Gene loci information

Transcript annotation

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

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.t5 isoform g3412.t5 25249076 25250198
chr_3 g3412 g3412.t5 exon g3412.t5.exon1 25249076 25249861
chr_3 g3412 g3412.t5 cds g3412.t5.CDS1 25249431 25249861
chr_3 g3412 g3412.t5 exon g3412.t5.exon2 25249948 25250062
chr_3 g3412 g3412.t5 cds g3412.t5.CDS2 25249948 25250062
chr_3 g3412 g3412.t5 exon g3412.t5.exon3 25250124 25250198
chr_3 g3412 g3412.t5 cds g3412.t5.CDS3 25250124 25250198
chr_3 g3412 g3412.t5 TSS g3412.t5 25250224 25250224
chr_3 g3412 g3412.t5 TTS g3412.t5 NA NA

Sequences

>g3412.t5 Gene=g3412 Length=976
ATGGCTCTGATGACAATGATTGCTAGAGTTATAGATGGATTACCTCTAGTAGGAACTATG
CAAGAGAATGAAGAATCAGGCAAGAGTGTTTTAGAATATCAGAATCAAGCAAAAATGCTA
TTCAGAAAGCTCGGACCTAATTCTCCAGCGAGATGCACTCTTGAAACAGGACCATATTTA
TTCCAGTTGATATGCTATCTCGTTTTGTGTGACAAAATGTTTTCAAAACGTCTTGCATTT
AATTATCTTGAGGATTTAGCACAAGAGTTTTACACAAATTATGGTAGAAAGATTAATACA
GTGACTAGACCTTATCAATTTATTGAGTTCGATATATACATTCAAAAAGCCAAGAAATCA
CTTACGGATCGTAGAAGAAATATCAACACAATAAATTCTCAACTTCAAGATGTGCAGCGA
ATAATGGTCCAAAATATTGATGATGTACTCCAACGGGGAGCAGTTTTGTCAGAATTAGAT
ACAAAAACACAAAATTTATCAATGCTCTCACAGAAATACAAAAAGAGTGCAACACAGTTA
AATCGAAGATCAATGTATGTTAAAGCAGCAGTAGCAAGTATCATTTTGATCGTTATTGGC
ATGTATTTTTGGTTATTCTGAGATCAAACTATTTCATTCATCTTCAAAAATGGTTTCAAC
TATTACTTTCGCGTTAAGGGATTTGAAATGTGGACTGGGACTATTTTTTCCAACATGCAT
ACCGACATACACACATATATAACATTATTATTATTATTCATAATAAAATATCGGATGAAA
GAGCAAAAAAAATATAAGGCGCGAATATATGTATAATATTTTTAAAGAATTGATTTTATT
ATTTCGTTAGAAAATGAAAAACAAAAAAAATTGTGTAAAGATTCAATTTGCAATAAAAAA
AACATTCTTATTTTGCAATTATATAAAATAGGACAATTAAGAGTCATTGCTCGAGAAGAA
CTTATGGGCATACATT

>g3412.t5 Gene=g3412 Length=206
MALMTMIARVIDGLPLVGTMQENEESGKSVLEYQNQAKMLFRKLGPNSPARCTLETGPYL
FQLICYLVLCDKMFSKRLAFNYLEDLAQEFYTNYGRKINTVTRPYQFIEFDIYIQKAKKS
LTDRRRNINTINSQLQDVQRIMVQNIDDVLQRGAVLSELDTKTQNLSMLSQKYKKSATQL
NRRSMYVKAAVASIILIVIGMYFWLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3412.t5 CDD cd14824 Longin 3 119 5.4321E-31
12 g3412.t5 CDD cd15866 R-SNARE_SEC22 125 188 5.55957E-28
8 g3412.t5 Gene3D G3DSA:3.30.450.50 - 1 121 1.7E-42
7 g3412.t5 Gene3D G3DSA:1.20.5.110 - 123 206 6.0E-16
3 g3412.t5 PANTHER PTHR45837:SF3 VESICLE-TRAFFICKING PROTEIN SEC22B 1 205 1.5E-72
4 g3412.t5 PANTHER PTHR45837 VESICLE-TRAFFICKING PROTEIN SEC22B 1 205 1.5E-72
1 g3412.t5 Pfam PF13774 Regulated-SNARE-like domain 37 111 1.4E-17
2 g3412.t5 Pfam PF00957 Synaptobrevin 125 203 5.8E-19
9 g3412.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 184 -
11 g3412.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 185 205 -
10 g3412.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 206 206 -
17 g3412.t5 ProSiteProfiles PS50859 Longin domain profile. 6 114 26.249
16 g3412.t5 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 127 187 14.728
15 g3412.t5 SMART SM01270 Longin_2 36 113 2.3E-24
5 g3412.t5 SUPERFAMILY SSF64356 SNARE-like 1 119 1.69E-32
6 g3412.t5 SUPERFAMILY SSF58038 SNARE fusion complex 125 184 1.67E-16
14 g3412.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 183 205 -

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