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.t25 TTS g12205.t25 21750629 21750629
chr_1 g12205 g12205.t25 isoform g12205.t25 21751222 21752250
chr_1 g12205 g12205.t25 exon g12205.t25.exon1 21751222 21751457
chr_1 g12205 g12205.t25 cds g12205.t25.CDS1 21751223 21751457
chr_1 g12205 g12205.t25 exon g12205.t25.exon2 21751516 21751614
chr_1 g12205 g12205.t25 cds g12205.t25.CDS2 21751516 21751614
chr_1 g12205 g12205.t25 exon g12205.t25.exon3 21751671 21751857
chr_1 g12205 g12205.t25 cds g12205.t25.CDS3 21751671 21751857
chr_1 g12205 g12205.t25 exon g12205.t25.exon4 21751913 21752250
chr_1 g12205 g12205.t25 cds g12205.t25.CDS4 21751913 21752198
chr_1 g12205 g12205.t25 TSS g12205.t25 21752830 21752830

Sequences

>g12205.t25 Gene=g12205 Length=860
ATTCAGACTCGAAAATTGTTGAGAGGCTAAACGGAGTGTAATATCGAGCATCATGTCTGA
ATATTGGCTAATATCTGCACCGGGTGACAAGACTTGCCAGCAAACATGGGAAACAATGAA
TAATGTCACGAGCAAGCAAAACAATTTGTGTGAGAACTTCAAGTTTCACATTCCCGATCT
TAAAGTCGGTACATTAGATCAACTGGTAGGCCTCTCAGATGATCTAGGTAAATTGGACTC
ATTTGTTGAACAAATCACACGAAAAGTCGCCAATTATTTGGGTGATGTGCTTGAAGATCA
ACGAGATAAGCTCATCGAAAATTTATTGGCTAATAATACTGATTTGTCACAGTATATAAC
AAGATTTCAATGGGATATGGCTAAATATCCAATTAAGCAGTCCTTGAGGAATATTGCCGA
TATTATTTCAAAACAAGTCGGTCAGATTGATGCTGATTTAAAAACAAAATCTGCAGCATA
TAACAGTTTGAAGGGCAATTTGCAAAATTTAGAAAAGAAGCAAACTGGAAGCTTGCTGAC
TAGAAATCTTGCTGATTTAGTTAAGAAAGAACACTTTATTTTGGACTCTGAGTATTTGAC
TACATTACTTGTAATTGTTCCTAAAATGCTCTTTAATGATTGGAATGCTGGCTATGAAAA
GCTCACTGACATGATTGTTCCACGCTCTTCGACACTCATCACACAAGATCAGGACTTTGG
TTTGTTTAACGTGACACTTTTCAAGAAGGTAGTTGACGAATTCAAGCTTCATGCGCGTGA
GAAGAAATTTGTTGTTCGCGATTTTACATATAATGAAGAAGAATTGGCAGCAGGCAAAAA
TGAAATTACCAAATTGGTTA

>g12205.t25 Gene=g12205 Length=269
MSEYWLISAPGDKTCQQTWETMNNVTSKQNNLCENFKFHIPDLKVGTLDQLVGLSDDLGK
LDSFVEQITRKVANYLGDVLEDQRDKLIENLLANNTDLSQYITRFQWDMAKYPIKQSLRN
IADIISKQVGQIDADLKTKSAAYNSLKGNLQNLEKKQTGSLLTRNLADLVKKEHFILDSE
YLTTLLVIVPKMLFNDWNAGYEKLTDMIVPRSSTLITQDQDFGLFNVTLFKKVVDEFKLH
AREKKFVVRDFTYNEEELAAGKNEITKLV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g12205.t25 CDD cd14785 V-ATPase_C 4 269 4.1878E-141
5 g12205.t25 Coils Coil Coil 136 156 -
4 g12205.t25 Gene3D G3DSA:1.20.1460.10 - 40 215 1.8E-50
2 g12205.t25 PANTHER PTHR10137 V-TYPE PROTON ATPASE SUBUNIT C 1 269 1.3E-128
1 g12205.t25 Pfam PF03223 V-ATPase subunit C 4 268 4.6E-129
3 g12205.t25 SUPERFAMILY SSF118203 Vacuolar ATP synthase subunit C 1 268 3.92E-106

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

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. There were no conditions that were differentially expressed