Gene loci information

Transcript annotation

  • This transcript has been annotated as Vesicle-trafficking protein SEC22b-B.

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_3 g3412 g3412.t7 isoform g3412.t7 25249076 25250427
chr_3 g3412 g3412.t7 exon g3412.t7.exon1 25249076 25249881
chr_3 g3412 g3412.t7 cds g3412.t7.CDS1 25249431 25249881
chr_3 g3412 g3412.t7 exon g3412.t7.exon2 25249953 25250058
chr_3 g3412 g3412.t7 cds g3412.t7.CDS2 25249953 25250023
chr_3 g3412 g3412.t7 exon g3412.t7.exon3 25250124 25250223
chr_3 g3412 g3412.t7 exon g3412.t7.exon4 25250283 25250427
chr_3 g3412 g3412.t7 TSS g3412.t7 25250774 25250774
chr_3 g3412 g3412.t7 TTS g3412.t7 NA NA

Sequences

>g3412.t7 Gene=g3412 Length=1157
TTTTAATTATAAACTAAAATAAATTTTTAGATACAAAAAAGTAATGTAAACAAAAGTTGG
CAAAAAAATTTCTGCGTAAATTTGATTTTTAAACGTTCGTTTTATTCTCTTTAAAAATAA
TAACGTTTTAATTTTCAAAACGTTGATTTATTATAAAGAATTTATTAAAAATGGCTCTGA
TGACAATGATTGCTAGAGTTATAGATGGATTACCTCTAGTAGGAACTATGCAAGAGAATG
AAGAAGCAAGAGTGTTTTAGAATATCAGAATCAAGCAAAAATGCTATTCAGAAAGCTCGG
ACCTAATTCTCCAGCGAGATGCACTCTTGAAACAGGACCATATTTATTCCATTATTTAAT
TGAGAATGAAGTATGCTATCTCGTTTTGTGTGACAAAATGTTTTCAAAACGTCTTGCATT
TAATTATCTTGAGGATTTAGCACAAGAGTTTTACACAAATTATGGTAGAAAGATTAATAC
AGTGACTAGACCTTATCAATTTATTGAGTTCGATATATACATTCAAAAAGCCAAGAAATC
ACTTACGGATCGTAGAAGAAATATCAACACAATAAATTCTCAACTTCAAGATGTGCAGCG
AATAATGGTCCAAAATATTGATGATGTACTCCAACGGGGAGCAGTTTTGTCAGAATTAGA
TACAAAAACACAAAATTTATCAATGCTCTCACAGAAATACAAAAAGAGTGCAACACAGTT
AAATCGAAGATCAATGTATGTTAAAGCAGCAGTAGCAAGTATCATTTTGATCGTTATTGG
CATGTATTTTTGGTTATTCTGAGATCAAACTATTTCATTCATCTTCAAAAATGGTTTCAA
CTATTACTTTCGCGTTAAGGGATTTGAAATGTGGACTGGGACTATTTTTTCCAACATGCA
TACCGACATACACACATATATAACATTATTATTATTATTCATAATAAAATATCGGATGAA
AGAGCAAAAAAAATATAAGGCGCGAATATATGTATAATATTTTTAAAGAATTGATTTTAT
TATTTCGTTAGAAAATGAAAAACAAAAAAAATTGTGTAAAGATTCAATTTGCAATAAAAA
AAACATTCTTATTTTGCAATTATATAAAATAGGACAATTAAGAGTCATTGCTCGAGAAGA
ACTTATGGGCATACATT

>g3412.t7 Gene=g3412 Length=173
MLFRKLGPNSPARCTLETGPYLFHYLIENEVCYLVLCDKMFSKRLAFNYLEDLAQEFYTN
YGRKINTVTRPYQFIEFDIYIQKAKKSLTDRRRNINTINSQLQDVQRIMVQNIDDVLQRG
AVLSELDTKTQNLSMLSQKYKKSATQLNRRSMYVKAAVASIILIVIGMYFWLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3412.t7 CDD cd14824 Longin 1 86 7.71353E-30
12 g3412.t7 CDD cd15866 R-SNARE_SEC22 92 155 1.18646E-28
8 g3412.t7 Gene3D G3DSA:3.30.450.50 - 1 88 3.6E-35
7 g3412.t7 Gene3D G3DSA:1.20.5.110 - 90 173 4.0E-16
3 g3412.t7 PANTHER PTHR45837:SF3 VESICLE-TRAFFICKING PROTEIN SEC22B 1 172 6.0E-65
4 g3412.t7 PANTHER PTHR45837 VESICLE-TRAFFICKING PROTEIN SEC22B 1 172 6.0E-65
1 g3412.t7 Pfam PF13774 Regulated-SNARE-like domain 2 78 7.3E-24
2 g3412.t7 Pfam PF00957 Synaptobrevin 92 170 3.9E-19
9 g3412.t7 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 151 -
11 g3412.t7 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 152 172 -
10 g3412.t7 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 173 173 -
17 g3412.t7 ProSiteProfiles PS50859 Longin domain profile. 1 81 29.386
16 g3412.t7 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 94 154 14.728
15 g3412.t7 SMART SM01270 Longin_2 1 80 7.7E-29
5 g3412.t7 SUPERFAMILY SSF64356 SNARE-like 1 86 3.52E-30
6 g3412.t7 SUPERFAMILY SSF58038 SNARE fusion complex 92 151 1.14E-16
14 g3412.t7 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 150 172 -

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