 148 1.7E-30
12 g12411.t3 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 127 -
14 g12411.t3 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 128 151 -
13 g12411.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 152 154 -
18 g12411.t3 ProSiteProfiles PS50859 Longin domain profile. 1 48 16.647
17 g12411.t3 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 63 123 16.74
8 g12411.t3 SUPERFAMILY SSF64356 SNARE-like 1 55 5.04E-11
9 g12411.t3 SUPERFAMILY SSF58038 SNARE fusion complex 59 124 3.14E-18
16 g12411.t3 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 128 150 -

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.

Raw TPM values