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.t8 isoform g3412.t8 25249076 25251047
chr_3 g3412 g3412.t8 exon g3412.t8.exon1 25249076 25249881
chr_3 g3412 g3412.t8 cds g3412.t8.CDS1 25249431 25249881
chr_3 g3412 g3412.t8 exon g3412.t8.exon2 25249953 25250062
chr_3 g3412 g3412.t8 cds g3412.t8.CDS2 25249953 25250062
chr_3 g3412 g3412.t8 exon g3412.t8.exon3 25250124 25250223
chr_3 g3412 g3412.t8 cds g3412.t8.CDS3 25250124 25250198
chr_3 g3412 g3412.t8 exon g3412.t8.exon4 25250283 25251047
chr_3 g3412 g3412.t8 TSS g3412.t8 NA NA
chr_3 g3412 g3412.t8 TTS g3412.t8 NA NA

Sequences

>g3412.t8 Gene=g3412 Length=1781
CGAATCTCTTTGATCTTCTTTATAATTTGATTCACGTGCTCTTTTTTTACTACTTTCCTC
TTTACTTCTTTTAGTGCTTGTAGTTTTAGATTCATATTCTCTGTGATTACTTTTACTTCT
TGATCGATCAATATGTGTTCTTTTTCTATCATATCGAGAATTTTTCCGTTCTGGTGATTC
TCTTCTTTTCCTACTATCAGTATTTCTTTCCTCTGAACGTCTCTTTGAATTATATTTATC
TTCAATTCGGCGAATTTCATTTTTAGTAGAACTAGTTTGTGTATATTTATCGCTTGTGTT
TTTACTAATCTTTGTTTTACGAAAAATTATTTCATCCTTTTCACGTTGCAATTCGCTATT
AGCAAGTCTTAATTCTTTAATTTGTGCATCTTTTCTCTCAATTTCGGCTTTCGCAGTTGC
CAATAAGATCGATAAATTTTTCTTAAGTTGTTCATTAGAATTTTCAAGTTTTTCAATCTT
TTCAAATGTTTCTTCTTTAAATTGTTTTTCTTTTTCTAATTTCACTAAATTCTCTACTGC
TTTCTTTTCTACTTCTTCTTGCAATGGTTCAATAAGTGCTTCATCTAAATCTCCATAAAT
ATCAAAGTTATCACTTGCCATTTTAATTATAAACTAAAATAAATTTTTAGATACAAAAAA
GTAATGTAAACAAAAGTTGGCAAAAAAATTTCTGCGTAAATTTGATTTTTAAACGTTCGT
TTTATTCTCTTTAAAAATAATAACGTTTTAATTTTCAAAACGTTGATTTATTATAAAGAA
TTTATTAAAAATGGCTCTGATGACAATGATTGCTAGAGTTATAGATGGATTACCTCTAGT
AGGAACTATGCAAGAGAATGAAGAATCAGGCAAGAGTGTTTTAGAATATCAGAATCAAGC
AAAAATGCTATTCAGAAAGCTCGGACCTAATTCTCCAGCGAGATGCACTCTTGAAACAGG
ACCATATTTATTCCATTATTTAATTGAGAATGAAGTATGCTATCTCGTTTTGTGTGACAA
AATGTTTTCAAAACGTCTTGCATTTAATTATCTTGAGGATTTAGCACAAGAGTTTTACAC
AAATTATGGTAGAAAGATTAATACAGTGACTAGACCTTATCAATTTATTGAGTTCGATAT
ATACATTCAAAAAGCCAAGAAATCACTTACGGATCGTAGAAGAAATATCAACACAATAAA
TTCTCAACTTCAAGATGTGCAGCGAATAATGGTCCAAAATATTGATGATGTACTCCAACG
GGGAGCAGTTTTGTCAGAATTAGATACAAAAACACAAAATTTATCAATGCTCTCACAGAA
ATACAAAAAGAGTGCAACACAGTTAAATCGAAGATCAATGTATGTTAAAGCAGCAGTAGC
AAGTATCATTTTGATCGTTATTGGCATGTATTTTTGGTTATTCTGAGATCAAACTATTTC
ATTCATCTTCAAAAATGGTTTCAACTATTACTTTCGCGTTAAGGGATTTGAAATGTGGAC
TGGGACTATTTTTTCCAACATGCATACCGACATACACACATATATAACATTATTATTATT
ATTCATAATAAAATATCGGATGAAAGAGCAAAAAAAATATAAGGCGCGAATATATGTATA
ATATTTTTAAAGAATTGATTTTATTATTTCGTTAGAAAATGAAAAACAAAAAAAATTGTG
TAAAGATTCAATTTGCAATAAAAAAAACATTCTTATTTTGCAATTATATAAAATAGGACA
ATTAAGAGTCATTGCTCGAGAAGAACTTATGGGCATACATT

>g3412.t8 Gene=g3412 Length=211
MALMTMIARVIDGLPLVGTMQENEESGKSVLEYQNQAKMLFRKLGPNSPARCTLETGPYL
FHYLIENEVCYLVLCDKMFSKRLAFNYLEDLAQEFYTNYGRKINTVTRPYQFIEFDIYIQ
KAKKSLTDRRRNINTINSQLQDVQRIMVQNIDDVLQRGAVLSELDTKTQNLSMLSQKYKK
SATQLNRRSMYVKAAVASIILIVIGMYFWLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3412.t8 CDD cd14824 Longin 3 124 1.64271E-38
12 g3412.t8 CDD cd15866 R-SNARE_SEC22 130 193 4.57371E-28
8 g3412.t8 Gene3D G3DSA:3.30.450.50 - 1 126 9.6E-51
7 g3412.t8 Gene3D G3DSA:1.20.5.110 - 128 211 6.4E-16
3 g3412.t8 PANTHER PTHR45837:SF3 VESICLE-TRAFFICKING PROTEIN SEC22B 1 210 2.9E-80
4 g3412.t8 PANTHER PTHR45837 VESICLE-TRAFFICKING PROTEIN SEC22B 1 210 2.9E-80
1 g3412.t8 Pfam PF13774 Regulated-SNARE-like domain 37 116 1.2E-24
2 g3412.t8 Pfam PF00957 Synaptobrevin 130 208 6.1E-19
9 g3412.t8 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 189 -
11 g3412.t8 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 190 210 -
10 g3412.t8 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 211 211 -
17 g3412.t8 ProSiteProfiles PS50859 Longin domain profile. 6 119 34.672
16 g3412.t8 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 132 192 14.728
15 g3412.t8 SMART SM01270 Longin_2 36 118 3.8E-34
5 g3412.t8 SUPERFAMILY SSF64356 SNARE-like 1 124 2.24E-39
6 g3412.t8 SUPERFAMILY SSF58038 SNARE fusion complex 130 189 1.73E-16
14 g3412.t8 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 188 210 -

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