General information for g12499.t1
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.t1 | isoform | g12499.t1 | 24011380 | 24016300 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS1 | 24011380 | 24011437 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon2 | 24013414 | 24013566 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS2 | 24013414 | 24013566 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS3 | 24013637 | 24014025 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon4 | 24014081 | 24014215 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS4 | 24014081 | 24014215 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon5 | 24015729 | 24015752 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS5 | 24015729 | 24015752 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon6 | 24015826 | 24015884 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS6 | 24015826 | 24015884 |
| chr_1 | g12499 | g12499.t1 | exon | g12499.t1.exon7 | 24016099 | 24016300 |
| chr_1 | g12499 | g12499.t1 | cds | g12499.t1.CDS7 | 24016099 | 24016300 |
| chr_1 | g12499 | g12499.t1 | TTS | g12499.t1 | 24016365 | 24016365 |
| chr_1 | g12499 | g12499.t1 | TSS | g12499.t1 | NA | NA |
Sequences
>g12499.t1 Gene=g12499 Length=1020
ATGTCGAAGCCCGAGAATGTTTTAATAATTGATCCGGCTCAAGAGCTGAAGTTTCGAGGC
CCATTCACACAGCCTGTGACTTCACATATGAGTCTGAAAAATCCTACTGACAAAAAAATC
GCATTCAAGATTAAAACAACAGCTCCGAAAAAATATTGTGTACGTCCTAATTGTGGAGTG
GTTGAACCAAAAAGCTCTGTGGAAATTGCTATTTGCCTGCAACCATTTGTATATGATCCA
AATGAGAAGAATAAGCATAAATTTATGGTACAATCAATGGTTGTTCCAGAGGGTGAAATT
AATATTGAGCAATTATGGAAGGATGTAAGTCCTGAGCAGTTAATGGATGCAAAATTACGT
TGCACATTTGAGACACCGAATGAGAAAGTCAGTGAAAAGAGCAGTGTTAGTCAATTAACA
ACGCAAATGATTCAAAATGAAGCGACTTTGTCAGACTCGCAACTGAAAACAGCTGTTGGA
ACATCTATTGTTGATTCCAGCAATAAACCAAGTGATGTTGATTTTGTTAGAGCAACTGCT
GAAGTACGAGATCTTCGTGAGGAGAACAGCAAAATGCATCAAGAAAATTTGGAACTAAAG
GAGCAAATTATTCGTTTGAAAGCTATGGTAGATAACCAAAAGGATACAACAAGTTCATCA
CCATCAGCTAAAATTATTTCAAATCCTTATTCACCACCACAACTTGGACAGCAGCAACAA
ATGCCCATTATATGGCAACTCGAGTCATTCACAAAAAATCAATATATAATGGAGAACGAC
GCTGGTGAATTCGTTGATTTATACTGCCCAAGAAAATGCTCGGCAAGTAACAGAATCATT
CATGCTAAAGATTATGCTTCAATTCAAATCAACTTGGTCGATGTTGATGAGGCCACAGGC
AGAATGCTTGATACAACCAAGACATATGCTATTTGCGGAGAAATCAGACGTATGGGTGAA
AGCGATGATTGTATCGCTCGATTGGCTAAGAAAGACGGAGTTCTCTCAAGAAACTATTAA
>g12499.t1 Gene=g12499 Length=339
MSKPENVLIIDPAQELKFRGPFTQPVTSHMSLKNPTDKKIAFKIKTTAPKKYCVRPNCGV
VEPKSSVEIAICLQPFVYDPNEKNKHKFMVQSMVVPEGEINIEQLWKDVSPEQLMDAKLR
CTFETPNEKVSEKSSVSQLTTQMIQNEATLSDSQLKTAVGTSIVDSSNKPSDVDFVRATA
EVRDLREENSKMHQENLELKEQIIRLKAMVDNQKDTTSSSPSAKIISNPYSPPQLGQQQQ
MPIIWQLESFTKNQYIMENDAGEFVDLYCPRKCSASNRIIHAKDYASIQINLVDVDEATG
RMLDTTKTYAICGEIRRMGESDDCIARLAKKDGVLSRNY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g12499.t1 | Coils | Coil | Coil | 175 | 216 | - |
| 7 | g12499.t1 | Gene3D | G3DSA:2.60.40.10 | Immunoglobulins | 1 | 125 | 5.5E-54 |
| 8 | g12499.t1 | Gene3D | G3DSA:3.30.1230.20 | - | 257 | 339 | 4.0E-41 |
| 3 | g12499.t1 | PANTHER | PTHR10809:SF131 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN A | 1 | 146 | 3.3E-53 |
| 4 | g12499.t1 | PANTHER | PTHR10809 | VESICLE-ASSOCIATED MEMBRANE PROTEIN-ASSOCIATED PROTEIN | 1 | 146 | 3.3E-53 |
| 2 | g12499.t1 | Pfam | PF00635 | MSP (Major sperm protein) domain | 8 | 104 | 1.1E-33 |
| 1 | g12499.t1 | Pfam | PF01249 | Ribosomal protein S21e | 257 | 335 | 2.7E-39 |
| 6 | g12499.t1 | ProSitePatterns | PS00996 | Ribosomal protein S21e signature. | 267 | 275 | - |
| 10 | g12499.t1 | ProSiteProfiles | PS50202 | Major sperm protein (MSP) domain profile. | 7 | 124 | 33.553 |
| 5 | g12499.t1 | SUPERFAMILY | SSF49354 | PapD-like | 3 | 128 | 3.4E-43 |
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:0005840 | ribosome | CC |
| GO:0006412 | translation | BP |
| GO:0005789 | endoplasmic reticulum membrane | CC |
| GO:0003735 | structural constituent of ribosome | MF |
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.
