Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Vesicle-associated membrane protein 714.

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 g12408 g12408.t2 isoform g12408.t2 23423279 23424173
chr_1 g12408 g12408.t2 exon g12408.t2.exon1 23423279 23423877
chr_1 g12408 g12408.t2 TTS g12408.t2 23423309 23423309
chr_1 g12408 g12408.t2 cds g12408.t2.CDS1 23423728 23423877
chr_1 g12408 g12408.t2 exon g12408.t2.exon2 23423935 23424173
chr_1 g12408 g12408.t2 cds g12408.t2.CDS2 23423935 23424132
chr_1 g12408 g12408.t2 TSS g12408.t2 23425105 23425105

Sequences

>g12408.t2 Gene=g12408 Length=838
CAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGCAATGAATACAGAATTCTCTC
GTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGGCGAGTATGATAGCATACAGC
GAGTACATGGACAAATTGATGAATTAAAAGATATTATGGTTAAAAATATTGAAAATATAA
CAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATCAGAAAGTTTACGAAATAATG
CTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACACTATTTTGGAGAAATGTAA
AAATGTATATTCTACTTGGTCTCTTAATGCTTTTTATAATATACATTATTGTTGCCATGT
TTTGTGGATTTGCTTTGAAATGTCGCTAAAGTGTTAAAACATAATTTATATTTTAAGCAA
AACAATAATATGATGGTAAGAGACTATGTGATTGTTAAATGTCTCTCGAAAAAAAATTGT
TTATTTCAACCACATAGATTCTCAGTTATGAATTTATCAATATTTATATATTATTATTTC
TAATGAGGGTAAGTGTTGAAATAAATGTGAAAGGAAGTCAATTTTAACTTCTAACAATCT
TATCAGTAGTTGATCAAAATTATATATGAGTGAAAAAATCTAATTAATCTTCTTCTCATC
AACACATGACCCTCATTCTTACATATACAAAAAAATTTATGTATCAACCACAATAAATAT
GATAAAAAATATTTTATTATTATTGACTACTGCACCAAAAAAACTCCGTTTTTATTAAAA
TATTGAATGTAATCAAAACTAAGAAGCGAGAAAAATAAATGAAAAATTTCTTAATGCA

>g12408.t2 Gene=g12408 Length=115
MNTEFSRVMSAEMKKCNESGEYDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKS
ESLRNNAVSFRQTSRTIARTLFWRNVKMYILLGLLMLFIIYIIVAMFCGFALKCR

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g12408.t2 Gene3D G3DSA:1.20.5.110 - 2 108 7.1E-27
2 g12408.t2 PANTHER PTHR21136:SF179 VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 1 108 9.0E-39
3 g12408.t2 PANTHER PTHR21136 SNARE PROTEINS 1 108 9.0E-39
5 g12408.t2 PRINTS PR00219 Synaptobrevin signature 29 48 7.1E-16
6 g12408.t2 PRINTS PR00219 Synaptobrevin signature 49 68 7.1E-16
4 g12408.t2 PRINTS PR00219 Synaptobrevin signature 85 104 7.1E-16
1 g12408.t2 Pfam PF00957 Synaptobrevin 23 109 2.8E-30
9 g12408.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 88 -
11 g12408.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 89 112 -
10 g12408.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 113 115 -
13 g12408.t2 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 24 84 16.74
7 g12408.t2 SUPERFAMILY SSF58038 SNARE fusion complex 20 85 1.47E-18
12 g12408.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 89 111 -

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