Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP synthase subunit alpha, 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_3 g1669 g1669.t2 TSS g1669.t2 12370666 12370666
chr_3 g1669 g1669.t2 isoform g1669.t2 12370737 12371818
chr_3 g1669 g1669.t2 exon g1669.t2.exon1 12370737 12370802
chr_3 g1669 g1669.t2 cds g1669.t2.CDS1 12370737 12370802
chr_3 g1669 g1669.t2 exon g1669.t2.exon2 12371165 12371401
chr_3 g1669 g1669.t2 cds g1669.t2.CDS2 12371165 12371401
chr_3 g1669 g1669.t2 exon g1669.t2.exon3 12371482 12371818
chr_3 g1669 g1669.t2 cds g1669.t2.CDS3 12371482 12371817
chr_3 g1669 g1669.t2 TTS g1669.t2 NA NA

Sequences

>g1669.t2 Gene=g1669 Length=640
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTC
TCTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCC
GCACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCT
CGTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTG
AAGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGAT
AAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTC
GGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGA
GAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGT
GTTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGTACCAATT
GGTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGA

>g1669.t2 Gene=g1669 Length=213
MSMLSARLAASVARNLPRSAQQVARVVVPASQIAARKIHVSAPAKGAEISSILEERIMGA
APKADLEETGRVLSIGDGIARVYGLKNIQADEMVEFSSGLKGMALNLEPDNVGVVVFGND
KLIREGDIVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEIKTKQRFRVGIKAPGIIPR
VSVREPMQTGIKAVDSLVPIGRGQRELIIGDRQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
13 g1669.t2 CDD cd18116 ATP-synt_F1_alpha_N 68 134 9.68706E-36
7 g1669.t2 Gene3D G3DSA:2.40.30.20 - 43 134 8.2E-41
6 g1669.t2 Gene3D G3DSA:3.40.50.300 - 135 213 3.7E-29
2 g1669.t2 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 44 213 2.1E-96
3 g1669.t2 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 44 213 2.1E-96
1 g1669.t2 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 67 133 4.6E-19
9 g1669.t2 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
10 g1669.t2 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
11 g1669.t2 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
12 g1669.t2 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 20 -
8 g1669.t2 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 213 -
4 g1669.t2 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 51 135 1.6E-28
5 g1669.t2 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 137 213 3.72E-21

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:0046034 ATP metabolic process BP
GO:1902600 proton transmembrane transport BP

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