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.t13 TTS g12411.t13 23431760 23431760
chr_1 g12411 g12411.t13 isoform g12411.t13 23432129 23433523
chr_1 g12411 g12411.t13 exon g12411.t13.exon1 23432129 23432709
chr_1 g12411 g12411.t13 cds g12411.t13.CDS1 23432327 23432709
chr_1 g12411 g12411.t13 exon g12411.t13.exon2 23432767 23432921
chr_1 g12411 g12411.t13 cds g12411.t13.CDS2 23432767 23432893
chr_1 g12411 g12411.t13 exon g12411.t13.exon3 23433374 23433523
chr_1 g12411 g12411.t13 TSS g12411.t13 23433461 23433461

Sequences

>g12411.t13 Gene=g12411 Length=886
AAAGTTTCTCGATTTTTAATTTTTCCACGAATTTCTTTCTTTTAATGTTAAGAAAGCAAA
GAAACAAGATAATAACTGTTTAAAGTTCTTATTTATCGTGAAGTTATAATTTTAAAGAAT
TCTGTGAAACTCAATAAGTATTGTTGGTGAACAGCAGGTTATCAACATCAACAACAAGAT
GCCTCTTCTATATGCAGTTATCACAAGAGGAAATACTGTATTGTGTAAATATGCCGACTG
CGTTGGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGACAAACCA
TAAAATGACATACACACATGGCCAATACCTTTTCCATTATATTTGTGCTGATAAAATAAT
TTACATGACCATAAGTGATGATGAGTTTCCACGACAGCGTGCCTTTCTATATCTCTCAGA
AATAAAACAGAAATTTTTAGCAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGC
AATGAATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGG
CGAGTATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAAGATATTATGGT
TAAAAATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATC
AGAAAGTTTACGAAATAATGTAAGTTAATTTAAATACAAAATAATTTGACATGTTTATTA
TTTTAATTTTTTATAGGCTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACACT
ATTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATACTTTTCATAATATA
CATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAA

>g12411.t13 Gene=g12411 Length=169
MPLLYAVITRGNTVLCKYADCVGNFSEVTENLISKIQLTNHKMTYTHGQYLFHYICADKI
IYMTISDDEFPRQRAFLYLSEIKQKFLATYGLTAATALPYAMNTEFSRVMSAEMKKCNES
GEYDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKSESLRNNVS

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g12411.t13 CDD cd14824 Longin 4 117 0.0000000
10 g12411.t13 Gene3D G3DSA:3.30.450.50 - 1 120 0.0000000
9 g12411.t13 Gene3D G3DSA:1.20.5.110 - 121 169 0.0000000
3 g12411.t13 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 168 0.0000000
4 g12411.t13 PANTHER PTHR21136 SNARE PROTEINS 1 168 0.0000000
6 g12411.t13 PRINTS PR00219 Synaptobrevin signature 130 149 0.0000021
5 g12411.t13 PRINTS PR00219 Synaptobrevin signature 150 169 0.0000021
1 g12411.t13 Pfam PF13774 Regulated-SNARE-like domain 31 107 0.0000000
2 g12411.t13 Pfam PF00957 Synaptobrevin 124 167 0.0000000
14 g12411.t13 ProSiteProfiles PS50859 Longin domain profile. 7 110 28.7580000
13 g12411.t13 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 125 169 13.8190000
12 g12411.t13 SMART SM01270 Longin_2 28 109 0.0000000
7 g12411.t13 SUPERFAMILY SSF64356 SNARE-like 3 117 0.0000000
8 g12411.t13 SUPERFAMILY SSF58038 SNARE fusion complex 121 167 0.0000000

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. There were no conditions that were differentially expressed