Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ATP synthase F(0) complex subunit C3, mitochondrial.

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 g9266 g9266.t4 TTS g9266.t4 1369645 1369645
chr_1 g9266 g9266.t4 isoform g9266.t4 1370090 1371702
chr_1 g9266 g9266.t4 exon g9266.t4.exon1 1370090 1370253
chr_1 g9266 g9266.t4 cds g9266.t4.CDS1 1370090 1370253
chr_1 g9266 g9266.t4 exon g9266.t4.exon2 1370810 1371014
chr_1 g9266 g9266.t4 cds g9266.t4.CDS2 1370810 1371014
chr_1 g9266 g9266.t4 exon g9266.t4.exon3 1371284 1371367
chr_1 g9266 g9266.t4 cds g9266.t4.CDS3 1371284 1371322
chr_1 g9266 g9266.t4 exon g9266.t4.exon4 1371484 1371702
chr_1 g9266 g9266.t4 TSS g9266.t4 1371819 1371819

Sequences

>g9266.t4 Gene=g9266 Length=672
TCTATCTTTATTTGCTAAATTTTACTTGTTTTTTATTTGAATACGGTTCAGTTAAAATTT
TTCGGCTAAATTTCCCGACAAACGCACCGCCATTTTGTATTTTGTGATAAGAAAATTGCA
ATTTCTTGCATAAATAGAAAGTTTTACAATCAAATTATATATGTAATTAATTATTGTGAA
TCAAAACTATCGAAATAAGTTATAATATTTCTAAATTAAATCCTCCTTTAAGCACCGGAC
AAAGTCAAAGAATTTAATTCAAAAATGTTCGTAACATCAGCTGCCCGCGTTGCTCCACGT
ATTGTCGCCAATGGCACAAAAGCTTATCTTAGACCTTTGAGCAGTGCTGTCATCTCACAA
AGCCAGACATTAGCAGCTCAAAACACAACGCCCGTAGCTCTTCTGCCACAGGTCAGATCA
TTCCAGACCTCAGTCGTAAAGAATGATATCGACTCAGCAGCCAAGTTCATCGGTGCTGGT
GCTGCCACAGTCGGAGTTGCTGGATCTGGTGCTGGTATCGGAACAGTATTCGGTTCACTC
ATCATTGGTTATGCCAGAAATCCATCACTCAAACAACAATTGTTCTCATATGCCATTTTG
GGTTTCGCCTTGTCTGAAGCTATGGGACTTTTCTGTCTTATGATGGCTTTCTTGCTGTTG
TTCGCTTTCTAA

>g9266.t4 Gene=g9266 Length=135
MFVTSAARVAPRIVANGTKAYLRPLSSAVISQSQTLAAQNTTPVALLPQVRSFQTSVVKN
DIDSAAKFIGAGAATVGVAGSGAGIGTVFGSLIIGYARNPSLKQQLFSYAILGFALSEAM
GLFCLMMAFLLLFAF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g9266.t4 CDD cd18182 ATP-synt_Fo_c_ATP5G3 67 131 5.15915E-29
9 g9266.t4 Gene3D G3DSA:1.20.20.10 F1FO ATP Synthase 62 133 2.2E-38
4 g9266.t4 Hamap MF_01396 ATP synthase subunit c [atpH]. 64 132 13.989817
2 g9266.t4 PANTHER PTHR10031:SF31 ATP SYNTHASE F(0) COMPLEX SUBUNIT C2, MITOCHONDRIAL 2 134 6.6E-56
3 g9266.t4 PANTHER PTHR10031 ATP SYNTHASE LIPID-BINDING PROTEIN, MITOCHONDRIAL 2 134 6.6E-56
7 g9266.t4 PRINTS PR00124 ATP synthase C subunit signature 69 88 1.0E-31
6 g9266.t4 PRINTS PR00124 ATP synthase C subunit signature 90 105 1.0E-31
5 g9266.t4 PRINTS PR00124 ATP synthase C subunit signature 107 132 1.0E-31
1 g9266.t4 Pfam PF00137 ATP synthase subunit C 69 131 1.1E-10
11 g9266.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 1 67 -
14 g9266.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 68 94 -
10 g9266.t4 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 95 105 -
13 g9266.t4 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 106 134 -
12 g9266.t4 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 135 135 -
18 g9266.t4 ProSitePatterns PS00605 ATP synthase c subunit signature. 97 118 -
8 g9266.t4 SUPERFAMILY SSF81333 F1F0 ATP synthase subunit C 63 134 1.96E-19
17 g9266.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 74 96 -
16 g9266.t4 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 133 -

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:0015986 ATP synthesis coupled proton transport BP
GO:1902600 proton transmembrane transport BP
GO:0045263 proton-transporting ATP synthase complex, coupling factor F(o) CC
GO:0033177 proton-transporting two-sector ATPase complex, proton-transporting domain CC
GO:0015078 proton transmembrane transporter activity MF

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