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.t6 TTS g11590.t6 17376550 17376550
chr_1 g11590 g11590.t6 isoform g11590.t6 17376817 17380714
chr_1 g11590 g11590.t6 exon g11590.t6.exon1 17376817 17377630
chr_1 g11590 g11590.t6 cds g11590.t6.CDS1 17377273 17377630
chr_1 g11590 g11590.t6 exon g11590.t6.exon2 17377699 17378237
chr_1 g11590 g11590.t6 cds g11590.t6.CDS2 17377699 17378216
chr_1 g11590 g11590.t6 exon g11590.t6.exon3 17380345 17380714
chr_1 g11590 g11590.t6 TSS g11590.t6 NA NA

Sequences

>g11590.t6 Gene=g11590 Length=1723
GCTTTGAAATGCGGGCAAAAAAGAAAGATTTGAGATTTGACGAAAAAAATGAAAAAAAAA
ATGTGAAGACGACTTTATTAATTTGAAGGTGTATTAGCATTTAAAAAAAATAAAAAAATT
AGAAGTTAATAAAAATTTAGAAAATCATACACTTATGGCGAATTAAAACTTTTTATTACT
TTAAAAATTATTTCGTGAAAATTACCGTTTTTTATTACAAAAATATTTATTAAAAAGAAT
AGTGGAATAAACACAAAACACAAACTCACAAATTACAAAGGAGAAAAATTGATTTTTTTT
ATCATCCTCAATTTTATATAGGTACTATAACAAAGTGAAAAAACCAAGTGCTTGATAAAT
AATAAATCAGTTACAACGTTTGGGATATAAAATGTCGCTTCGACATTCAAGCTCCCTAAA
TAATGTTCGTCAATCATCTAGTCTGAAGATGAAAAGTTCAAAATCTTCACCAAATGGTTC
TCTTTCTTCGGAAAGCTCTGGTAGCATTACTGAAAAAGAGCGTTTAAAGAGAGAACGAGA
AAGCATTAAACTCTGGATTCATCCAGTTTTGACGATCAAATATTGTTTCTTTGAAGTAGC
AACTCTTTTTCAAATTTATAAGCGTAGCATATTAAACCATAAAAAGACCATAGGATTTGT
TATGACATTGCTAATAGCATTTTTTACGCTCTGGTATATACCTGGAAAGCATCAAATTTA
CGTTGAATTTATAAGAAAAAATGCATTCTTCGTAACATATTGGATTGGTTTGGGTGTAAT
ATCGAGTATTGGATTGGGAACAGGACTGCATACATTTATATTATATTTAGGACCACATAT
AGCCAGTGTAACATTAGCGGCATATGAATGTGGATCTCTAGATTTTCCTTCTCCCCCTTA
TCCTGACGAAATAATTTGTCCAGATAGTCCTACGCCAGGTTTTGTGCCGTCATTATGGAG
CATAATGAGCAAAGTTCGTTTAGAATCATTCCTTTGGGGTGCTGGAACTGCACTGGGAGA
ACTACCACCTTATTTTATGGCGCGTGCAGCTCGTTTAAGTGGTTATGATCCTGAGGATGC
AGAAGATTTACAAGAATTTGAAGAATTACAGAAAAAACGTGAATTGGGTGAAAAACTAAG
TTATTTTGAAAAATTGAAATTGGGTATGGAAAGAATTGTTGAGCGTGTTGGATTTTTTGG
AATTTTGGCTTGTGCAAGTGTACGTTACATATTGCATAAAATTAGAATGATTATTGTTTT
ATTATAATATAAATTTTTATTTTATTTGTAGGTTCCAAATCCACTTTTTGATTTGGCAGG
TATCACATGCGGTCACTTTTTGGTACCATTTTGGACGTTCTTTGGTGCAACATTAATTGG
AAAGGCTGTGATTAAAATGCATCTTCAGAAAATAGTAGTAATTGTAGCATTCAACGAACT
ATTGCTTGAGAAGGCTGTTGATTTATTGGCTCTTATTCCTGTCGTTGGAAAAAAGTTTCA
AGAACCATTCAAAACTTTCCTTCAAAACCAAAAAGAAAAATTACATCGTGGTAAGATTAC
TAAGAACAAGGGTAATCTTCTTCAAAAAGTTTTTGAAGTTTTTGTCATTGGCATGATTCT
CTATTTCATTCTTTCAATTATCAACTCGTTAGCCCAGAGTTGGCACAAACGAATTCACAA
AAAATCCAACAAGAAACAACGTAAAGTAATTAAAGATAATTAA

>g11590.t6 Gene=g11590 Length=291
MSLRHSSSLNNVRQSSSLKMKSSKSSPNGSLSSESSGSITEKERLKRERESIKLWIHPVL
TIKYCFFEVATLFQIYKRSILNHKKTIGFVMTLLIAFFTLWYIPGKHQIYVEFIRKNAFF
VTYWIGLGVISSIGLGTGLHTFILYLGPHIASVTLAAYECGSLDFPSPPYPDEIICPDSP
TPGFVPSLWSIMSKVRLESFLWGAGTALGELPPYFMARAARLSGYDPEDAEDLQEFEELQ
KKRELGEKLSYFEKLKLGMERIVERVGFFGILACASVRYILHKIRMIIVLL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g11590.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 42 -
7 g11590.t6 MobiDBLite mobidb-lite consensus disorder prediction 1 38 -
1 g11590.t6 PANTHER PTHR10281 MEMBRANE-ASSOCIATED PROGESTERONE RECEPTOR COMPONENT-RELATED 48 277 8.9E-67
2 g11590.t6 PANTHER PTHR10281:SF1 VACUOLE MEMBRANE PROTEIN 1 48 277 8.9E-67
12 g11590.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 53 -
16 g11590.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 54 75 -
9 g11590.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 76 86 -
14 g11590.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 87 103 -
11 g11590.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 104 122 -
15 g11590.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 123 146 -
8 g11590.t6 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 147 261 -
13 g11590.t6 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 262 281 -
10 g11590.t6 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 282 291 -
3 g11590.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 54 76 -
4 g11590.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 86 105 -
5 g11590.t6 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 118 140 -

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.

Raw TPM values