General information for g11590.t1
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.t1 | TTS | g11590.t1 | 17376550 | 17376550 |
| chr_1 | g11590 | g11590.t1 | isoform | g11590.t1 | 17376817 | 17379630 |
| chr_1 | g11590 | g11590.t1 | exon | g11590.t1.exon1 | 17376817 | 17377248 |
| chr_1 | g11590 | g11590.t1 | cds | g11590.t1.CDS1 | 17376817 | 17377248 |
| chr_1 | g11590 | g11590.t1 | exon | g11590.t1.exon2 | 17377321 | 17377630 |
| chr_1 | g11590 | g11590.t1 | cds | g11590.t1.CDS2 | 17377321 | 17377630 |
| chr_1 | g11590 | g11590.t1 | exon | g11590.t1.exon3 | 17377699 | 17378237 |
| chr_1 | g11590 | g11590.t1 | cds | g11590.t1.CDS3 | 17377699 | 17378237 |
| chr_1 | g11590 | g11590.t1 | exon | g11590.t1.exon4 | 17379331 | 17379630 |
| chr_1 | g11590 | g11590.t1 | cds | g11590.t1.CDS4 | 17379331 | 17379630 |
| chr_1 | g11590 | g11590.t1 | TSS | g11590.t1 | 17380627 | 17380627 |
Sequences
>g11590.t1 Gene=g11590 Length=1581
ATGACTCGAAAAAGAACTAGTCAGGCAGGATCAAATTCGGCTACAGCAAAATTGATAAAT
AAGATCAATAAATTTAATCAGAATAATACGATCAACAACAATTTTATTGCGGAATCCAAT
GAGCAAGAGACACGTATAGTAAAAAATAATAACTATGATGAGGATGAAGTTTTCATTTTG
ACTGAAAAGCAAAAACAACAATTGCAACGAAACGAATATTTAGAATCGTTAACCAAAGAT
CGACTCAAAACTGAGGCTAAGCGTAGAGGACAGAAAACTTCAGGAACTAAATCTGAATTG
TTACAACGTTTGGGATATAAAATGTCGCTTCGACATTCAAGCTCCCTAAATAATGTTCGT
CAATCATCTAGTCTGAAGATGAAAAGTTCAAAATCTTCACCAAATGGTTCTCTTTCTTCG
GAAAGCTCTGGTAGCATTACTGAAAAAGAGCGTTTAAAGAGAGAACGAGAAAGCATTAAA
CTCTGGATTCATCCAGTTTTGACGATCAAATATTGTTTCTTTGAAGTAGCAACTCTTTTT
CAAATTTATAAGCGTAGCATATTAAACCATAAAAAGACCATAGGATTTGTTATGACATTG
CTAATAGCATTTTTTACGCTCTGGTATATACCTGGAAAGCATCAAATTTACGTTGAATTT
ATAAGAAAAAATGCATTCTTCGTAACATATTGGATTGGTTTGGGTGTAATATCGAGTATT
GGATTGGGAACAGGACTGCATACATTTATATTATATTTAGGACCACATATAGCCAGTGTA
ACATTAGCGGCATATGAATGTGGATCTCTAGATTTTCCTTCTCCCCCTTATCCTGACGAA
ATAATTTGTCCAGATAGTCCTACGCCAGGTTTTGTGCCGTCATTATGGAGCATAATGAGC
AAAGTTCGTTTAGAATCATTCCTTTGGGGTGCTGGAACTGCACTGGGAGAACTACCACCT
TATTTTATGGCGCGTGCAGCTCGTTTAAGTGGTTATGATCCTGAGGATGCAGAAGATTTA
CAAGAATTTGAAGAATTACAGAAAAAACGTGAATTGGGTGAAAAACTAAGTTATTTTGAA
AAATTGAAATTGGGTATGGAAAGAATTGTTGAGCGTGTTGGATTTTTTGGAATTTTGGCT
TGTGCAAGTGTTCCAAATCCACTTTTTGATTTGGCAGGTATCACATGCGGTCACTTTTTG
GTACCATTTTGGACGTTCTTTGGTGCAACATTAATTGGAAAGGCTGTGATTAAAATGCAT
CTTCAGAAAATAGTAGTAATTGTAGCATTCAACGAACTATTGCTTGAGAAGGCTGTTGAT
TTATTGGCTCTTATTCCTGTCGTTGGAAAAAAGTTTCAAGAACCATTCAAAACTTTCCTT
CAAAACCAAAAAGAAAAATTACATCGTGGTAAGATTACTAAGAACAAGGGTAATCTTCTT
CAAAAAGTTTTTGAAGTTTTTGTCATTGGCATGATTCTCTATTTCATTCTTTCAATTATC
AACTCGTTAGCCCAGAGTTGGCACAAACGAATTCACAAAAAATCCAACAAGAAACAACGT
AAAGTAATTAAAGATAATTAA
>g11590.t1 Gene=g11590 Length=526
MTRKRTSQAGSNSATAKLINKINKFNQNNTINNNFIAESNEQETRIVKNNNYDEDEVFIL
TEKQKQQLQRNEYLESLTKDRLKTEAKRRGQKTSGTKSELLQRLGYKMSLRHSSSLNNVR
QSSSLKMKSSKSSPNGSLSSESSGSITEKERLKRERESIKLWIHPVLTIKYCFFEVATLF
QIYKRSILNHKKTIGFVMTLLIAFFTLWYIPGKHQIYVEFIRKNAFFVTYWIGLGVISSI
GLGTGLHTFILYLGPHIASVTLAAYECGSLDFPSPPYPDEIICPDSPTPGFVPSLWSIMS
KVRLESFLWGAGTALGELPPYFMARAARLSGYDPEDAEDLQEFEELQKKRELGEKLSYFE
KLKLGMERIVERVGFFGILACASVPNPLFDLAGITCGHFLVPFWTFFGATLIGKAVIKMH
LQKIVVIVAFNELLLEKAVDLLALIPVVGKKFQEPFKTFLQNQKEKLHRGKITKNKGNLL
QKVFEVFVIGMILYFILSIINSLAQSWHKRIHKKSNKKQRKVIKDN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g11590.t1 | Gene3D | G3DSA:1.10.720.30 | - | 60 | 118 | 5.8E-6 |
| 10 | g11590.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 79 | 94 | - |
| 11 | g11590.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 79 | 98 | - |
| 8 | g11590.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 149 | - |
| 9 | g11590.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 116 | 145 | - |
| 1 | g11590.t1 | PANTHER | PTHR10281 | MEMBRANE-ASSOCIATED PROGESTERONE RECEPTOR COMPONENT-RELATED | 157 | 521 | 6.4E-124 |
| 2 | g11590.t1 | PANTHER | PTHR10281:SF1 | VACUOLE MEMBRANE PROTEIN 1 | 157 | 521 | 6.4E-124 |
| 17 | g11590.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 192 | - |
| 24 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 193 | 210 | - |
| 18 | g11590.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 211 | 229 | - |
| 22 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 230 | 253 | - |
| 16 | g11590.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 254 | 368 | - |
| 25 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 369 | 385 | - |
| 20 | g11590.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 386 | 390 | - |
| 21 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 412 | - |
| 15 | g11590.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 413 | 423 | - |
| 26 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 424 | 448 | - |
| 19 | g11590.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 449 | 482 | - |
| 23 | g11590.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 483 | 504 | - |
| 14 | g11590.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 505 | 526 | - |
| 13 | g11590.t1 | ProSiteProfiles | PS50800 | SAP motif profile. | 74 | 108 | 9.666 |
| 7 | g11590.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 161 | 183 | - |
| 3 | g11590.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 193 | 212 | - |
| 5 | g11590.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 224 | 246 | - |
| 4 | g11590.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 391 | 413 | - |
| 6 | g11590.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 483 | 505 | - |
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 transcript has been annotated with K21248 (vacuole membrane protein 1)
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.
