General information for g3412.t6
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vesicle-trafficking protein SEC22b-B.
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.t6 | isoform | g3412.t6 | 25249076 | 25250198 |
| chr_3 | g3412 | g3412.t6 | exon | g3412.t6.exon1 | 25249076 | 25249881 |
| chr_3 | g3412 | g3412.t6 | cds | g3412.t6.CDS1 | 25249431 | 25249881 |
| chr_3 | g3412 | g3412.t6 | exon | g3412.t6.exon2 | 25249953 | 25250198 |
| chr_3 | g3412 | g3412.t6 | cds | g3412.t6.CDS2 | 25249953 | 25250023 |
| chr_3 | g3412 | g3412.t6 | TSS | g3412.t6 | 25250224 | 25250224 |
| chr_3 | g3412 | g3412.t6 | TTS | g3412.t6 | NA | NA |
Sequences
>g3412.t6 Gene=g3412 Length=1052
ATGGCTCTGATGACAATGATTGCTAGAGTTATAGATGGATTACCTCTAGTAGGAACTATG
CAAGAGAATGAAGAAGTAAGATTTTTCAATAAAATATTTATTTGTAAATAAATTGTTCTC
TCTTTATAATTTTTAGTCAGGCAAGAGTGTTTTAGAATATCAGAATCAAGCAAAAATGCT
ATTCAGAAAGCTCGGACCTAATTCTCCAGCGAGATGCACTCTTGAAACAGGACCATATTT
ATTCCATTATTTAATTGAGAATGAAGTATGCTATCTCGTTTTGTGTGACAAAATGTTTTC
AAAACGTCTTGCATTTAATTATCTTGAGGATTTAGCACAAGAGTTTTACACAAATTATGG
TAGAAAGATTAATACAGTGACTAGACCTTATCAATTTATTGAGTTCGATATATACATTCA
AAAAGCCAAGAAATCACTTACGGATCGTAGAAGAAATATCAACACAATAAATTCTCAACT
TCAAGATGTGCAGCGAATAATGGTCCAAAATATTGATGATGTACTCCAACGGGGAGCAGT
TTTGTCAGAATTAGATACAAAAACACAAAATTTATCAATGCTCTCACAGAAATACAAAAA
GAGTGCAACACAGTTAAATCGAAGATCAATGTATGTTAAAGCAGCAGTAGCAAGTATCAT
TTTGATCGTTATTGGCATGTATTTTTGGTTATTCTGAGATCAAACTATTTCATTCATCTT
CAAAAATGGTTTCAACTATTACTTTCGCGTTAAGGGATTTGAAATGTGGACTGGGACTAT
TTTTTCCAACATGCATACCGACATACACACATATATAACATTATTATTATTATTCATAAT
AAAATATCGGATGAAAGAGCAAAAAAAATATAAGGCGCGAATATATGTATAATATTTTTA
AAGAATTGATTTTATTATTTCGTTAGAAAATGAAAAACAAAAAAAATTGTGTAAAGATTC
AATTTGCAATAAAAAAAACATTCTTATTTTGCAATTATATAAAATAGGACAATTAAGAGT
CATTGCTCGAGAAGAACTTATGGGCATACATT
>g3412.t6 Gene=g3412 Length=173
MLFRKLGPNSPARCTLETGPYLFHYLIENEVCYLVLCDKMFSKRLAFNYLEDLAQEFYTN
YGRKINTVTRPYQFIEFDIYIQKAKKSLTDRRRNINTINSQLQDVQRIMVQNIDDVLQRG
AVLSELDTKTQNLSMLSQKYKKSATQLNRRSMYVKAAVASIILIVIGMYFWLF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g3412.t6 | CDD | cd14824 | Longin | 1 | 86 | 7.71353E-30 |
| 12 | g3412.t6 | CDD | cd15866 | R-SNARE_SEC22 | 92 | 155 | 1.18646E-28 |
| 8 | g3412.t6 | Gene3D | G3DSA:3.30.450.50 | - | 1 | 88 | 3.6E-35 |
| 7 | g3412.t6 | Gene3D | G3DSA:1.20.5.110 | - | 90 | 173 | 4.0E-16 |
| 3 | g3412.t6 | PANTHER | PTHR45837:SF3 | VESICLE-TRAFFICKING PROTEIN SEC22B | 1 | 172 | 6.0E-65 |
| 4 | g3412.t6 | PANTHER | PTHR45837 | VESICLE-TRAFFICKING PROTEIN SEC22B | 1 | 172 | 6.0E-65 |
| 1 | g3412.t6 | Pfam | PF13774 | Regulated-SNARE-like domain | 2 | 78 | 7.3E-24 |
| 2 | g3412.t6 | Pfam | PF00957 | Synaptobrevin | 92 | 170 | 3.9E-19 |
| 9 | g3412.t6 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 151 | - |
| 11 | g3412.t6 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 152 | 172 | - |
| 10 | g3412.t6 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 173 | 173 | - |
| 17 | g3412.t6 | ProSiteProfiles | PS50859 | Longin domain profile. | 1 | 81 | 29.386 |
| 16 | g3412.t6 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 94 | 154 | 14.728 |
| 15 | g3412.t6 | SMART | SM01270 | Longin_2 | 1 | 80 | 7.7E-29 |
| 5 | g3412.t6 | SUPERFAMILY | SSF64356 | SNARE-like | 1 | 86 | 3.52E-30 |
| 6 | g3412.t6 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 92 | 151 | 1.14E-16 |
| 14 | g3412.t6 | 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.
