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.t10 TSS g1669.t10 12370666 12370666
chr_3 g1669 g1669.t10 isoform g1669.t10 12370737 12372963
chr_3 g1669 g1669.t10 exon g1669.t10.exon1 12370737 12370806
chr_3 g1669 g1669.t10 exon g1669.t10.exon2 12371482 12371822
chr_3 g1669 g1669.t10 cds g1669.t10.CDS1 12371485 12371822
chr_3 g1669 g1669.t10 exon g1669.t10.exon3 12371888 12372521
chr_3 g1669 g1669.t10 cds g1669.t10.CDS2 12371888 12372521
chr_3 g1669 g1669.t10 exon g1669.t10.exon4 12372586 12372963
chr_3 g1669 g1669.t10 cds g1669.t10.CDS3 12372586 12372963
chr_3 g1669 g1669.t10 TTS g1669.t10 12373358 12373358

Sequences

>g1669.t10 Gene=g1669 Length=1423
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTATGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGG
TAATGATAAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGT
TCCAGTCGGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGG
AAAGGGAGAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTAT
TCCACGTGTTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGT
ACCAATTGGTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGACTGGTAAAACTGC
TTTGGCCATTGATACAATCATCAATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAA
GAAATTGTACTGTATTTATGTTGCCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGT
CAAGCGTTTGAGTGATGCTGGTGCTATGGATTATACCATCATTGTCTCAGCTACTGCTTC
AGATGCTGCTCCATTGCAATATTTGGCACCATATTCTGGCTGTGCCATGGGTGAATACTT
CCGTGACAATGGCAAACACGCTCTTATCATTTATGATGACTTGTCAAAACAAGCTGTTGC
CTATCGTCAAATGTCACTGTTGTTGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGA
TGTCTTCTATCTTCACAGCCGTTTGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGG
CGGTGGATCATTGACTGCCTTGCCAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTA
CATTCCCACAAATGTCATCTCAATTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTT
CTACAAAGGTATTCGTCCAGCTATTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGC
TGCTCAAACCAGAGCCATGAAACAGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTA
TCGTGAGGTTGCTGCCTTCGCTCAATTCGGTTCAGATCTCGATGCTGCCACACAACAACT
TTTGAATCGTGGTGTTCGTTTGACAGAATTATTGAAACAAGGTCAATATGTACCAATGGC
TATTGAAGAACAAGTTGCAGTCATTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGA
ACCATCAAAGATCACAGCATTCGAAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAA
GGCATTGTTGCAACAAATTGCCAGCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCT
TAAATCGATTGTAACCAGTTTCCTCTCGACATACAGCGGTTAA

>g1669.t10 Gene=g1669 Length=449
MALNLEPDNVGVVVFGNDKLIREGDIVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEI
KTKQRFRVGIKAPGIIPRVSVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTALAID
TIINQKRFNDGQDESKKLYCIYVAIGQKRSTVAQIVKRLSDAGAMDYTIIVSATASDAAP
LQYLAPYSGCAMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYL
HSRLLERAAKMSPAHGGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGI
RPAINVGLSVSRVGSAAQTRAMKQVAGSMKLELAQYREVAAFAQFGSDLDAATQQLLNRG
VRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKMEPSKITAFEKEFLAHIKTNEKALLQ
QIASEGKISDEVDAKLKSIVTSFLSTYSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1669.t10 CDD cd01132 F1_ATPase_alpha 33 314 0.0
13 g1669.t10 CDD cd18113 ATP-synt_F1_alpha_C 322 447 1.14371E-68
12 g1669.t10 Gene3D G3DSA:2.40.30.20 - 1 32 1.1E-11
10 g1669.t10 Gene3D G3DSA:3.40.50.300 - 33 318 2.1E-134
11 g1669.t10 Gene3D G3DSA:1.20.150.20 - 319 448 9.0E-61
6 g1669.t10 Hamap MF_01346 ATP synthase subunit alpha [atpA]. 1 448 44.191345
4 g1669.t10 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 1 447 3.7E-285
5 g1669.t10 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 1 447 3.7E-285
1 g1669.t10 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 1 31 5.9E-6
3 g1669.t10 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 88 311 3.4E-72
2 g1669.t10 Pfam PF00306 ATP synthase alpha/beta chain, C terminal domain 318 443 9.6E-48
15 g1669.t10 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 302 311 -
7 g1669.t10 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 1 33 1.02E-7
8 g1669.t10 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 35 317 3.64E-103
9 g1669.t10 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 320 447 1.2E-45
16 g1669.t10 TIGRFAM TIGR00962 atpA: ATP synthase F1, alpha subunit 1 447 1.1E-226

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:0045261 proton-transporting ATP synthase complex, catalytic core F(1) CC
GO:0015986 ATP synthesis coupled proton transport BP
GO:1902600 proton transmembrane transport BP
GO:0005524 ATP binding MF
GO:0032559 adenyl ribonucleotide 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