Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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.t2 isoform g3412.t2 25249076 25249878
chr_3 g3412 g3412.t2 exon g3412.t2.exon1 25249076 25249878
chr_3 g3412 g3412.t2 cds g3412.t2.CDS1 25249431 25249835
chr_3 g3412 g3412.t2 TSS g3412.t2 25250224 25250224
chr_3 g3412 g3412.t2 TTS g3412.t2 NA NA

Sequences

>g3412.t2 Gene=g3412 Length=803
TTTAATTGAGAATGAAGTATGCTATCTCGTTTTGTGTGACAAAATGTTTTCAAAACGTCT
TGCATTTAATTATCTTGAGGATTTAGCACAAGAGTTTTACACAAATTATGGTAGAAAGAT
TAATACAGTGACTAGACCTTATCAATTTATTGAGTTCGATATATACATTCAAAAAGCCAA
GAAATCACTTACGGATCGTAGAAGAAATATCAACACAATAAATTCTCAACTTCAAGATGT
GCAGCGAATAATGGTCCAAAATATTGATGATGTACTCCAACGGGGAGCAGTTTTGTCAGA
ATTAGATACAAAAACACAAAATTTATCAATGCTCTCACAGAAATACAAAAAGAGTGCAAC
ACAGTTAAATCGAAGATCAATGTATGTTAAAGCAGCAGTAGCAAGTATCATTTTGATCGT
TATTGGCATGTATTTTTGGTTATTCTGAGATCAAACTATTTCATTCATCTTCAAAAATGG
TTTCAACTATTACTTTCGCGTTAAGGGATTTGAAATGTGGACTGGGACTATTTTTTCCAA
CATGCATACCGACATACACACATATATAACATTATTATTATTATTCATAATAAAATATCG
GATGAAAGAGCAAAAAAAATATAAGGCGCGAATATATGTATAATATTTTTAAAGAATTGA
TTTTATTATTTCGTTAGAAAATGAAAAACAAAAAAAATTGTGTAAAGATTCAATTTGCAA
TAAAAAAAACATTCTTATTTTGCAATTATATAAAATAGGACAATTAAGAGTCATTGCTCG
AGAAGAACTTATGGGCATACATT

>g3412.t2 Gene=g3412 Length=134
MFSKRLAFNYLEDLAQEFYTNYGRKINTVTRPYQFIEFDIYIQKAKKSLTDRRRNINTIN
SQLQDVQRIMVQNIDDVLQRGAVLSELDTKTQNLSMLSQKYKKSATQLNRRSMYVKAAVA
SIILIVIGMYFWLF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g3412.t2 CDD cd14824 Longin 2 47 1.71162E-11
12 g3412.t2 CDD cd15866 R-SNARE_SEC22 53 116 4.15061E-27
8 g3412.t2 Gene3D G3DSA:3.30.450.50 - 1 49 1.9E-15
7 g3412.t2 Gene3D G3DSA:1.20.5.110 - 51 134 2.1E-16
3 g3412.t2 PANTHER PTHR45837:SF3 VESICLE-TRAFFICKING PROTEIN SEC22B 2 133 2.0E-44
4 g3412.t2 PANTHER PTHR45837 VESICLE-TRAFFICKING PROTEIN SEC22B 2 133 2.0E-44
1 g3412.t2 Pfam PF13774 Regulated-SNARE-like domain 2 39 2.8E-8
2 g3412.t2 Pfam PF00957 Synaptobrevin 53 131 2.0E-19
9 g3412.t2 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 112 -
11 g3412.t2 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 113 133 -
10 g3412.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 134 134 -
16 g3412.t2 ProSiteProfiles PS50859 Longin domain profile. 1 42 13.471
15 g3412.t2 ProSiteProfiles PS50892 v-SNARE coiled-coil homology domain profile. 55 115 14.728
5 g3412.t2 SUPERFAMILY SSF64356 SNARE-like 2 47 6.41E-13
6 g3412.t2 SUPERFAMILY SSF58038 SNARE fusion complex 53 112 6.21E-17
14 g3412.t2 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 133 -

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