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.t7 TSS g1669.t7 12370666 12370666
chr_3 g1669 g1669.t7 isoform g1669.t7 12370737 12372963
chr_3 g1669 g1669.t7 exon g1669.t7.exon1 12370737 12370802
chr_3 g1669 g1669.t7 exon g1669.t7.exon2 12371165 12371401
chr_3 g1669 g1669.t7 exon g1669.t7.exon3 12371482 12371746
chr_3 g1669 g1669.t7 exon g1669.t7.exon4 12371888 12372521
chr_3 g1669 g1669.t7 cds g1669.t7.CDS1 12372042 12372521
chr_3 g1669 g1669.t7 exon g1669.t7.exon5 12372586 12372963
chr_3 g1669 g1669.t7 cds g1669.t7.CDS2 12372586 12372963
chr_3 g1669 g1669.t7 TTS g1669.t7 12373358 12373358

Sequences

>g1669.t7 Gene=g1669 Length=1580
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTC
TCTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCC
GCACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCT
CGTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTG
AAGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGAT
AAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTC
GGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGA
GAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGT
GTTTCTGTACGTGAGCCTATGCAGACCGTAAAACTGCTTTGGCCATTGATACAATCATCA
ATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAAGAAATTGTACTGTATTTATGTTG
CCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGTCAAGCGTTTGAGTGATGCTGGTG
CTATGGATTATACCATCATTGTCTCAGCTACTGCTTCAGATGCTGCTCCATTGCAATATT
TGGCACCATATTCTGGCTGTGCCATGGGTGAATACTTCCGTGACAATGGCAAACACGCTC
TTATCATTTATGATGACTTGTCAAAACAAGCTGTTGCCTATCGTCAAATGTCACTGTTGT
TGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGATGTCTTCTATCTTCACAGCCGTT
TGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGGCGGTGGATCATTGACTGCCTTGC
CAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTACATTCCCACAAATGTCATCTCAA
TTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTTCTACAAAGGTATTCGTCCAGCTA
TTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGCTGCTCAAACCAGAGCCATGAAAC
AGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTATCGTGAGGTTGCTGCCTTCGCTC
AATTCGGTTCAGATCTCGATGCTGCCACACAACAACTTTTGAATCGTGGTGTTCGTTTGA
CAGAATTATTGAAACAAGGTCAATATGTACCAATGGCTATTGAAGAACAAGTTGCAGTCA
TTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGAACCATCAAAGATCACAGCATTCG
AAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAAGGCATTGTTGCAACAAATTGCCA
GCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCTTAAATCGATTGTAACCAGTTTCC
TCTCGACATACAGCGGTTAA

>g1669.t7 Gene=g1669 Length=285
MDYTIIVSATASDAAPLQYLAPYSGCAMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLL
RRPPGREAYPGDVFYLHSRLLERAAKMSPAHGGGSLTALPVIETQAGDVSAYIPTNVISI
TDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGSMKLELAQYREVAAFAQ
FGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKMEPSKITAFE
KEFLAHIKTNEKALLQQIASEGKISDEVDAKLKSIVTSFLSTYSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g1669.t7 CDD cd18113 ATP-synt_F1_alpha_C 158 283 2.60498E-70
8 g1669.t7 Gene3D G3DSA:3.40.50.300 - 1 154 5.4E-73
9 g1669.t7 Gene3D G3DSA:1.20.150.20 - 155 284 3.4E-61
3 g1669.t7 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 1 283 1.5E-175
4 g1669.t7 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 1 283 1.5E-175
2 g1669.t7 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 1 147 9.8E-51
1 g1669.t7 Pfam PF00306 ATP synthase alpha/beta chain, C terminal domain 154 279 3.7E-48
7 g1669.t7 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 138 147 -
5 g1669.t7 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 1 153 6.28E-56
6 g1669.t7 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 156 283 4.45E-46
10 g1669.t7 TIGRFAM TIGR00962 atpA: ATP synthase F1, alpha subunit 1 283 1.9E-146

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:0045261 proton-transporting ATP synthase complex, catalytic core F(1) CC
GO:0015986 ATP synthesis coupled proton transport BP
GO:0005524 ATP binding MF
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism MF

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