Gene loci information

Transcript annotation

  • This transcript has been annotated as Vacuole membrane protein 1.

Parent gene

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.t5 TTS g11590.t5 17376550 17376550
chr_1 g11590 g11590.t5 isoform g11590.t5 17376817 17380714
chr_1 g11590 g11590.t5 exon g11590.t5.exon1 17376817 17377248
chr_1 g11590 g11590.t5 cds g11590.t5.CDS1 17376817 17377248
chr_1 g11590 g11590.t5 exon g11590.t5.exon2 17377321 17377630
chr_1 g11590 g11590.t5 cds g11590.t5.CDS2 17377321 17377630
chr_1 g11590 g11590.t5 exon g11590.t5.exon3 17377699 17378237
chr_1 g11590 g11590.t5 cds g11590.t5.CDS3 17377699 17378216
chr_1 g11590 g11590.t5 exon g11590.t5.exon4 17380345 17380714
chr_1 g11590 g11590.t5 TSS g11590.t5 NA NA

Sequences

>g11590.t5 Gene=g11590 Length=1651
GCTTTGAAATGCGGGCAAAAAAGAAAGATTTGAGATTTGACGAAAAAAATGAAAAAAAAA
ATGTGAAGACGACTTTATTAATTTGAAGGTGTATTAGCATTTAAAAAAAATAAAAAAATT
AGAAGTTAATAAAAATTTAGAAAATCATACACTTATGGCGAATTAAAACTTTTTATTACT
TTAAAAATTATTTCGTGAAAATTACCGTTTTTTATTACAAAAATATTTATTAAAAAGAAT
AGTGGAATAAACACAAAACACAAACTCACAAATTACAAAGGAGAAAAATTGATTTTTTTT
ATCATCCTCAATTTTATATAGGTACTATAACAAAGTGAAAAAACCAAGTGCTTGATAAAT
AATAAATCAGTTACAACGTTTGGGATATAAAATGTCGCTTCGACATTCAAGCTCCCTAAA
TAATGTTCGTCAATCATCTAGTCTGAAGATGAAAAGTTCAAAATCTTCACCAAATGGTTC
TCTTTCTTCGGAAAGCTCTGGTAGCATTACTGAAAAAGAGCGTTTAAAGAGAGAACGAGA
AAGCATTAAACTCTGGATTCATCCAGTTTTGACGATCAAATATTGTTTCTTTGAAGTAGC
AACTCTTTTTCAAATTTATAAGCGTAGCATATTAAACCATAAAAAGACCATAGGATTTGT
TATGACATTGCTAATAGCATTTTTTACGCTCTGGTATATACCTGGAAAGCATCAAATTTA
CGTTGAATTTATAAGAAAAAATGCATTCTTCGTAACATATTGGATTGGTTTGGGTGTAAT
ATCGAGTATTGGATTGGGAACAGGACTGCATACATTTATATTATATTTAGGACCACATAT
AGCCAGTGTAACATTAGCGGCATATGAATGTGGATCTCTAGATTTTCCTTCTCCCCCTTA
TCCTGACGAAATAATTTGTCCAGATAGTCCTACGCCAGGTTTTGTGCCGTCATTATGGAG
CATAATGAGCAAAGTTCGTTTAGAATCATTCCTTTGGGGTGCTGGAACTGCACTGGGAGA
ACTACCACCTTATTTTATGGCGCGTGCAGCTCGTTTAAGTGGTTATGATCCTGAGGATGC
AGAAGATTTACAAGAATTTGAAGAATTACAGAAAAAACGTGAATTGGGTGAAAAACTAAG
TTATTTTGAAAAATTGAAATTGGGTATGGAAAGAATTGTTGAGCGTGTTGGATTTTTTGG
AATTTTGGCTTGTGCAAGTGTTCCAAATCCACTTTTTGATTTGGCAGGTATCACATGCGG
TCACTTTTTGGTACCATTTTGGACGTTCTTTGGTGCAACATTAATTGGAAAGGCTGTGAT
TAAAATGCATCTTCAGAAAATAGTAGTAATTGTAGCATTCAACGAACTATTGCTTGAGAA
GGCTGTTGATTTATTGGCTCTTATTCCTGTCGTTGGAAAAAAGTTTCAAGAACCATTCAA
AACTTTCCTTCAAAACCAAAAAGAAAAATTACATCGTGGTAAGATTACTAAGAACAAGGG
TAATCTTCTTCAAAAAGTTTTTGAAGTTTTTGTCATTGGCATGATTCTCTATTTCATTCT
TTCAATTATCAACTCGTTAGCCCAGAGTTGGCACAAACGAATTCACAAAAAATCCAACAA
GAAACAACGTAAAGTAATTAAAGATAATTAA

>g11590.t5 Gene=g11590 Length=419
MSLRHSSSLNNVRQSSSLKMKSSKSSPNGSLSSESSGSITEKERLKRERESIKLWIHPVL
TIKYCFFEVATLFQIYKRSILNHKKTIGFVMTLLIAFFTLWYIPGKHQIYVEFIRKNAFF
VTYWIGLGVISSIGLGTGLHTFILYLGPHIASVTLAAYECGSLDFPSPPYPDEIICPDSP
TPGFVPSLWSIMSKVRLESFLWGAGTALGELPPYFMARAARLSGYDPEDAEDLQEFEELQ
KKRELGEKLSYFEKLKLGMERIVERVGFFGILACASVPNPLFDLAGITCGHFLVPFWTFF
GATLIGKAVIKMHLQKIVVIVAFNELLLEKAVDLLALIPVVGKKFQEPFKTFLQNQKEKL
HRGKITKNKGNLLQKVFEVFVIGMILYFILSIINSLAQSWHKRIHKKSNKKQRKVIKDN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g11590.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
9 g11590.t5 MobiDBLite mobidb-lite consensus disorder prediction 1 38 -
1 g11590.t5 PANTHER PTHR10281 MEMBRANE-ASSOCIATED PROGESTERONE RECEPTOR COMPONENT-RELATED 50 414 3.4E-124
2 g11590.t5 PANTHER PTHR10281:SF1 VACUOLE MEMBRANE PROTEIN 1 50 414 3.4E-124
16 g11590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 53 -
24 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 75 -
11 g11590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 86 -
19 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 103 -
15 g11590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 104 122 -
23 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 146 -
10 g11590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 261 -
22 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 262 278 -
17 g11590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 279 283 -
18 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 284 305 -
13 g11590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 306 316 -
21 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 317 341 -
14 g11590.t5 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 342 375 -
20 g11590.t5 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 376 397 -
12 g11590.t5 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 398 419 -
3 g11590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
6 g11590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -
4 g11590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 117 139 -
7 g11590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 284 306 -
5 g11590.t5 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 376 398 -

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

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.

Raw TPM values