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.t6 isoform g12411.t6 23431665 23433523
chr_1 g12411 g12411.t6 exon g12411.t6.exon1 23431665 23432278
chr_1 g12411 g12411.t6 cds g12411.t6.CDS1 23432129 23432278
chr_1 g12411 g12411.t6 exon g12411.t6.exon2 23432336 23432697
chr_1 g12411 g12411.t6 cds g12411.t6.CDS2 23432336 23432697
chr_1 g12411 g12411.t6 exon g12411.t6.exon3 23432767 23432921
chr_1 g12411 g12411.t6 cds g12411.t6.CDS3 23432767 23432893
chr_1 g12411 g12411.t6 exon g12411.t6.exon4 23433378 23433523
chr_1 g12411 g12411.t6 TSS g12411.t6 23433461 23433461
chr_1 g12411 g12411.t6 TTS g12411.t6 NA NA

Sequences

>g12411.t6 Gene=g12411 Length=1277
AAAGTTTCTCGATTTTTAATTTTTCCACGAATTTCTTTCTTTTAATGTTAAGAAAGCAAA
GAAACAAGATAATAACTGTTTAAAGTTCTTATTTATCGTGAAGTTATAATTTTAAAGAAT
TCTGTGAAACTCAATAAGTATTGTTGACAGCAGGTTATCAACATCAACAACAAGATGCCT
CTTCTATATGCAGTTATCACAAGAGGAAATACTGTATTGTGTAAATATGCCGACTGCGTT
GGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGACAAACCATAAA
AATGGCCAATACCTTTTCCATTATATTTGTGCTGATAAAATAATTTACATGACCATAAGT
GATGATGAGTTTCCACGACAGCGTGCCTTTCTATATCTCTCAGAAATAAAACAGAAATTT
TTAGCAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGCAATGAATACAGAATTC
TCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGGCGAGTATGATAGCATA
CAGCGAGTACATGGACAAATTGATGAATTAAAAGATATTATGGTTAAAAATATTGAAAAT
ATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATCAGAAAGTTTACGAAAT
AATGCTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACACTATTTTGGAGAAAT
GTAAAAATGTATATTCTACTTGGTCTCTTAATACTTTTCATAATATACATTATTGTTGCC
ATGTTTTGTGGATTTGCTTTGAAATGTCGCTAAAGTGTTAAAACATAATTTATATTTTAA
GCAAAACAATAATATGATGGTAAGAGACTATGTGATTGTTAAATGTCTCTCGAAAAAAAA
TTGTTTATTTCAACCACATAGATTCTCAGTTATGAATTTATCAATATTTTATACATTATT
ATTTCTAATGAGGGTAAGTGTTGAAATAAATGTGAAAGGAAGTCAATTTTAACTTCTAAC
AATCTTATCAGTAGTTGATCAAAATTATATATGAGTGAAAAAATCTAATTAATCTTCTTC
TCATCAACACATGACCCTCATTCTTACATATACAAAAAAATTTATGTATCAACCACAATA
AATATGATAAAAATAATTTTATTATTATTTGACTACTGCACCAAAAAAACTCCGTTTTTA
TTAAAATATTGAATGTAATCAAAACTAAGAAGCGAGAAAAATAAATGAAAAATTTCTTAA
TGCAAAATAAAACTTTT

>g12411.t6 Gene=g12411 Length=212
MPLLYAVITRGNTVLCKYADCVGNFSEVTENLISKIQLTNHKNGQYLFHYICADKIIYMT
ISDDEFPRQRAFLYLSEIKQKFLATYGLTAATALPYAMNTEFSRVMSAEMKKCNESGEYD
SIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKSESLRNNAVSFRQTSRTIARTLFW
RNVKMYILLGLLILFIIYIIVAMFCGFALKCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g12411.t6 CDD cd14824 Longin 4 113 2.56209E-29
11 g12411.t6 Gene3D G3DSA:3.30.450.50 - 1 118 1.1E-37
10 g12411.t6 Gene3D G3DSA:1.20.5.110 - 119 205 9.3E-26
3 g12411.t6 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 205 7.2E-87
4 g12411.t6 PANTHER PTHR21136 SNARE PROTEINS 1 205 7.2E-87
7 g12411.t6 PRINTS PR00219 Synaptobrevin signature 126 145 1.2E-15
6 g12411.t6 PRINTS PR00219 Synaptobrevin signature 146 165 1.2E-15
5 g12411.t6 PRINTS PR00219 Synaptobrevin signature 182 201 1.2E-15
1 g12411.t6 Pfam PF13774 Regulated-SNARE-like domain 38 103 5.3E-20
2 g12411.t6 Pfam PF00957 Synaptobrevin 120 206 3.9E-30
12 g12411.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 185 -
14 g12411.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 186 209 -
13 g12411.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 210 212 -
19 g12411.t6 ProSiteProfiles PS50859 Longin domain profile. 7 106 24.518
18 g12411.t6 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 121 181 16.74
17 g12411.t6 SMART SM01270 Longin_2 28 105 7.3E-23
8 g12411.t6 SUPERFAMILY SSF64356 SNARE-like 3 113 6.87E-25
9 g12411.t6 SUPERFAMILY SSF58038 SNARE fusion complex 117 182 6.28E-18
16 g12411.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 186 208 -

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