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.t19 TTS g8067.t19 28397737 28397737
chr_2 g8067 g8067.t19 isoform g8067.t19 28397946 28401068
chr_2 g8067 g8067.t19 exon g8067.t19.exon1 28397946 28398161
chr_2 g8067 g8067.t19 cds g8067.t19.CDS1 28398145 28398161
chr_2 g8067 g8067.t19 exon g8067.t19.exon2 28400067 28400374
chr_2 g8067 g8067.t19 cds g8067.t19.CDS2 28400067 28400374
chr_2 g8067 g8067.t19 exon g8067.t19.exon3 28401040 28401068
chr_2 g8067 g8067.t19 cds g8067.t19.CDS3 28401040 28401068
chr_2 g8067 g8067.t19 TSS g8067.t19 28401654 28401654

Sequences

>g8067.t19 Gene=g8067 Length=553
ATGGCAGATCAAGGAACATCAAATGGAGCTTTTCCATCAATTCCACCTCCCCCTCAAAAT
AGCGGATCAACTGGTACTCAGAATAATAATAATCGTCTCAAACAAACACAACAAAAAGTC
GATGAAGTCGTGGGAATCATGCGAGTAAATGTTGAAAAAGTATTAGAGCGTGATCAGAAA
CTGTCTGAACTGGATCATCGAGCTGACGCTTTACAACATGGTGCATCACAATTTGAACAA
CAGGCTGGTAAATTAAAGAGAAAACAATGGTGGGCGAACATGAAAATGATGATTATAATG
GGAGTCATTGGTGTTATCCTATTAATCATCATCATAGTTCTTCTCTTCAAATAATGGCAA
AATTTTATTTTTCAAATGAATAAATGTTGTAAGGAGCATTACGATAGGTTTACCAATTTA
TTGATAAATTTTTTGAATGCATAACAAAGAAGCACAGAATATCATTAATCTTAATTATGT
TATAAAATAATATAACTTTTCAATCTATACTTATTTTTTCCAATTTGGTATTGTTATACG
TGAAAAGGGGAAG

>g8067.t19 Gene=g8067 Length=117
MADQGTSNGAFPSIPPPPQNSGSTGTQNNNNRLKQTQQKVDEVVGIMRVNVEKVLERDQK
LSELDHRADALQHGASQFEQQAGKLKRKQWWANMKMMIIMGVIGVILLIIIIVLLFK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g8067.t19 CDD cd15870 R-SNARE_VAMP2 32 93 3.26727E-34
8 g8067.t19 Gene3D G3DSA:1.20.5.110 - 3 116 7.8E-46
16 g8067.t19 MobiDBLite mobidb-lite consensus disorder prediction 1 38 -
15 g8067.t19 MobiDBLite mobidb-lite consensus disorder prediction 20 38 -
2 g8067.t19 PANTHER PTHR45701:SF10 SYNAPTOBREVIN 7 115 5.4E-57
3 g8067.t19 PANTHER PTHR45701 SYNAPTOBREVIN FAMILY MEMBER 7 115 5.4E-57
12 g8067.t19 PIRSF PIRSF005409 VAMP-5_synaptobrevin 11 117 8.9E-41
6 g8067.t19 PRINTS PR00219 Synaptobrevin signature 37 56 5.7E-29
4 g8067.t19 PRINTS PR00219 Synaptobrevin signature 57 76 5.7E-29
5 g8067.t19 PRINTS PR00219 Synaptobrevin signature 93 112 5.7E-29
1 g8067.t19 Pfam PF00957 Synaptobrevin 30 116 4.8E-34
9 g8067.t19 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 95 -
11 g8067.t19 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 96 116 -
10 g8067.t19 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 117 117 -
17 g8067.t19 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 32 92 17.415
7 g8067.t19 SUPERFAMILY SSF58038 SNARE fusion complex 28 94 4.08E-20
14 g8067.t19 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 97 116 -

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