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.t10 isoform g8067.t10 28391916 28401590
chr_2 g8067 g8067.t10 exon g8067.t10.exon1 28391916 28392232
chr_2 g8067 g8067.t10 TTS g8067.t10 28391931 28391931
chr_2 g8067 g8067.t10 cds g8067.t10.CDS1 28392168 28392232
chr_2 g8067 g8067.t10 exon g8067.t10.exon2 28400067 28400341
chr_2 g8067 g8067.t10 cds g8067.t10.CDS2 28400067 28400341
chr_2 g8067 g8067.t10 exon g8067.t10.exon3 28401040 28401123
chr_2 g8067 g8067.t10 cds g8067.t10.CDS3 28401040 28401068
chr_2 g8067 g8067.t10 exon g8067.t10.exon4 28401574 28401590
chr_2 g8067 g8067.t10 TSS g8067.t10 28401654 28401654

Sequences

>g8067.t10 Gene=g8067 Length=693
TCTGCCTAAAAAGTCATTCTCTGATCATCATCTTCATCTTAAATAAATAATAATTAATAG
ACGCATTTGAAAATGGCAGATCAAGGAACATCAAATGGAGCCGGATCAACTGGTACTCAG
AATAATAATAATCGTCTCAAACAAACACAACAAAAAGTCGATGAAGTCGTGGGAATCATG
CGAGTAAATGTTGAAAAAGTATTAGAGCGTGATCAGAAACTGTCTGAACTGGATCATCGA
GCTGACGCTTTACAACATGGTGCATCACAATTTGAACAACAGGCTGGTAAATTAAAGAGA
AAACAATGGTGGGCGAACATGAAAATGATGATTATAATGGGAGTCATTGGTGTTATCCTA
TTAATCATCATCATAGTTCTTCTTCATCTATCTGTCTGTTTTTTTTCTTTCAAATACAGT
TTTCAATATATTTCAATTTAAATACGATAAACGTGACTTTTATTTATCAACAAAAAGTGC
CTACGATGTGTGTGCAAATATTAAATAATGTCAATAAAATTGTGCATGGCAGACAGTGAG
ATGAAAATCAAACGAGATGGAAATGTGCACAATATAAAATAGATTTTTTATATTTATTAT
ATCATAGTTTATACATCACAATATGTCTACCCTTTTGTAAATTGTAATCTAAATAAAAAA
TGTTATCCTTCAACCAGCAACTAATTTTTGTAT

>g8067.t10 Gene=g8067 Length=122
MADQGTSNGAGSTGTQNNNNRLKQTQQKVDEVVGIMRVNVEKVLERDQKLSELDHRADAL
QHGASQFEQQAGKLKRKQWWANMKMMIIMGVIGVILLIIIIVLLHLSVCFFSFKYSFQYI
SI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g8067.t10 CDD cd15870 R-SNARE_VAMP2 21 82 1.80984E-34
8 g8067.t10 Gene3D G3DSA:1.20.5.110 - 1 105 1.2E-44
14 g8067.t10 MobiDBLite mobidb-lite consensus disorder prediction 1 26 -
2 g8067.t10 PANTHER PTHR45701:SF10 SYNAPTOBREVIN 6 106 3.1E-54
3 g8067.t10 PANTHER PTHR45701 SYNAPTOBREVIN FAMILY MEMBER 6 106 3.1E-54
5 g8067.t10 PRINTS PR00219 Synaptobrevin signature 26 45 6.2E-29
6 g8067.t10 PRINTS PR00219 Synaptobrevin signature 46 65 6.2E-29
4 g8067.t10 PRINTS PR00219 Synaptobrevin signature 82 101 6.2E-29
1 g8067.t10 Pfam PF00957 Synaptobrevin 19 103 7.6E-34
9 g8067.t10 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 84 -
11 g8067.t10 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 85 113 -
10 g8067.t10 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 114 122 -
15 g8067.t10 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 21 81 17.415
7 g8067.t10 SUPERFAMILY SSF58038 SNARE fusion complex 17 83 4.6E-20
13 g8067.t10 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 108 -

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