Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Synaptobrevin.

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_2 g8067 g8067.t2 TTS g8067.t2 28397737 28397737
chr_2 g8067 g8067.t2 isoform g8067.t2 28398145 28401068
chr_2 g8067 g8067.t2 exon g8067.t2.exon1 28398145 28398161
chr_2 g8067 g8067.t2 cds g8067.t2.CDS1 28398145 28398161
chr_2 g8067 g8067.t2 exon g8067.t2.exon2 28400067 28400341
chr_2 g8067 g8067.t2 cds g8067.t2.CDS2 28400067 28400341
chr_2 g8067 g8067.t2 exon g8067.t2.exon3 28401040 28401068
chr_2 g8067 g8067.t2 cds g8067.t2.CDS3 28401040 28401068
chr_2 g8067 g8067.t2 TSS g8067.t2 28401654 28401654

Sequences

>g8067.t2 Gene=g8067 Length=321
ATGGCAGATCAAGGAACATCAAATGGAGCCGGATCAACTGGTACTCAGAATAATAATAAT
CGTCTCAAACAAACACAACAAAAAGTCGATGAAGTCGTGGGAATCATGCGAGTAAATGTT
GAAAAAGTATTAGAGCGTGATCAGAAACTGTCTGAACTGGATCATCGAGCTGACGCTTTA
CAACATGGTGCATCACAATTTGAACAACAGGCTGGTAAATTAAAGAGAAAACAATGGTGG
GCGAACATGAAAATGATGATTATAATGGGAGTCATTGGTGTTATCCTATTAATCATCATC
ATAGTTCTTCTCTTCAAATAA

>g8067.t2 Gene=g8067 Length=106
MADQGTSNGAGSTGTQNNNNRLKQTQQKVDEVVGIMRVNVEKVLERDQKLSELDHRADAL
QHGASQFEQQAGKLKRKQWWANMKMMIIMGVIGVILLIIIIVLLFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8067.t2 CDD cd15870 R-SNARE_VAMP2 21 82 1.64873E-31
8 g8067.t2 Gene3D G3DSA:1.20.5.110 - 1 105 6.7E-45
15 g8067.t2 MobiDBLite mobidb-lite consensus disorder prediction 1 24 -
2 g8067.t2 PANTHER PTHR45701:SF10 SYNAPTOBREVIN 6 104 5.5E-53
3 g8067.t2 PANTHER PTHR45701 SYNAPTOBREVIN FAMILY MEMBER 6 104 5.5E-53
12 g8067.t2 PIRSF PIRSF005409 VAMP-5_synaptobrevin 1 106 7.2E-40
5 g8067.t2 PRINTS PR00219 Synaptobrevin signature 26 45 4.8E-29
6 g8067.t2 PRINTS PR00219 Synaptobrevin signature 46 65 4.8E-29
4 g8067.t2 PRINTS PR00219 Synaptobrevin signature 82 101 4.8E-29
1 g8067.t2 Pfam PF00957 Synaptobrevin 19 105 3.4E-34
9 g8067.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 84 -
11 g8067.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 105 -
10 g8067.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 106 106 -
16 g8067.t2 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 21 81 17.415
7 g8067.t2 SUPERFAMILY SSF58038 SNARE fusion complex 17 83 3.09E-20
14 g8067.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -

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.

Raw TPM values