General information for g1669.t16
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.t16 | TSS | g1669.t16 | 12370666 | 12370666 |
| chr_3 | g1669 | g1669.t16 | isoform | g1669.t16 | 12371599 | 12372963 |
| chr_3 | g1669 | g1669.t16 | exon | g1669.t16.exon1 | 12371599 | 12371807 |
| chr_3 | g1669 | g1669.t16 | cds | g1669.t16.CDS1 | 12371737 | 12371807 |
| chr_3 | g1669 | g1669.t16 | exon | g1669.t16.exon2 | 12371888 | 12372521 |
| chr_3 | g1669 | g1669.t16 | cds | g1669.t16.CDS2 | 12371888 | 12372521 |
| chr_3 | g1669 | g1669.t16 | exon | g1669.t16.exon3 | 12372586 | 12372963 |
| chr_3 | g1669 | g1669.t16 | cds | g1669.t16.CDS3 | 12372586 | 12372963 |
| chr_3 | g1669 | g1669.t16 | TTS | g1669.t16 | 12373358 | 12373358 |
Sequences
>g1669.t16 Gene=g1669 Length=1221
GGTGATGAGCTTTTGGGACGTGTCGTTGATGCTTTGGGTAACACAATTGATGGAAAGGGA
GAAATCAAAACAAAACAACGTTTCCGTGTCGGTATTAAGGCTCCAGGTATTATTCCACGT
GTTTCTGTACGTGAGCCTATGCAGACCGGTATTAAGGCCGTCGATTCATTGGTACCAATT
GGTCGTGGTCAACGTGAATTGATTATTGGTAAAACTGCTTTGGCCATTGATACAATCATC
AATCAAAAGCGTTTCAATGATGGACAAGATGAATCAAAGAAATTGTACTGTATTTATGTT
GCCATTGGTCAAAAACGTTCAACTGTCGCTCAAATTGTCAAGCGTTTGAGTGATGCTGGT
GCTATGGATTATACCATCATTGTCTCAGCTACTGCTTCAGATGCTGCTCCATTGCAATAT
TTGGCACCATATTCTGGCTGTGCCATGGGTGAATACTTCCGTGACAATGGCAAACACGCT
CTTATCATTTATGATGACTTGTCAAAACAAGCTGTTGCCTATCGTCAAATGTCACTGTTG
TTGCGTCGTCCACCAGGTCGTGAGGCCTATCCTGGTGATGTCTTCTATCTTCACAGCCGT
TTGTTGGAACGTGCTGCCAAAATGTCACCTGCTCATGGCGGTGGATCATTGACTGCCTTG
CCAGTTATCGAAACACAAGCTGGTGATGTGTCAGCTTACATTCCCACAAATGTCATCTCA
ATTACTGATGGTCAAATTTTCTTGGAAACTGAATTGTTCTACAAAGGTATTCGTCCAGCT
ATTAACGTCGGTTTGTCTGTCTCACGTGTAGGATCAGCTGCTCAAACCAGAGCCATGAAA
CAGGTCGCCGGTTCAATGAAATTGGAACTTGCTCAGTATCGTGAGGTTGCTGCCTTCGCT
CAATTCGGTTCAGATCTCGATGCTGCCACACAACAACTTTTGAATCGTGGTGTTCGTTTG
ACAGAATTATTGAAACAAGGTCAATATGTACCAATGGCTATTGAAGAACAAGTTGCAGTC
ATTTACTGCGGTGTCCGCGGTCATTTGGATAAGATGGAACCATCAAAGATCACAGCATTC
GAAAAAGAGTTCTTGGCACACATCAAGACAAACGAAAAGGCATTGTTGCAACAAATTGCC
AGCGAAGGAAAGATCAGTGACGAAGTTGATGCTAAGCTTAAATCGATTGTAACCAGTTTC
CTCTCGACATACAGCGGTTAA
>g1669.t16 Gene=g1669 Length=360
MQTGIKAVDSLVPIGRGQRELIIGKTALAIDTIINQKRFNDGQDESKKLYCIYVAIGQKR
STVAQIVKRLSDAGAMDYTIIVSATASDAAPLQYLAPYSGCAMGEYFRDNGKHALIIYDD
LSKQAVAYRQMSLLLRRPPGREAYPGDVFYLHSRLLERAAKMSPAHGGGSLTALPVIETQ
AGDVSAYIPTNVISITDGQIFLETELFYKGIRPAINVGLSVSRVGSAAQTRAMKQVAGSM
KLELAQYREVAAFAQFGSDLDAATQQLLNRGVRLTELLKQGQYVPMAIEEQVAVIYCGVR
GHLDKMEPSKITAFEKEFLAHIKTNEKALLQQIASEGKISDEVDAKLKSIVTSFLSTYSG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 11 | g1669.t16 | CDD | cd18113 | ATP-synt_F1_alpha_C | 233 | 358 | 5.27522E-69 |
| 8 | g1669.t16 | Gene3D | G3DSA:3.40.50.300 | - | 1 | 229 | 8.9E-107 |
| 9 | g1669.t16 | Gene3D | G3DSA:1.20.150.20 | - | 230 | 359 | 5.8E-61 |
| 3 | g1669.t16 | PANTHER | PTHR48082:SF3 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 1 | 358 | 7.1E-223 |
| 4 | g1669.t16 | PANTHER | PTHR48082 | ATP SYNTHASE SUBUNIT ALPHA, MITOCHONDRIAL | 1 | 358 | 7.1E-223 |
| 2 | g1669.t16 | Pfam | PF00006 | ATP synthase alpha/beta family, nucleotide-binding domain | 4 | 222 | 3.9E-68 |
| 1 | g1669.t16 | Pfam | PF00306 | ATP synthase alpha/beta chain, C terminal domain | 229 | 354 | 6.2E-48 |
| 7 | g1669.t16 | ProSitePatterns | PS00152 | ATP synthase alpha and beta subunits signature. | 213 | 222 | - |
| 5 | g1669.t16 | SUPERFAMILY | SSF52540 | P-loop containing nucleoside triphosphate hydrolases | 1 | 228 | 8.69E-82 |
| 6 | g1669.t16 | SUPERFAMILY | SSF47917 | C-terminal domain of alpha and beta subunits of F1 ATP synthase | 231 | 358 | 7.59E-46 |
| 10 | g1669.t16 | TIGRFAM | TIGR00962 | atpA: ATP synthase F1, alpha subunit | 1 | 358 | 3.1E-182 |
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.
