General information for g1669.t13
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.t13 | TSS | g1669.t13 | 12370666 | 12370666 |
| chr_3 | g1669 | g1669.t13 | isoform | g1669.t13 | 12370737 | 12373382 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon1 | 12370737 | 12370802 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon2 | 12371165 | 12371401 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon3 | 12371482 | 12371689 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon4 | 12371743 | 12371822 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon5 | 12371888 | 12372521 |
| chr_3 | g1669 | g1669.t13 | cds | g1669.t13.CDS1 | 12372042 | 12372521 |
| chr_3 | g1669 | g1669.t13 | exon | g1669.t13.exon6 | 12372586 | 12373382 |
| chr_3 | g1669 | g1669.t13 | cds | g1669.t13.CDS2 | 12372586 | 12372963 |
| chr_3 | g1669 | g1669.t13 | TTS | g1669.t13 | 12373358 | 12373358 |
Sequences
>g1669.t13 Gene=g1669 Length=2022
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCATGTC
TCTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGGCGCC
GCACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTATTGCT
CGTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGGCTTG
AAGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAATGAT
AAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCCAGTC
GGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGA
GAAATCAAAACAAAACAACGTTTCCGTGTCGACCGGTATTAAGGCCGTCGATTCATTGGT
ACCAATTGGTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGACTGGTAAAACTGC
TTTGGCCATTGATACAATCATCAATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAA
GAAATTGTACTGTATTTATGTTGCCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGT
CAAGCGTTTGAGTGATGCTGGTGCTATGGATTATACCATCATTGTCTCAGCTACTGCTTC
AGATGCTGCTCCATTGCAATATTTGGCACCATATTCTGGCTGTGCCATGGGTGAATACTT
CCGTGACAATGGCAAACACGCTCTTATCATTTATGATGACTTGTCAAAACAAGCTGTTGC
CTATCGTCAAATGTCACTGTTGTTGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGA
TGTCTTCTATCTTCACAGCCGTTTGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGG
CGGTGGATCATTGACTGCCTTGCCAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTA
CATTCCCACAAATGTCATCTCAATTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTT
CTACAAAGGTATTCGTCCAGCTATTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGC
TGCTCAAACCAGAGCCATGAAACAGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTA
TCGTGAGGTTGCTGCCTTCGCTCAATTCGGTTCAGATCTCGATGCTGCCACACAACAACT
TTTGAATCGTGGTGTTCGTTTGACAGAATTATTGAAACAAGGTCAATATGTACCAATGGC
TATTGAAGAACAAGTTGCAGTCATTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGA
ACCATCAAAGATCACAGCATTCGAAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAA
GGCATTGTTGCAACAAATTGCCAGCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCT
TAAATCGATTGTAACCAGTTTCCTCTCGACATACAGCGGTTAAATTAATCGCAATTAAGT
GCTTAGTTTTGCAAAAACATAAAACATTAAAAATTATCTAAAAAAGTAATAATTCTGTTT
TTTTGTCATAGTTGGTTAAGAGAAGAAAAGTGAAAAAAATATTAAGGGAGGATAAAAACA
ATTTCACATCTATAAGCGGATACGAAAGGATAACTGATTTAAAAAAATATATTTCCACCT
TTAAACAAAACTTCAAAGAAAATCCCAAGAAAATTTAAATGTATTCACACAAAACATGAG
TAAGAATTAATTAGAGGAATGATTACACACATACACGACACAGTAAAAGAAAAAATTCTC
AAGCGAACACGAACATGATTTTTCTTTTTGCGATTTACATCTTGAAAATGGAAGGAATAA
AATTATCAATAAAAATTTAAATATAAAAGTTCTTTTATTTAT
>g1669.t13 Gene=g1669 Length=285
MDYTIIVSATASDAAPLQYLAPYSGCAMGEYFRDNGKHALIIYDDLSKQAVAYRQMSLLL
RRPPGREAYPGDVFYLHSRLLERAAKMSPAHGGGSLTALPVIETQAGDVSAYIPTNVISI
TDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGSMKLELAQYREVAAFAQ
FGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVRGHLDKMEPSKITAFE
KEFLAHIKTNEKALLQQIASEGKISDEVDAKLKSIVTSFLSTYSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1669.t13 | CDD | cd18113 | ATP-synt_F1_alpha_C | 158 | 283 | 2.60498E-70 |
| 8 | g1669.t13 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 154 | 5.4E-73 |
| 9 | g1669.t13 | Gene3D | G3DSA:1.20.150.20 | - | 155 | 284 | 3.4E-61 |
| 3 | g1669.t13 | PANTHER | PTHR48082:SF3 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 1 | 283 | 1.5E-175 |
| 4 | g1669.t13 | PANTHER | PTHR48082 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 1 | 283 | 1.5E-175 |
| 2 | g1669.t13 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 1 | 147 | 9.8E-51 |
| 1 | g1669.t13 | Pfam | PF00306 | ATP synthase alpha/beta chain, C terminal domain | 154 | 279 | 3.7E-48 |
| 7 | g1669.t13 | ProSitePatterns | PS00152 | ATP synthase alpha and beta subunits signature. | 138 | 147 | - |
| 5 | g1669.t13 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 153 | 6.28E-56 |
| 6 | g1669.t13 | SUPERFAMILY | SSF47917 | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 156 | 283 | 4.45E-46 |
| 10 | g1669.t13 | TIGRFAM | TIGR00962 | atpA: ATP synthase F1, alpha subunit | 1 | 283 | 1.9E-146 |
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:0045261 | proton-transporting ATP synthase complex, catalytic core F(1) | CC |
| GO:0015986 | ATP synthesis coupled proton transport | BP |
| GO:0005524 | ATP 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.
