General information for g11590.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Vacuole membrane protein 1.
Parent gene
- The parent gene g11590 is located on chr_1: 17379104..17380714 (- 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 | g11590 | g11590.t3 | isoform | g11590.t3 | 17376327 | 17377630 |
| chr_1 | g11590 | g11590.t3 | exon | g11590.t3.exon1 | 17376327 | 17377248 |
| chr_1 | g11590 | g11590.t3 | cds | g11590.t3.CDS1 | 17376817 | 17377248 |
| chr_1 | g11590 | g11590.t3 | exon | g11590.t3.exon2 | 17377321 | 17377630 |
| chr_1 | g11590 | g11590.t3 | cds | g11590.t3.CDS2 | 17377321 | 17377575 |
| chr_1 | g11590 | g11590.t3 | TSS | g11590.t3 | NA | NA |
| chr_1 | g11590 | g11590.t3 | TTS | g11590.t3 | NA | NA |
Sequences
>g11590.t3 Gene=g11590 Length=1232
AATAATTTGTCCAGATAGTCCTACGCCAGGTTTTGTGCCGTCATTATGGAGCATAATGAG
CAAAGTTCGTTTAGAATCATTCCTTTGGGGTGCTGGAACTGCACTGGGAGAACTACCACC
TTATTTTATGGCGCGTGCAGCTCGTTTAAGTGGTTATGATCCTGAGGATGCAGAAGATTT
ACAAGAATTTGAAGAATTACAGAAAAAACGTGAATTGGGTGAAAAACTAAGTTATTTTGA
AAAATTGAAATTGGGTATGGAAAGAATTGTTGAGCGTGTTGGATTTTTTGGAATTTTGGC
TTGTGCAAGTGTTCCAAATCCACTTTTTGATTTGGCAGGTATCACATGCGGTCACTTTTT
GGTACCATTTTGGACGTTCTTTGGTGCAACATTAATTGGAAAGGCTGTGATTAAAATGCA
TCTTCAGAAAATAGTAGTAATTGTAGCATTCAACGAACTATTGCTTGAGAAGGCTGTTGA
TTTATTGGCTCTTATTCCTGTCGTTGGAAAAAAGTTTCAAGAACCATTCAAAACTTTCCT
TCAAAACCAAAAAGAAAAATTACATCGTGGTAAGATTACTAAGAACAAGGGTAATCTTCT
TCAAAAAGTTTTTGAAGTTTTTGTCATTGGCATGATTCTCTATTTCATTCTTTCAATTAT
CAACTCGTTAGCCCAGAGTTGGCACAAACGAATTCACAAAAAATCCAACAAGAAACAACG
TAAAGTAATTAAAGATAATTAAGTGTAAAGACAACAAAAGAATCTTAAATTATATAAAAA
CTAGTAAAATATTGTTTCATCGATAACATGAAAAGAACATTTTCTAAAATATGTGTGTGT
ATGCCCTTATCCCAAAAATTTGTGTAGAAATGTTAAGGAATGTTTTGAAACTAGCTCAAG
GCTCAGTAATGCATTGTAAAATGCTACTTGAGCAAAAAATAATATAGATAGGTAGTAAAT
TTTGTGCTAAATTTATTATTTTCCAATAAATTATCATTTTATAAATATGAAATTTTTGTG
TCATTTTTTTACCTAATCTTTTTGTAAGATCGATATTAAAAAAATGTTTTAAGATTCATT
TCTATACATTCTTTATTTCTTCACGAATTCAATGTAAGAGTATGAGGAATAATCTTAATT
TAATGAATTTTAGAAAACGATGAAGTTATTAGCAGGTTTTATAAATAAAGACATTAATAG
TGTTTGTGCACTTATACATCGTTTTAAACAGG
>g11590.t3 Gene=g11590 Length=228
MSKVRLESFLWGAGTALGELPPYFMARAARLSGYDPEDAEDLQEFEELQKKRELGEKLSY
FEKLKLGMERIVERVGFFGILACASVPNPLFDLAGITCGHFLVPFWTFFGATLIGKAVIK
MHLQKIVVIVAFNELLLEKAVDLLALIPVVGKKFQEPFKTFLQNQKEKLHRGKITKNKGN
LLQKVFEVFVIGMILYFILSIINSLAQSWHKRIHKKSNKKQRKVIKDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 1 | g11590.t3 | PANTHER | PTHR10281 | MEMBRANE-ASSOCIATED PROGESTERONE RECEPTOR COMPONENT-RELATED | 1 | 223 | 1.9E-75 |
| 2 | g11590.t3 | PANTHER | PTHR10281:SF1 | VACUOLE MEMBRANE PROTEIN 1 | 1 | 223 | 1.9E-75 |
| 6 | g11590.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 70 | - |
| 10 | g11590.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 71 | 87 | - |
| 8 | g11590.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 88 | 92 | - |
| 11 | g11590.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 114 | - |
| 7 | g11590.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 115 | 125 | - |
| 12 | g11590.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 126 | 150 | - |
| 9 | g11590.t3 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 151 | 184 | - |
| 13 | g11590.t3 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 185 | 206 | - |
| 5 | g11590.t3 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 207 | 228 | - |
| 3 | g11590.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 93 | 115 | - |
| 4 | g11590.t3 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 185 | 207 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
