General information for g12408.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle-associated membrane protein 714.
Parent gene
- The parent gene g12408 is located on chr_1: 23423728..23425422 (- 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_1 | g12408 | g12408.t3 | isoform | g12408.t3 | 23423279 | 23425422 |
| chr_1 | g12408 | g12408.t3 | exon | g12408.t3.exon1 | 23423279 | 23423877 |
| chr_1 | g12408 | g12408.t3 | TTS | g12408.t3 | 23423309 | 23423309 |
| chr_1 | g12408 | g12408.t3 | cds | g12408.t3.CDS1 | 23423728 | 23423877 |
| chr_1 | g12408 | g12408.t3 | exon | g12408.t3.exon2 | 23423935 | 23424307 |
| chr_1 | g12408 | g12408.t3 | cds | g12408.t3.CDS2 | 23423935 | 23424132 |
| chr_1 | g12408 | g12408.t3 | exon | g12408.t3.exon3 | 23424365 | 23424518 |
| chr_1 | g12408 | g12408.t3 | exon | g12408.t3.exon4 | 23424974 | 23425422 |
| chr_1 | g12408 | g12408.t3 | TSS | g12408.t3 | NA | NA |
Sequences
>g12408.t3 Gene=g12408 Length=1575
TTTTCGGTAAAAACGTTTTTTAATTTGCTGTGATACGATTGAAAAATTCTTTATATTCGG
CAGTAAGTGCTTCGTGTTACTCAGCTGTTTGAAGACTAGTGACGTGAAACTCATAAAAGA
TAAGTGAATAAAAACAGCTCGAAAATCCAAAACACACGATCGATAAAAATATTTTGAGGA
CTGACAACTGAAATATGACACAAGTTTGAAAACATTTTGACAGTTTCTTCATATTTATTT
TAACGGTAAGAAGAAACTTTAAATTTTTGTATTGAAAACCTCTCTAATTCAAATCAAAAC
ACAAAGTTTCTCGATTTTTAATTTTTCCACGAATTTCTTTCTTTTAATGTTAAGAAAGCA
AAAAAACAAGATAATAACTGTTTAAAGTTCTTATTTATCGTGAAGTTATAATTTTAAAAG
AATTCTGTGAAACTCAATAAGTATTGTTGACAGCAGGTTATCAACATCAACAACAAGATG
CCTCTCTATATGCAGTTATCACAAGAGGAAATACTGTATGTGTTAAATATGCCGACTGCG
TTGGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATTCAATTGACAAACCATA
AAATGACATACACACATGGCCAATACCTTTTCCATTATATTTGTGCTGATAAAATAATTT
ACATGACCATAAGTGATGATGAGTTTCCACGACAGCGTGCCTTTCTATATCTCTCAGAAA
TAAAACGAAAATTTTAGCAACTTATGGTTTGACAGCAGCAACAGCTCTTCCTTATGCAAT
GAATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAATGAAAGTGGCGA
GTATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAAGATATTATGGTTAA
AAATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTTAATAAATCAGA
AAGTTTACGAAATAATGCTGTTTCATTCAGACAAACAAGTAGAACAATAGCAAGAACACT
ATTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATGCTTTTTATAATATA
CATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAAAGTGTTAAAACATA
ATTTATATTTTAAGCAAAACAATAATATGATGGTAAGAGACTATGTGATTGTTAAATGTC
TCTCGAAAAAAAATTGTTTATTTCAACCACATAGATTCTCAGTTATGAATTTATCAATAT
TTATATATTATTATTTCTAATGAGGGTAAGTGTTGAAATAAATGTGAAAGGAAGTCAATT
TTAACTTCTAACAATCTTATCAGTAGTTGATCAAAATTATATATGAGTGAAAAAATCTAA
TTAATCTTCTTCTCATCAACACATGACCCTCATTCTTACATATACAAAAAAATTTATGTA
TCAACCACAATAAATATGATAAAAAATATTTTATTATTATTGACTACTGCACCAAAAAAA
CTCCGTTTTTATTAAAATATTGAATGTAATCAAAACTAAGAAGCGAGAAAAATAAATGAA
AAATTTCTTAATGCA
>g12408.t3 Gene=g12408 Length=115
MNTEFSRVMSAEMKKCNESGEYDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKS
ESLRNNAVSFRQTSRTIARTLFWRNVKMYILLGLLMLFIIYIIVAMFCGFALKCR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12408.t3 | Gene3D | G3DSA:1.20.5.110 | - | 2 | 108 | 7.1E-27 |
| 2 | g12408.t3 | PANTHER | PTHR21136:SF179 | VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 | 1 | 108 | 9.0E-39 |
| 3 | g12408.t3 | PANTHER | PTHR21136 | SNARE PROTEINS | 1 | 108 | 9.0E-39 |
| 5 | g12408.t3 | PRINTS | PR00219 | Synaptobrevin signature | 29 | 48 | 7.1E-16 |
| 6 | g12408.t3 | PRINTS | PR00219 | Synaptobrevin signature | 49 | 68 | 7.1E-16 |
| 4 | g12408.t3 | PRINTS | PR00219 | Synaptobrevin signature | 85 | 104 | 7.1E-16 |
| 1 | g12408.t3 | Pfam | PF00957 | Synaptobrevin | 23 | 109 | 2.8E-30 |
| 9 | g12408.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 88 | - |
| 11 | g12408.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 89 | 112 | - |
| 10 | g12408.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 113 | 115 | - |
| 13 | g12408.t3 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 24 | 84 | 16.74 |
| 7 | g12408.t3 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 20 | 85 | 1.47E-18 |
| 12 | g12408.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 89 | 111 | - |
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.
