General information for g3412.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vesicle-trafficking protein SEC22b.
Parent gene
- The parent gene g3412 is located on chr_3: 25249431..25251047 (- strand)
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.t1 | TTS | g3412.t1 | 25249131 | 25249131 |
| chr_3 | g3412 | g3412.t1 | isoform | g3412.t1 | 25249431 | 25250198 |
| chr_3 | g3412 | g3412.t1 | exon | g3412.t1.exon1 | 25249431 | 25249881 |
| chr_3 | g3412 | g3412.t1 | cds | g3412.t1.CDS1 | 25249431 | 25249881 |
| chr_3 | g3412 | g3412.t1 | exon | g3412.t1.exon2 | 25249953 | 25250062 |
| chr_3 | g3412 | g3412.t1 | cds | g3412.t1.CDS2 | 25249953 | 25250062 |
| chr_3 | g3412 | g3412.t1 | exon | g3412.t1.exon3 | 25250124 | 25250198 |
| chr_3 | g3412 | g3412.t1 | cds | g3412.t1.CDS3 | 25250124 | 25250198 |
| chr_3 | g3412 | g3412.t1 | TSS | g3412.t1 | 25250224 | 25250224 |
Sequences
>g3412.t1 Gene=g3412 Length=636
ATGGCTCTGATGACAATGATTGCTAGAGTTATAGATGGATTACCTCTAGTAGGAACTATG
CAAGAGAATGAAGAATCAGGCAAGAGTGTTTTAGAATATCAGAATCAAGCAAAAATGCTA
TTCAGAAAGCTCGGACCTAATTCTCCAGCGAGATGCACTCTTGAAACAGGACCATATTTA
TTCCATTATTTAATTGAGAATGAAGTATGCTATCTCGTTTTGTGTGACAAAATGTTTTCA
AAACGTCTTGCATTTAATTATCTTGAGGATTTAGCACAAGAGTTTTACACAAATTATGGT
AGAAAGATTAATACAGTGACTAGACCTTATCAATTTATTGAGTTCGATATATACATTCAA
AAAGCCAAGAAATCACTTACGGATCGTAGAAGAAATATCAACACAATAAATTCTCAACTT
CAAGATGTGCAGCGAATAATGGTCCAAAATATTGATGATGTACTCCAACGGGGAGCAGTT
TTGTCAGAATTAGATACAAAAACACAAAATTTATCAATGCTCTCACAGAAATACAAAAAG
AGTGCAACACAGTTAAATCGAAGATCAATGTATGTTAAAGCAGCAGTAGCAAGTATCATT
TTGATCGTTATTGGCATGTATTTTTGGTTATTCTGA
>g3412.t1 Gene=g3412 Length=211
MALMTMIARVIDGLPLVGTMQENEESGKSVLEYQNQAKMLFRKLGPNSPARCTLETGPYL
FHYLIENEVCYLVLCDKMFSKRLAFNYLEDLAQEFYTNYGRKINTVTRPYQFIEFDIYIQ
KAKKSLTDRRRNINTINSQLQDVQRIMVQNIDDVLQRGAVLSELDTKTQNLSMLSQKYKK
SATQLNRRSMYVKAAVASIILIVIGMYFWLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3412.t1 | CDD | cd14824 | Longin | 3 | 124 | 1.64271E-38 |
| 12 | g3412.t1 | CDD | cd15866 | R-SNARE_SEC22 | 130 | 193 | 4.57371E-28 |
| 8 | g3412.t1 | Gene3D | G3DSA:3.30.450.50 | - | 1 | 126 | 9.6E-51 |
| 7 | g3412.t1 | Gene3D | G3DSA:1.20.5.110 | - | 128 | 211 | 6.4E-16 |
| 3 | g3412.t1 | PANTHER | PTHR45837:SF3 | VESICLE-TRAFFICKING PROTEIN SEC22B | 1 | 210 | 2.9E-80 |
| 4 | g3412.t1 | PANTHER | PTHR45837 | VESICLE-TRAFFICKING PROTEIN SEC22B | 1 | 210 | 2.9E-80 |
| 1 | g3412.t1 | Pfam | PF13774 | Regulated-SNARE-like domain | 37 | 116 | 1.2E-24 |
| 2 | g3412.t1 | Pfam | PF00957 | Synaptobrevin | 130 | 208 | 6.1E-19 |
| 9 | g3412.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 189 | - |
| 11 | g3412.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 190 | 210 | - |
| 10 | g3412.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 211 | 211 | - |
| 17 | g3412.t1 | ProSiteProfiles | PS50859 | Longin domain profile. | 6 | 119 | 34.672 |
| 16 | g3412.t1 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 132 | 192 | 14.728 |
| 15 | g3412.t1 | SMART | SM01270 | Longin_2 | 36 | 118 | 3.8E-34 |
| 5 | g3412.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 124 | 2.24E-39 |
| 6 | g3412.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 130 | 189 | 1.73E-16 |
| 14 | g3412.t1 | 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
- This transcript has been annotated with K08517 (vesicle transport protein SEC22)
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.
