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.t12 TSS g1669.t12 12370666 12370666
chr_3 g1669 g1669.t12 isoform g1669.t12 12370737 12373382
chr_3 g1669 g1669.t12 exon g1669.t12.exon1 12370737 12370802
chr_3 g1669 g1669.t12 cds g1669.t12.CDS1 12370737 12370802
chr_3 g1669 g1669.t12 exon g1669.t12.exon2 12371165 12371401
chr_3 g1669 g1669.t12 cds g1669.t12.CDS2 12371165 12371401
chr_3 g1669 g1669.t12 exon g1669.t12.exon3 12371482 12371822
chr_3 g1669 g1669.t12 cds g1669.t12.CDS3 12371482 12371822
chr_3 g1669 g1669.t12 exon g1669.t12.exon4 12371888 12372521
chr_3 g1669 g1669.t12 cds g1669.t12.CDS4 12371888 12372521
chr_3 g1669 g1669.t12 exon g1669.t12.exon5 12372586 12372978
chr_3 g1669 g1669.t12 cds g1669.t12.CDS5 12372586 12372963
chr_3 g1669 g1669.t12 exon g1669.t12.exon6 12373221 12373382
chr_3 g1669 g1669.t12 TTS g1669.t12 12373358 12373358

Sequences

>g1669.t12 Gene=g1669 Length=1833
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTC
TCTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCC
GCACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCT
CGTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTG
AAGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGAT
AAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTC
GGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGA
GAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGT
GTTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGTACCAATT
GGTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGACTGGTAAAACTGCTTTGGCC
ATTGATACAATCATCAATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAAGAAATTG
TACTGTATTTATGTTGCCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGTCAAGCGT
TTGAGTGATGCTGGTGCTATGGATTATACCATCATTGTCTCAGCTACTGCTTCAGATGCT
GCTCCATTGCAATATTTGGCACCATATTCTGGCTGTGCCATGGGTGAATACTTCCGTGAC
AATGGCAAACACGCTCTTATCATTTATGATGACTTGTCAAAACAAGCTGTTGCCTATCGT
CAAATGTCACTGTTGTTGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGATGTCTTC
TATCTTCACAGCCGTTTGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGGCGGTGGA
TCATTGACTGCCTTGCCAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTACATTCCC
ACAAATGTCATCTCAATTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTTCTACAAA
GGTATTCGTCCAGCTATTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGCTGCTCAA
ACCAGAGCCATGAAACAGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTATCGTGAG
GTTGCTGCCTTCGCTCAATTCGGTTCAGATCTCGATGCTGCCACACAACAACTTTTGAAT
CGTGGTGTTCGTTTGACAGAATTATTGAAACAAGGTCAATATGTACCAATGGCTATTGAA
GAACAAGTTGCAGTCATTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGAACCATCA
AAGATCACAGCATTCGAAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAAGGCATTG
TTGCAACAAATTGCCAGCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCTTAAATCG
ATTGTAACCAGTTTCCTCTCGACATACAGCGGTTAAATTAATCGCAATTAATAAGAATTA
ATTAGAGGAATGATTACACACATACACGACACAGTAAAAGAAAAAATTCTCAAGCGAACA
CGAACATGATTTTTCTTTTTGCGATTTACATCTTGAAAATGGAAGGAATAAAATTATCAA
TAAAAATTTAAATATAAAAGTTCTTTTATTTAT

>g1669.t12 Gene=g1669 Length=551
MSMLSARLAASVARNLPRSAQQVARVVVPASQIAARKIHVSAPAKGAEISSILEERIMGA
APKADLEETGRVLSIGDGIARVYGLKNIQADEMVEFSSGLKGMALNLEPDNVGVVVFGND
KLIREGDIVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEIKTKQRFRVGIKAPGIIPR
VSVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKTALAIDTIINQKRFNDGQDESKKL
YCIYVAIGQKRSTVAQIVKRLSDAGAMDYTIIVSATASDAAPLQYLAPYSGCAMGEYFRD
NGKHALIIYDDLSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSPAHGGG
SLTALPVIETQAGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQ
TRAMKQVAGSMKLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIE
EQVAVIYCGVRGHLDKMEPSKITAFEKEFLAHIKTNEKALLQQIASEGKISDEVDAKLKS
IVTSFLSTYSG

Protein features from InterProScan

Transcript Database ID Name Start End E.value
19 g1669.t12 CDD cd18116 ATP-synt_F1_alpha_N 68 134 5.12115E-36
21 g1669.t12 CDD cd01132 F1_ATPase_alpha 135 416 0.0
20 g1669.t12 CDD cd18113 ATP-synt_F1_alpha_C 424 549 1.68662E-67
12 g1669.t12 Gene3D G3DSA:2.40.30.20 - 43 134 4.9E-40
10 g1669.t12 Gene3D G3DSA:3.40.50.300 - 135 420 3.6E-134
11 g1669.t12 Gene3D G3DSA:1.20.150.20 - 421 550 1.3E-60
6 g1669.t12 Hamap MF_01346 ATP synthase subunit alpha [atpA]. 42 550 50.141045
4 g1669.t12 PANTHER PTHR48082:SF3 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 44 549 0.0
5 g1669.t12 PANTHER PTHR48082 ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL 44 549 0.0
18 g1669.t12 PIRSF PIRSF039088 F_ATPase_subunit_alpha 42 551 7.3E-284
1 g1669.t12 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 67 133 2.2E-18
3 g1669.t12 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 190 413 5.6E-72
2 g1669.t12 Pfam PF00306 ATP synthase alpha/beta chain, C terminal domain 420 545 1.4E-47
14 g1669.t12 Phobius SIGNAL_PEPTIDE Signal peptide region 1 20 -
15 g1669.t12 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 3 -
16 g1669.t12 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 4 12 -
17 g1669.t12 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 13 20 -
13 g1669.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 21 551 -
22 g1669.t12 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 404 413 -
7 g1669.t12 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 51 135 9.42E-28
8 g1669.t12 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 137 419 7.09E-103
9 g1669.t12 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 422 549 2.01E-45
23 g1669.t12 TIGRFAM TIGR00962 atpA: ATP synthase F1, alpha subunit 46 549 2.9E-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.

Raw TPM values