Gene loci information

Transcript annotation

  • This transcript has been annotated as V-type proton ATPase subunit C.

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 g12205 g12205.t15 TTS g12205.t15 21750129 21750129
chr_1 g12205 g12205.t15 isoform g12205.t15 21750691 21752670
chr_1 g12205 g12205.t15 exon g12205.t15.exon1 21750691 21750786
chr_1 g12205 g12205.t15 cds g12205.t15.CDS1 21750691 21750786
chr_1 g12205 g12205.t15 exon g12205.t15.exon2 21750850 21750985
chr_1 g12205 g12205.t15 cds g12205.t15.CDS2 21750850 21750985
chr_1 g12205 g12205.t15 exon g12205.t15.exon3 21751047 21751144
chr_1 g12205 g12205.t15 cds g12205.t15.CDS3 21751047 21751144
chr_1 g12205 g12205.t15 exon g12205.t15.exon4 21751202 21751457
chr_1 g12205 g12205.t15 cds g12205.t15.CDS4 21751202 21751457
chr_1 g12205 g12205.t15 exon g12205.t15.exon5 21751516 21751614
chr_1 g12205 g12205.t15 cds g12205.t15.CDS5 21751516 21751614
chr_1 g12205 g12205.t15 exon g12205.t15.exon6 21751671 21751857
chr_1 g12205 g12205.t15 cds g12205.t15.CDS6 21751671 21751857
chr_1 g12205 g12205.t15 exon g12205.t15.exon7 21751913 21752250
chr_1 g12205 g12205.t15 cds g12205.t15.CDS7 21751913 21752198
chr_1 g12205 g12205.t15 exon g12205.t15.exon8 21752500 21752670
chr_1 g12205 g12205.t15 TSS g12205.t15 21752830 21752830

Sequences

>g12205.t15 Gene=g12205 Length=1381
TCTGTGAGAAAAAAAGAATTTTAAAAGAACAATTTATTTTTCAAAATAATACAATTAAGA
AAAATTTAATTTCTTCAGTTTGTGTGTTCTCTACCTGCAATCATTTGCTTGTATTAATTA
TAAATTACTTTATTACATCAGATCAACTACAATTTATCAGTGAAAAAGATCATTCAGACT
CGAAAATTGTTGAGAGGCTAAACGGAGTGTAATATCGAGCATCATGTCTGAATATTGGCT
AATATCTGCACCGGGTGACAAGACTTGCCAGCAAACATGGGAAACAATGAATAATGTCAC
GAGCAAGCAAAACAATTTGTGTGAGAACTTCAAGTTTCACATTCCCGATCTTAAAGTCGG
TACATTAGATCAACTGGTAGGCCTCTCAGATGATCTAGGTAAATTGGACTCATTTGTTGA
ACAAATCACACGAAAAGTCGCCAATTATTTGGGTGATGTGCTTGAAGATCAACGAGATAA
GCTCATCGAAAATTTATTGGCTAATAATACTGATTTGTCACAGTATATAACAAGATTTCA
ATGGGATATGGCTAAATATCCAATTAAGCAGTCCTTGAGGAATATTGCCGATATTATTTC
AAAACAAGTCGGTCAGATTGATGCTGATTTAAAAACAAAATCTGCAGCATATAACAGTTT
GAAGGGCAATTTGCAAAATTTAGAAAAGAAGCAAACTGGAAGCTTGCTGACTAGAAATCT
TGCTGATTTAGTTAAGAAAGAACACTTTATTTTGGACTCTGAGTATTTGACTACATTACT
TGTAATTGTTCCTAAAATGCTCTTTAATGATTGGAATGCTGGCTATGAAAAGCTCACTGA
CATGATTGTTCCACGCTCTTCGACACTCATCACACAAGATCAGGACTTTGGTTTGTTTAA
CGTGACACTTTTCAAGAAGGTAGTTGACGAATTCAAGCTTCATGCGCGTGAGAAGAAATT
TGTTGTTCGCGATTTTACATATAATGAAGAAGAATTGGCAGCAGGCAAAAATGAAATTAC
CAAATTGGTTACTGATAAGAAGAAGCAATTTGGTCCACTCGTAAGATGGTTAAAAGTGAA
CTTTAGCGAATGTTTCTGTGCATGGATTCATGTTAAAGCACTTCGCGTTTTTGTGGAATC
TGTTTTAAGATATGGATTACCTGTCAACTTCCAAGCCATCCTCATTCATCCAAATAAAAA
GAACCAGAAACGACTTCGTGATGTTCTTAATCAATTATATGGACACCTTGATGGTTCTGC
ATCATCTTCATCAAACAACGCTGATAATGTAGATATTCCCGGCTTGGGCTTTGGTCAATC
AGAATACTATCCATATGTATTTTACAAATTATCGATCGATATGGTCGAAACCAAAATTTA
A

>g12205.t15 Gene=g12205 Length=385
MSEYWLISAPGDKTCQQTWETMNNVTSKQNNLCENFKFHIPDLKVGTLDQLVGLSDDLGK
LDSFVEQITRKVANYLGDVLEDQRDKLIENLLANNTDLSQYITRFQWDMAKYPIKQSLRN
IADIISKQVGQIDADLKTKSAAYNSLKGNLQNLEKKQTGSLLTRNLADLVKKEHFILDSE
YLTTLLVIVPKMLFNDWNAGYEKLTDMIVPRSSTLITQDQDFGLFNVTLFKKVVDEFKLH
AREKKFVVRDFTYNEEELAAGKNEITKLVTDKKKQFGPLVRWLKVNFSECFCAWIHVKAL
RVFVESVLRYGLPVNFQAILIHPNKKNQKRLRDVLNQLYGHLDGSASSSSNNADNVDIPG
LGFGQSEYYPYVFYKLSIDMVETKI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g12205.t15 CDD cd14785 V-ATPase_C 4 376 0.0
8 g12205.t15 Coils Coil Coil 136 156 -
6 g12205.t15 Gene3D G3DSA:3.30.70.1180 Vacuolar atp synthase subunit c; domain 1 3 346 2.2E-98
7 g12205.t15 Gene3D G3DSA:1.20.1460.10 - 40 313 2.2E-98
5 g12205.t15 Gene3D G3DSA:3.30.70.100 - 163 252 2.2E-98
2 g12205.t15 PANTHER PTHR10137:SF5 V-TYPE PROTON ATPASE SUBUNIT C 1 1 384 4.5E-184
3 g12205.t15 PANTHER PTHR10137 V-TYPE PROTON ATPASE SUBUNIT C 1 384 4.5E-184
1 g12205.t15 Pfam PF03223 V-ATPase subunit C 4 372 2.3E-182
4 g12205.t15 SUPERFAMILY SSF118203 Vacuolar ATP synthase subunit C 1 377 5.1E-150

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:1902600 proton transmembrane transport BP
GO:0015078 proton transmembrane transporter activity MF
GO:0033180 proton-transporting V-type ATPase, V1 domain CC

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