General information for g1669.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as ATP synthase subunit alpha, mitochondrial.
Parent gene
- The parent gene g1669 is located on chr_3: 12372583..12373382 (+ strand)
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.t1 | TSS | g1669.t1 | 12370666 | 12370666 |
| chr_3 | g1669 | g1669.t1 | isoform | g1669.t1 | 12370737 | 12372963 |
| chr_3 | g1669 | g1669.t1 | exon | g1669.t1.exon1 | 12370737 | 12370802 |
| chr_3 | g1669 | g1669.t1 | cds | g1669.t1.CDS1 | 12370737 | 12370802 |
| chr_3 | g1669 | g1669.t1 | exon | g1669.t1.exon2 | 12371165 | 12371401 |
| chr_3 | g1669 | g1669.t1 | cds | g1669.t1.CDS2 | 12371165 | 12371401 |
| chr_3 | g1669 | g1669.t1 | exon | g1669.t1.exon3 | 12371482 | 12371822 |
| chr_3 | g1669 | g1669.t1 | cds | g1669.t1.CDS3 | 12371482 | 12371822 |
| chr_3 | g1669 | g1669.t1 | exon | g1669.t1.exon4 | 12371888 | 12372521 |
| chr_3 | g1669 | g1669.t1 | cds | g1669.t1.CDS4 | 12371888 | 12372521 |
| chr_3 | g1669 | g1669.t1 | exon | g1669.t1.exon5 | 12372586 | 12372963 |
| chr_3 | g1669 | g1669.t1 | cds | g1669.t1.CDS5 | 12372586 | 12372963 |
| chr_3 | g1669 | g1669.t1 | TTS | g1669.t1 | 12373358 | 12373358 |
Sequences
>g1669.t1 Gene=g1669 Length=1656
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
ATTGTAACCAGTTTCCTCTCGACATACAGCGGTTAA
>g1669.t1 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.t1 | CDD | cd18116 | ATP-synt_F1_alpha_N | 68 | 134 | 5.12115E-36 |
| 21 | g1669.t1 | CDD | cd01132 | F1_ATPase_alpha | 135 | 416 | 0.0 |
| 20 | g1669.t1 | CDD | cd18113 | ATP-synt_F1_alpha_C | 424 | 549 | 1.68662E-67 |
| 12 | g1669.t1 | Gene3D | G3DSA:2.40.30.20 | - | 43 | 134 | 4.9E-40 |
| 10 | g1669.t1 | Gene3D | G3DSA:3.40.50.300 | - | 135 | 420 | 3.6E-134 |
| 11 | g1669.t1 | Gene3D | G3DSA:1.20.150.20 | - | 421 | 550 | 1.3E-60 |
| 6 | g1669.t1 | Hamap | MF_01346 | ATP synthase subunit alpha [atpA]. | 42 | 550 | 50.141045 |
| 4 | g1669.t1 | PANTHER | PTHR48082:SF3 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 44 | 549 | 0.0 |
| 5 | g1669.t1 | PANTHER | PTHR48082 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 44 | 549 | 0.0 |
| 18 | g1669.t1 | PIRSF | PIRSF039088 | F_ATPase_subunit_alpha | 42 | 551 | 7.3E-284 |
| 1 | g1669.t1 | Pfam | PF02874 | ATP synthase alpha/beta family, beta-barrel domain | 67 | 133 | 2.2E-18 |
| 3 | g1669.t1 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 190 | 413 | 5.6E-72 |
| 2 | g1669.t1 | Pfam | PF00306 | ATP synthase alpha/beta chain, C terminal domain | 420 | 545 | 1.4E-47 |
| 14 | g1669.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 20 | - |
| 15 | g1669.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 3 | - |
| 16 | g1669.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 4 | 12 | - |
| 17 | g1669.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 13 | 20 | - |
| 13 | g1669.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 21 | 551 | - |
| 22 | g1669.t1 | ProSitePatterns | PS00152 | ATP synthase alpha and beta subunits signature. | 404 | 413 | - |
| 7 | g1669.t1 | SUPERFAMILY | SSF50615 | N-terminal domain of alpha and beta subunits of F1 ATP synthase | 51 | 135 | 9.42E-28 |
| 8 | g1669.t1 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 137 | 419 | 7.09E-103 |
| 9 | g1669.t1 | SUPERFAMILY | SSF47917 | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 422 | 549 | 2.01E-45 |
| 23 | g1669.t1 | 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
- This transcript has been annotated with K02132 (F-type H+-transporting ATPase subunit alpha)
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.
