General information for g1669.t3
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.t3 | TSS | g1669.t3 | 12370666 | 12370666 |
| chr_3 | g1669 | g1669.t3 | isoform | g1669.t3 | 12370737 | 12371894 |
| chr_3 | g1669 | g1669.t3 | exon | g1669.t3.exon1 | 12370737 | 12370806 |
| chr_3 | g1669 | g1669.t3 | exon | g1669.t3.exon2 | 12371165 | 12371401 |
| chr_3 | g1669 | g1669.t3 | cds | g1669.t3.CDS1 | 12371270 | 12371401 |
| chr_3 | g1669 | g1669.t3 | exon | g1669.t3.exon3 | 12371482 | 12371822 |
| chr_3 | g1669 | g1669.t3 | cds | g1669.t3.CDS2 | 12371482 | 12371822 |
| chr_3 | g1669 | g1669.t3 | exon | g1669.t3.exon4 | 12371888 | 12371894 |
| chr_3 | g1669 | g1669.t3 | cds | g1669.t3.CDS3 | 12371888 | 12371894 |
| chr_3 | g1669 | g1669.t3 | TTS | g1669.t3 | NA | NA |
Sequences
>g1669.t3 Gene=g1669 Length=655
ATGTCGATGTTATCAGCACGTTTAGCTGCCTCGGTTGCTCGCAACCTTCCACGATCAGCA
CAACAGGTATGTTGCAAGAGTAGTCGTTCCAGCCTCACAGATTGCAGCTCGTAAAATTCA
TGTCTCTGCACCAGCCAAAGGTGCTGAAATCAGCTCAATTCTTGAGGAAAGAATCATGGG
CGCCGCACCAAAAGCTGATTTGGAAGAAACTGGACGTGTCTTGAGCATCGGTGACGGTAT
TGCTCGTGTCTATGGTTTAAAGAACATCCAAGCTGACGAGATGGTGGAGTTTTCATCAGG
CTTGAAGGGTATGGCTCTTAACTTGGAACCTGATAATGTTGGTGTTGTCGTATTCGGTAA
TGATAAGCTCATTCGTGAAGGCGATATCGTCAAGCGTACCGGTGCTATTGTCGATGTTCC
AGTCGGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAA
GGGAGAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCC
ACGTGTTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGTACC
AATTGGTCGTGGTCAACGTGAATTGATTATTGGAGACAGACAGACTGGTAAAACT
>g1669.t3 Gene=g1669 Length=160
MGAAPKADLEETGRVLSIGDGIARVYGLKNIQADEMVEFSSGLKGMALNLEPDNVGVVVF
GNDKLIREGDIVKRTGAIVDVPVGDELLGRVVDALGNTIDGKGEIKTKQRFRVGIKAPGI
IPRVSVREPMQTGIKAVDSLVPIGRGQRELIIGDRQTGKT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1669.t3 | CDD | cd18116 | ATP-synt_F1_alpha_N | 11 | 77 | 0 |
| 7 | g1669.t3 | Gene3D | G3DSA:2.40.30.20 | - | 8 | 77 | 0 |
| 6 | g1669.t3 | Gene3D | G3DSA:3.40.50.300 | - | 78 | 160 | 0 |
| 2 | g1669.t3 | PANTHER | PTHR48082:SF3 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 2 | 160 | 0 |
| 3 | g1669.t3 | PANTHER | PTHR48082 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 2 | 160 | 0 |
| 1 | g1669.t3 | Pfam | PF02874 | ATP synthase alpha/beta family, beta-barrel domain | 10 | 76 | 0 |
| 4 | g1669.t3 | SUPERFAMILY | SSF50615 | N-terminal domain of alpha and beta subunits of F1 ATP synthase | 6 | 78 | 0 |
| 5 | g1669.t3 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 80 | 160 | 0 |
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:1902600 | proton transmembrane transport | BP |
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. There were no conditions that were differentially expressed