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.t14 TSS g1669.t14 12370666 12370666
chr_3 g1669 g1669.t14 isoform g1669.t14 12371160 12372963
chr_3 g1669 g1669.t14 exon g1669.t14.exon1 12371160 12371401
chr_3 g1669 g1669.t14 cds g1669.t14.CDS1 12371270 12371401
chr_3 g1669 g1669.t14 exon g1669.t14.exon2 12371482 12371822
chr_3 g1669 g1669.t14 cds g1669.t14.CDS2 12371482 12371822
chr_3 g1669 g1669.t14 exon g1669.t14.exon3 12371888 12372521
chr_3 g1669 g1669.t14 cds g1669.t14.CDS3 12371888 12372521
chr_3 g1669 g1669.t14 exon g1669.t14.exon4 12372586 12372963
chr_3 g1669 g1669.t14 cds g1669.t14.CDS4 12372586 12372963
chr_3 g1669 g1669.t14 TTS g1669.t14 12373358 12373358

Sequences

>g1669.t14 Gene=g1669 Length=1595
AACAGGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTCT
CTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCCG
CACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCTC
GTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTGA
AGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGATA
AGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTCG
GTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGAG
AAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGTG
TTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGTACCAATTG
GTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGACTGGTAAAACTGCTTTGGCCA
TTGATACAATCATCAATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAAGAAATTGT
ACTGTATTTATGTTGCCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGTCAAGCGTT
TGAGTGATGCTGGTGCTATGGATTATACCATCATTGTCTCAGCTACTGCTTCAGATGCTG
CTCCATTGCAATATTTGGCACCATATTCTGGCTGTGCCATGGGTGAATACTTCCGTGACA
ATGGCAAACACGCTCTTATCATTTATGATGACTTGTCAAAACAAGCTGTTGCCTATCGTC
AAATGTCACTGTTGTTGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGATGTCTTCT
ATCTTCACAGCCGTTTGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGGCGGTGGAT
CATTGACTGCCTTGCCAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTACATTCCCA
CAAATGTCATCTCAATTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTTCTACAAAG
GTATTCGTCCAGCTATTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGCTGCTCAAA
CCAGAGCCATGAAACAGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTATCGTGAGG
TTGCTGCCTTCGCTCAATTCGGTTCAGATCTCGATGCTGCCACACAACAACTTTTGAATC
GTGGTGTTCGTTTGACAGAATTATTGAAACAAGGTCAATATGTACCAATGGCTATTGAAG
AACAAGTTGCAGTCATTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGAACCATCAA
AGATCACAGCATTCGAAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAAGGCATTGT
TGCAACAAATTGCCAGCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCTTAAATCGA
TTGTAACCAGTTTCCTCTCGACATACAGCGGTTAA

>g1669.t14 Gene=g1669 Length=494
MGAAPKADLEETGRVLSIGDGIARVYGLKNIQADEMVEFSSGLKGMALNLEPDNVGVVVF
GNDKLIREGDIVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEIKTKQRFRVGIKAPGI
IPRVSVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTALAIDTIINQKRFNDGQDES
KKLYCIYVAIGQKRSTVAQIVKRLSDAGAMDYTIIVSATASDAAPLQYLAPYSGCAMGEY
FRDNGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSPAH
GGGSLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGS
AAQTRAMKQVAGSMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPM
AIEEQVAVIYCGVRGHLDKMEPSKITAFEKEFLAHIKTNEKALLQQIASEGKISDEVDAK
LKSIVTSFLSTYSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g1669.t14 CDD cd18116 ATP-synt_F1_alpha_N 11 77 5.33199E-36
16 g1669.t14 CDD cd01132 F1_ATPase_alpha 78 359 0.0
15 g1669.t14 CDD cd18113 ATP-synt_F1_alpha_C 367 492 3.63639E-68
12 g1669.t14 Gene3D G3DSA:2.40.30.20 - 8 77 4.2E-35
10 g1669.t14 Gene3D G3DSA:3.40.50.300 - 78 363 2.7E-134
11 g1669.t14 Gene3D G3DSA:1.20.150.20 - 364 493 1.1E-60
6 g1669.t14 Hamap MF_01346 ATP synthase subunit alpha [atpA]. 1 493 48.559135
4 g1669.t14 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 2 492 0.0
5 g1669.t14 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 2 492 0.0
13 g1669.t14 PIRSF PIRSF039088 F_ATPase_subunit_alpha 1 494 6.0E-279
1 g1669.t14 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 10 76 1.9E-18
3 g1669.t14 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 133 356 4.4E-72
2 g1669.t14 Pfam PF00306 ATP synthase alpha/beta chain, C terminal domain 363 488 1.1E-47
17 g1669.t14 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 347 356 -
7 g1669.t14 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 6 78 4.45E-26
8 g1669.t14 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 80 362 5.32E-103
9 g1669.t14 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 365 492 1.65E-45
18 g1669.t14 TIGRFAM TIGR00962 atpA: ATP synthase F1, alpha subunit 6 492 2.3E-242

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

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