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.t9 TSS g1669.t9 12370666 12370666
chr_3 g1669 g1669.t9 isoform g1669.t9 12370737 12372963
chr_3 g1669 g1669.t9 exon g1669.t9.exon1 12370737 12370781
chr_3 g1669 g1669.t9 cds g1669.t9.CDS1 12370737 12370781
chr_3 g1669 g1669.t9 exon g1669.t9.exon2 12371165 12371401
chr_3 g1669 g1669.t9 cds g1669.t9.CDS2 12371165 12371401
chr_3 g1669 g1669.t9 exon g1669.t9.exon3 12371482 12371822
chr_3 g1669 g1669.t9 cds g1669.t9.CDS3 12371482 12371822
chr_3 g1669 g1669.t9 exon g1669.t9.exon4 12371888 12372521
chr_3 g1669 g1669.t9 cds g1669.t9.CDS4 12371888 12372521
chr_3 g1669 g1669.t9 exon g1669.t9.exon5 12372586 12372963
chr_3 g1669 g1669.t9 cds g1669.t9.CDS5 12372586 12372963
chr_3 g1669 g1669.t9 TTS g1669.t9 12373358 12373358

Sequences

>g1669.t9 Gene=g1669 Length=1635
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACGTTGCAAGAGTAGTC
GTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTCTCTGCACCAGCCAAAGGTGCT
GAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCCGCACCAAAAGCTGATTTGGAA
GAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCTCGTGTCTATGGTTTAAAGAAC
ATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTGAAGGGTATGGCTCTTAACTTG
GAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGATAAGCTCATTCGTGAAGGCGAT
ATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTCGGTGATGAGCTTTTGGGACGT
GTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGAGAAATCAAAACAAAACAACGT
TTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGTGTTTCTGTACGTGAGCCTATG
CAGACCGGTATTAAGGCCGTCGATTCATTGGTACCAATTGGTCGTGGTCAACGTGAATTG
ATTATTGGAGACAGACAGACTGGTAAAACTGCTTTGGCCATTGATACAATCATCAATCAA
AAGCGTTTCAATGATGGACAAGATGAATCAAAGAAATTGTACTGTATTTATGTTGCCATT
GGTCAAAAACGTTCAACTGTCGCTCAAATTGTCAAGCGTTTGAGTGATGCTGGTGCTATG
GATTATACCATCATTGTCTCAGCTACTGCTTCAGATGCTGCTCCATTGCAATATTTGGCA
CCATATTCTGGCTGTGCCATGGGTGAATACTTCCGTGACAATGGCAAACACGCTCTTATC
ATTTATGATGACTTGTCAAAACAAGCTGTTGCCTATCGTCAAATGTCACTGTTGTTGCGT
CGTCCACCAGGTCGTGAGGCCTATCCTGGTGATGTCTTCTATCTTCACAGCCGTTTGTTG
GAACGTGCTGCCAAAATGTCACCTGCTCATGGCGGTGGATCATTGACTGCCTTGCCAGTT
ATCGAAACACAAGCTGGTGATGTGTCAGCTTACATTCCCACAAATGTCATCTCAATTACT
GATGGTCAAATTTTCTTGGAAACTGAATTGTTCTACAAAGGTATTCGTCCAGCTATTAAC
GTCGGTTTGTCTGTCTCACGTGTAGGATCAGCTGCTCAAACCAGAGCCATGAAACAGGTC
GCCGGTTCAATGAAATTGGAACTTGCTCAGTATCGTGAGGTTGCTGCCTTCGCTCAATTC
GGTTCAGATCTCGATGCTGCCACACAACAACTTTTGAATCGTGGTGTTCGTTTGACAGAA
TTATTGAAACAAGGTCAATATGTACCAATGGCTATTGAAGAACAAGTTGCAGTCATTTAC
TGCGGTGTCCGCGGTCATTTGGATAAGATGGAACCATCAAAGATCACAGCATTCGAAAAA
GAGTTCTTGGCACACATCAAGACAAACGAAAAGGCATTGTTGCAACAAATTGCCAGCGAA
GGAAAGATCAGTGACGAAGTTGATGCTAAGCTTAAATCGATTGTAACCAGTTTCCTCTCG
ACATACAGCGGTTAA

>g1669.t9 Gene=g1669 Length=544
MSMLSARLAASVARNVARVVVPASQIAARKIHVSAPAKGAEISSILEERIMGAAPKADLE
ETGRVLSIGDGIARVYGLKNIQADEMVEFSSGLKGMALNLEPDNVGVVVFGNDKLIREGD
IVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEIKTKQRFRVGIKAPGIIPRVSVREPM
QTGIKAVDSLVPIGRGQRELIIGDRQTGKTALAIDTIINQKRFNDGQDESKKLYCIYVAI
GQKRSTVAQIVKRLSDAGAMDYTIIVSATASDAAPLQYLAPYSGCAMGEYFRDNGKHALI
IYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSPAHGGGSLTALPV
IETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQV
AGSMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIY
CGVRGHLDKMEPSKITAFEKEFLAHIKTNEKALLQQIASEGKISDEVDAKLKSIVTSFLS
TYSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g1669.t9 CDD cd18116 ATP-synt_F1_alpha_N 61 127 4.42406E-36
21 g1669.t9 CDD cd01132 F1_ATPase_alpha 128 409 0.0
20 g1669.t9 CDD cd18113 ATP-synt_F1_alpha_C 417 542 1.62026E-67
12 g1669.t9 Gene3D G3DSA:2.40.30.20 - 36 127 4.8E-40
10 g1669.t9 Gene3D G3DSA:3.40.50.300 - 128 413 3.5E-134
11 g1669.t9 Gene3D G3DSA:1.20.150.20 - 414 543 1.3E-60
6 g1669.t9 Hamap MF_01346 ATP synthase subunit alpha [atpA]. 35 543 50.141045
4 g1669.t9 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 37 542 0.0
5 g1669.t9 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 37 542 0.0
18 g1669.t9 PIRSF PIRSF039088 F_ATPase_subunit_alpha 35 544 7.0E-284
1 g1669.t9 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 60 126 2.2E-18
3 g1669.t9 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 183 406 5.5E-72
2 g1669.t9 Pfam PF00306 ATP synthase alpha/beta chain, C terminal domain 413 538 1.4E-47
14 g1669.t9 Phobius SIGNAL_PEPTIDE Signal peptide region 1 18 -
15 g1669.t9 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
16 g1669.t9 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 13 -
17 g1669.t9 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 14 18 -
13 g1669.t9 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 19 544 -
22 g1669.t9 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 397 406 -
7 g1669.t9 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 44 128 9.16E-28
8 g1669.t9 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 130 412 6.79E-103
9 g1669.t9 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 415 542 1.96E-45
23 g1669.t9 TIGRFAM TIGR00962 atpA: ATP synthase F1, alpha subunit 39 542 2.8E-245

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. There were no conditions that were differentially expressed