General information for g12408.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle-associated membrane protein 7.
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.t1 | TTS | g12408.t1 | 23423309 | 23423309 |
| chr_1 | g12408 | g12408.t1 | isoform | g12408.t1 | 23423728 | 23424921 |
| chr_1 | g12408 | g12408.t1 | exon | g12408.t1.exon1 | 23423728 | 23423877 |
| chr_1 | g12408 | g12408.t1 | cds | g12408.t1.CDS1 | 23423728 | 23423877 |
| chr_1 | g12408 | g12408.t1 | exon | g12408.t1.exon2 | 23423935 | 23424173 |
| chr_1 | g12408 | g12408.t1 | cds | g12408.t1.CDS2 | 23423935 | 23424173 |
| chr_1 | g12408 | g12408.t1 | exon | g12408.t1.exon3 | 23424239 | 23424307 |
| chr_1 | g12408 | g12408.t1 | cds | g12408.t1.CDS3 | 23424239 | 23424307 |
| chr_1 | g12408 | g12408.t1 | exon | g12408.t1.exon4 | 23424365 | 23424518 |
| chr_1 | g12408 | g12408.t1 | cds | g12408.t1.CDS4 | 23424365 | 23424518 |
| chr_1 | g12408 | g12408.t1 | exon | g12408.t1.exon5 | 23424877 | 23424921 |
| chr_1 | g12408 | g12408.t1 | cds | g12408.t1.CDS5 | 23424877 | 23424921 |
| chr_1 | g12408 | g12408.t1 | TSS | g12408.t1 | 23425105 | 23425105 |
Sequences
>g12408.t1 Gene=g12408 Length=657
ATGAAGTTTCTTGTTATTTCTAAGTTCATTGACAACATTCCATTCACAGCAGGTTATCAA
CATCAACAACAAGATGCCTCTCTATATGCAGTTATCACAAGAGGAAATACTGTATGTGTT
AAATATGCCGACTGCGTTGGAAACTTTTCAGAAGTCACAGAAAATCTCATCTCAAAAATT
CAATTGACAAACCATAAAATGACATACACACATGGCCAATACCTTTTCCATTATATTTGT
GCTGATAAAATAATTTACATGACCATAACAACTTATGGTTTGACAGCAGCAACAGCTCTT
CCTTATGCAATGAATACAGAATTCTCTCGTGTGATGTCAGCCGAAATGAAGAAATGCAAT
GAAAGTGGCGAGTATGATAGCATACAGCGAGTACATGGACAAATTGATGAATTAAAAGAT
ATTATGGTTAAAAATATTGAAAATATAACAACAAGAGGAGAAAGACTTGAATTGCTGGTT
AATAAATCAGAAAGTTTACGAAATAATGCTGTTTCATTCAGACAAACAAGTAGAACAATA
GCAAGAACACTATTTTGGAGAAATGTAAAAATGTATATTCTACTTGGTCTCTTAATGCTT
TTTATAATATACATTATTGTTGCCATGTTTTGTGGATTTGCTTTGAAATGTCGCTAA
>g12408.t1 Gene=g12408 Length=218
MKFLVISKFIDNIPFTAGYQHQQQDASLYAVITRGNTVCVKYADCVGNFSEVTENLISKI
QLTNHKMTYTHGQYLFHYICADKIIYMTITTYGLTAATALPYAMNTEFSRVMSAEMKKCN
ESGEYDSIQRVHGQIDELKDIMVKNIENITTRGERLELLVNKSESLRNNAVSFRQTSRTI
ARTLFWRNVKMYILLGLLMLFIIYIIVAMFCGFALKCR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g12408.t1 | CDD | cd14824 | Longin | 28 | 119 | 2.08038E-16 |
| 17 | g12408.t1 | CDD | cd15871 | R-SNARE_VAMP7 | 126 | 190 | 1.27235E-33 |
| 13 | g12408.t1 | Gene3D | G3DSA:3.30.450.50 | - | 16 | 91 | 8.2E-19 |
| 12 | g12408.t1 | Gene3D | G3DSA:1.20.5.110 | - | 93 | 211 | 1.9E-26 |
| 4 | g12408.t1 | PANTHER | PTHR21136:SF179 | VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 | 28 | 90 | 1.1E-71 |
| 6 | g12408.t1 | PANTHER | PTHR21136 | SNARE PROTEINS | 28 | 90 | 1.1E-71 |
| 3 | g12408.t1 | PANTHER | PTHR21136:SF179 | VESICLE-ASSOCIATED MEMBRANE PROTEIN 7 | 90 | 211 | 1.1E-71 |
| 5 | g12408.t1 | PANTHER | PTHR21136 | SNARE PROTEINS | 90 | 211 | 1.1E-71 |
| 9 | g12408.t1 | PRINTS | PR00219 | Synaptobrevin signature | 132 | 151 | 2.7E-15 |
| 7 | g12408.t1 | PRINTS | PR00219 | Synaptobrevin signature | 152 | 171 | 2.7E-15 |
| 8 | g12408.t1 | PRINTS | PR00219 | Synaptobrevin signature | 188 | 207 | 2.7E-15 |
| 1 | g12408.t1 | Pfam | PF13774 | Regulated-SNARE-like domain | 55 | 94 | 2.1E-7 |
| 2 | g12408.t1 | Pfam | PF00957 | Synaptobrevin | 126 | 212 | 1.0E-29 |
| 14 | g12408.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 191 | - |
| 16 | g12408.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 192 | 215 | - |
| 15 | g12408.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 216 | 218 | - |
| 23 | g12408.t1 | ProSiteProfiles | PS50859 | Longin domain profile. | 31 | 90 | 12.387 |
| 22 | g12408.t1 | ProSiteProfiles | PS50892 | v-SNARE coiled-coil homology domain profile. | 127 | 187 | 16.74 |
| 21 | g12408.t1 | SMART | SM01270 | Longin_2 | 52 | 111 | 3.9E-7 |
| 10 | g12408.t1 | SUPERFAMILY | SSF64356 | SNARE-like | 28 | 119 | 4.03E-14 |
| 11 | g12408.t1 | SUPERFAMILY | SSF58038 | SNARE fusion complex | 123 | 188 | 6.8E-18 |
| 20 | g12408.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 74 | 96 | - |
| 19 | g12408.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 193 | 215 | - |
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. There were no conditions that were differentially expressed