General information for g12499.t3
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.t3 | isoform | g12499.t3 | 24011380 | 24014215 |
| chr_1 | g12499 | g12499.t3 | exon | g12499.t3.exon1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t3 | exon | g12499.t3.exon2 | 24013428 | 24013566 |
| chr_1 | g12499 | g12499.t3 | cds | g12499.t3.CDS1 | 24013443 | 24013566 |
| chr_1 | g12499 | g12499.t3 | exon | g12499.t3.exon3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t3 | cds | g12499.t3.CDS2 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t3 | exon | g12499.t3.exon4 | 24014081 | 24014215 |
| chr_1 | g12499 | g12499.t3 | cds | g12499.t3.CDS3 | 24014081 | 24014215 |
| chr_1 | g12499 | g12499.t3 | TSS | g12499.t3 | NA | NA |
| chr_1 | g12499 | g12499.t3 | TTS | g12499.t3 | NA | NA |
Sequences
>g12499.t3 Gene=g12499 Length=721
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGCC
TGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAAATCGCATTCAAGATTAA
AACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGAGTGGTTGAACCAAAAAG
CTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGATCCAAATGAGAAGAATAA
GCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAAATTAATATTGAGCAATT
ATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTACGTTGCACATTTGAGAC
ACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTAACAACGCAAATGATTCA
AAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTTGGAACATCTATTGTTGA
TTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACTGCTGAAGTACGAGATCT
TCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAACTAAAGGAGCAAATTATTCG
TTTGAAAGCTATGGTAGATAACCAAAAGGATACAACAAGTTCATCACCATCAGCTAAAAT
TATTTCAAATCCTTATTCACCACCACAACTTGGACAGCAGCAACAAATGCCCATTATATG
G
>g12499.t3 Gene=g12499 Length=216
MSLKNPTDKKIAFKIKTTAPKKYCVRPNCGVVEPKSSVEIAICLQPFVYDPNEKNKHKFM
VQSMVVPEGEINIEQLWKDVSPEQLMDAKLRCTFETPNEKVSEKSSVSQLTTQMIQNEAT
LSDSQLKTAVGTSIVDSSNKPSDVDFVRATAEVRDLREENSKMHQENLELKEQIIRLKAM
VDNQKDTTSSSPSAKIISNPYSPPQLGQQQQMPIIW
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12499.t3 | Coils | Coil | Coil | 146 | 187 | - |
| 5 | g12499.t3 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 99 | 1.1E-43 |
| 8 | g12499.t3 | MobiDBLite | mobidb-lite | consensus disorder prediction | 183 | 216 | - |
| 2 | g12499.t3 | PANTHER | PTHR10809:SF12 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN B/C | 1 | 178 | 1.1E-41 |
| 3 | g12499.t3 | PANTHER | PTHR10809 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN | 1 | 178 | 1.1E-41 |
| 7 | g12499.t3 | PIRSF | PIRSF019693 | VAMP_assoc_prot | 1 | 212 | 2.5E-49 |
| 1 | g12499.t3 | Pfam | PF00635 | MSP (Major sperm protein) domain | 1 | 76 | 4.2E-28 |
| 9 | g12499.t3 | ProSiteProfiles | PS50202 | Major sperm protein (MSP) domain profile. | 1 | 95 | 28.198 |
| 4 | g12499.t3 | SUPERFAMILY | SSF49354 | PapD-like | 1 | 99 | 4.45E-35 |
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. There were no conditions that were differentially expressed