General information for g12499.t7
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Vesicle-associated membrane protein/synaptobrevin-binding protein.
Parent gene
- The parent gene g12499 is located on chr_1: 24016098..24016328 (+ 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 | g12499 | g12499.t7 | isoform | g12499.t7 | 24011380 | 24014781 |
| chr_1 | g12499 | g12499.t7 | exon | g12499.t7.exon1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t7 | cds | g12499.t7.CDS1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t7 | exon | g12499.t7.exon2 | 24013411 | 24013566 |
| chr_1 | g12499 | g12499.t7 | cds | g12499.t7.CDS2 | 24013411 | 24013566 |
| chr_1 | g12499 | g12499.t7 | exon | g12499.t7.exon3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t7 | cds | g12499.t7.CDS3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t7 | exon | g12499.t7.exon4 | 24014081 | 24014781 |
| chr_1 | g12499 | g12499.t7 | cds | g12499.t7.CDS4 | 24014081 | 24014275 |
| chr_1 | g12499 | g12499.t7 | TSS | g12499.t7 | NA | NA |
| chr_1 | g12499 | g12499.t7 | TTS | g12499.t7 | NA | NA |
Sequences
>g12499.t7 Gene=g12499 Length=1304
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGAA
GGCCCATTCACACAGCCTGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAA
ATCGCATTCAAGATTAAAACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGA
GTGGTTGAACCAAAAAGCTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGAT
CCAAATGAGAAGAATAAGCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAA
ATTAATATTGAGCAATTATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTA
CGTTGCACATTTGAGACACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTA
ACAACGCAAATGATTCAAAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTT
GGAACATCTATTGTTGATTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACT
GCTGAAGTACGAGATCTTCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAACTA
AAGGAGCAAATTATTCGTTTGAAAGCTATGGTAGATAACCAAAAGGATACAACAAGTTCA
TCACCATCAGCTAAAATTATTTCAAATCCTTATTCACCACCACAACTTGGACAGCAGCAA
CAAATGCCCATTATATGGGTGATTGCAGCTGTTGCAATGGCCATTTTCGGTTTGATCCTT
GGCAAATTTGTCCTTTGAACGCATTAAGACTACAAAGCATGAAAAGCATACAGCAAACAC
AAGCAACAAGAAAAATGAATGATAAAAAAAATATAAAAAAGTAGCTCATCGTTTTTATTT
CCAGCCAATGTGTCCAATTATGTGACAATTAATTATTCTTGTGGAGAGACATATGATGAT
GATGGTATAAAAATTAAAGTGTTGGGATGGGCGTAAAGAATCATAATTTACATTAAAGAT
TTTTCCTAAAAACAAACATTATTACGACAGAAAGTTAAACTGTGGTCAAAACCAATAATG
TAATGTCATATATTTCTTTTCAATTAGAAAATTGTATTTAATGAAAAATTTTGAAACTAT
AAAATATAACTCATCAATTGGATTGAATGATTCTTCTTTCAGAAGTGATTCATTCTCTCT
CTCTCTCCTTTCCTTTCCATAATCTTTTTATTTTATTAAAAGAAAAATAAAAATAATGAG
TAAAAAAGTCAAACTTAATATAAAGAAAACATATATATAAAAAA
>g12499.t7 Gene=g12499 Length=265
MSKPENVLIIDPAQELKFREGPFTQPVTSHMSLKNPTDKKIAFKIKTTAPKKYCVRPNCG
VVEPKSSVEIAICLQPFVYDPNEKNKHKFMVQSMVVPEGEINIEQLWKDVSPEQLMDAKL
RCTFETPNEKVSEKSSVSQLTTQMIQNEATLSDSQLKTAVGTSIVDSSNKPSDVDFVRAT
AEVRDLREENSKMHQENLELKEQIIRLKAMVDNQKDTTSSSPSAKIISNPYSPPQLGQQQ
QMPIIWVIAAVAMAIFGLILGKFVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12499.t7 | Coils | Coil | Coil | 176 | 217 | - |
| 5 | g12499.t7 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 126 | 1.4E-52 |
| 2 | g12499.t7 | PANTHER | PTHR10809:SF131 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A | 1 | 146 | 2.1E-53 |
| 3 | g12499.t7 | PANTHER | PTHR10809 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN | 1 | 146 | 2.1E-53 |
| 10 | g12499.t7 | PIRSF | PIRSF019693 | VAMP_assoc_prot | 1 | 265 | 1.5E-61 |
| 1 | g12499.t7 | Pfam | PF00635 | MSP (Major sperm protein) domain | 8 | 106 | 1.4E-32 |
| 8 | g12499.t7 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 243 | - |
| 9 | g12499.t7 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 244 | 264 | - |
| 7 | g12499.t7 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 265 | 265 | - |
| 12 | g12499.t7 | ProSiteProfiles | PS50202 | Major sperm protein (MSP) domain profile. | 7 | 125 | 31.52 |
| 4 | g12499.t7 | SUPERFAMILY | SSF49354 | PapD-like | 3 | 129 | 1.07E-41 |
| 11 | g12499.t7 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 242 | 264 | - |
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:0005789 | endoplasmic reticulum membrane | CC |
KEGG
Orthology
- This transcript has been annotated with K06096 (vesicle-associated membrane protein-associated protein A)
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.
