General information for g12499.t9
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.t9 | isoform | g12499.t9 | 24011380 | 24014781 |
| chr_1 | g12499 | g12499.t9 | exon | g12499.t9.exon1 | 24011380 | 24011606 |
| chr_1 | g12499 | g12499.t9 | exon | g12499.t9.exon2 | 24013414 | 24013566 |
| chr_1 | g12499 | g12499.t9 | cds | g12499.t9.CDS1 | 24013443 | 24013566 |
| chr_1 | g12499 | g12499.t9 | exon | g12499.t9.exon3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t9 | cds | g12499.t9.CDS2 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t9 | exon | g12499.t9.exon4 | 24014081 | 24014781 |
| chr_1 | g12499 | g12499.t9 | cds | g12499.t9.CDS3 | 24014081 | 24014275 |
| chr_1 | g12499 | g12499.t9 | TSS | g12499.t9 | NA | NA |
| chr_1 | g12499 | g12499.t9 | TTS | g12499.t9 | NA | NA |
Sequences
>g12499.t9 Gene=g12499 Length=1470
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGGT
AAGTTTTGTGCAAAAATGAAATTGTGAATGAAAAAAATTTGTCTTGCACAAAAAGAAAAA
ATTTTCACCCGCAAAAAAACAACATCATGGAGTCATTTGCAATAAACAGAATTGCAAAAA
CAACTAATTGTGCCGCGAATATAGTGCATCACATGTCAAAAACGAGGGCCCATTCACACA
GCCTGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAAATCGCATTCAAGAT
TAAAACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGAGTGGTTGAACCAAA
AAGCTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGATCCAAATGAGAAGAA
TAAGCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAAATTAATATTGAGCA
ATTATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTACGTTGCACATTTGA
GACACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTAACAACGCAAATGAT
TCAAAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTTGGAACATCTATTGT
TGATTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACTGCTGAAGTACGAGA
TCTTCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAACTAAAGGAGCAAATTAT
TCGTTTGAAAGCTATGGTAGATAACCAAAAGGATACAACAAGTTCATCACCATCAGCTAA
AATTATTTCAAATCCTTATTCACCACCACAACTTGGACAGCAGCAACAAATGCCCATTAT
ATGGGTGATTGCAGCTGTTGCAATGGCCATTTTCGGTTTGATCCTTGGCAAATTTGTCCT
TTGAACGCATTAAGACTACAAAGCATGAAAAGCATACAGCAAACACAAGCAACAAGAAAA
ATGAATGATAAAAAAAATATAAAAAAGTAGCTCATCGTTTTTATTTCCAGCCAATGTGTC
CAATTATGTGACAATTAATTATTCTTGTGGAGAGACATATGATGATGATGGTATAAAAAT
TAAAGTGTTGGGATGGGCGTAAAGAATCATAATTTACATTAAAGATTTTTCCTAAAAACA
AACATTATTACGACAGAAAGTTAAACTGTGGTCAAAACCAATAATGTAATGTCATATATT
TCTTTTCAATTAGAAAATTGTATTTAATGAAAAATTTTGAAACTATAAAATATAACTCAT
CAATTGGATTGAATGATTCTTCTTTCAGAAGTGATTCATTCTCTCTCTCTCTCCTTTCCT
TTCCATAATCTTTTTATTTTATTAAAAGAAAAATAAAAATAATGAGTAAAAAAGTCAAAC
TTAATATAAAGAAAACATATATATAAAAAA
>g12499.t9 Gene=g12499 Length=235
MSLKNPTDKKIAFKIKTTAPKKYCVRPNCGVVEPKSSVEIAICLQPFVYDPNEKNKHKFM
VQSMVVPEGEINIEQLWKDVSPEQLMDAKLRCTFETPNEKVSEKSSVSQLTTQMIQNEAT
LSDSQLKTAVGTSIVDSSNKPSDVDFVRATAEVRDLREENSKMHQENLELKEQIIRLKAM
VDNQKDTTSSSPSAKIISNPYSPPQLGQQQQMPIIWVIAAVAMAIFGLILGKFVL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12499.t9 | Coils | Coil | Coil | 146 | 187 | - |
| 5 | g12499.t9 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 99 | 1.3E-43 |
| 2 | g12499.t9 | PANTHER | PTHR10809:SF131 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A | 2 | 117 | 1.0E-42 |
| 3 | g12499.t9 | PANTHER | PTHR10809 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN | 2 | 117 | 1.0E-42 |
| 10 | g12499.t9 | PIRSF | PIRSF019693 | VAMP_assoc_prot | 1 | 235 | 8.6E-53 |
| 1 | g12499.t9 | Pfam | PF00635 | MSP (Major sperm protein) domain | 1 | 76 | 5.0E-28 |
| 7 | g12499.t9 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 213 | - |
| 9 | g12499.t9 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 214 | 234 | - |
| 8 | g12499.t9 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 235 | 235 | - |
| 12 | g12499.t9 | ProSiteProfiles | PS50202 | Major sperm protein (MSP) domain profile. | 1 | 95 | 28.198 |
| 4 | g12499.t9 | SUPERFAMILY | SSF49354 | PapD-like | 1 | 99 | 5.49E-35 |
| 11 | g12499.t9 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 212 | 234 | - |
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 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.
