General information for g12499.t2
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.t2 | isoform | g12499.t2 | 24011380 | 24014019 |
| chr_1 | g12499 | g12499.t2 | exon | g12499.t2.exon1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t2 | cds | g12499.t2.CDS1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t2 | exon | g12499.t2.exon2 | 24013414 | 24013566 |
| chr_1 | g12499 | g12499.t2 | cds | g12499.t2.CDS2 | 24013414 | 24013566 |
| chr_1 | g12499 | g12499.t2 | exon | g12499.t2.exon3 | 24013637 | 24014019 |
| chr_1 | g12499 | g12499.t2 | cds | g12499.t2.CDS3 | 24013637 | 24014019 |
| chr_1 | g12499 | g12499.t2 | TSS | g12499.t2 | NA | NA |
| chr_1 | g12499 | g12499.t2 | TTS | g12499.t2 | NA | NA |
Sequences
>g12499.t2 Gene=g12499 Length=594
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGGC
CCATTCACACAGCCTGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAAATC
GCATTCAAGATTAAAACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGAGTG
GTTGAACCAAAAAGCTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGATCCA
AATGAGAAGAATAAGCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAAATT
AATATTGAGCAATTATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTACGT
TGCACATTTGAGACACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTAACA
ACGCAAATGATTCAAAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTTGGA
ACATCTATTGTTGATTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACTGCT
GAAGTACGAGATCTTCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAA
>g12499.t2 Gene=g12499 Length=198
MSKPENVLIIDPAQELKFRGPFTQPVTSHMSLKNPTDKKIAFKIKTTAPKKYCVRPNCGV
VEPKSSVEIAICLQPFVYDPNEKNKHKFMVQSMVVPEGEINIEQLWKDVSPEQLMDAKLR
CTFETPNEKVSEKSSVSQLTTQMIQNEATLSDSQLKTAVGTSIVDSSNKPSDVDFVRATA
EVRDLREENSKMHQENLE
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g12499.t2 | Coils | Coil | Coil | 175 | 195 | - |
| 5 | g12499.t2 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 125 | 1.4E-54 |
| 2 | g12499.t2 | PANTHER | PTHR10809:SF131 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A | 1 | 151 | 1.2E-53 |
| 3 | g12499.t2 | PANTHER | PTHR10809 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN | 1 | 151 | 1.2E-53 |
| 8 | g12499.t2 | PIRSF | PIRSF019693 | VAMP_assoc_prot | 1 | 198 | 4.2E-60 |
| 1 | g12499.t2 | Pfam | PF00635 | MSP (Major sperm protein) domain | 8 | 105 | 3.6E-34 |
| 7 | g12499.t2 | ProSiteProfiles | PS50202 | Major sperm protein (MSP) domain profile. | 7 | 124 | 33.553 |
| 4 | g12499.t2 | SUPERFAMILY | SSF49354 | PapD-like | 3 | 128 | 8.9E-44 |
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 K10707 (vesicle-associated membrane protein-associated protein B)
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. There were no conditions that were differentially expressed