General information for g5732.t30
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative ATP synthase subunit b, mitochondrial.
Parent gene
- The parent gene g5732 is located on chr_2: 11446662..11447330 (- 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_2 | g5732 | g5732.t30 | TTS | g5732.t30 | 11445921 | 11445921 |
| chr_2 | g5732 | g5732.t30 | isoform | g5732.t30 | 11446662 | 11447330 |
| chr_2 | g5732 | g5732.t30 | exon | g5732.t30.exon1 | 11446662 | 11446861 |
| chr_2 | g5732 | g5732.t30 | cds | g5732.t30.CDS1 | 11446663 | 11446861 |
| chr_2 | g5732 | g5732.t30 | exon | g5732.t30.exon2 | 11446929 | 11447052 |
| chr_2 | g5732 | g5732.t30 | cds | g5732.t30.CDS2 | 11446929 | 11447052 |
| chr_2 | g5732 | g5732.t30 | exon | g5732.t30.exon3 | 11447300 | 11447330 |
| chr_2 | g5732 | g5732.t30 | cds | g5732.t30.CDS3 | 11447300 | 11447330 |
| chr_2 | g5732 | g5732.t30 | TSS | g5732.t30 | 11447399 | 11447399 |
Sequences
>g5732.t30 Gene=g5732 Length=355
ATGCTTTCTCGCGCGGCTTTGTTGTCTACAGCCCAAAAGACGTCAGTCATGGCGCTTGCA
ACAAGAGGATCAGCCTCATCAACACCAGGCTTTGAACGACCAGTTCGTCTTGAACATCCT
GGCAAAGTCCGCATGGGATTCATTCCTGATGAATGGTTTAAATTCTTTTATCCAAAAACA
GGTGTCACTGGTCCCTATGTATTCTTAGCTGGTCTCTCAACATACTTGTTTTCAAAGGAA
ATCTATGTTATGGAGCACGAATACTATACTGGACTTTCAATTCTTATTGCTGTCGTTTAT
GCCACGAAGAAATTTGGTCCATCAGTCGCTAAATCACTCGATAAAGAAGTCGATG
>g5732.t30 Gene=g5732 Length=118
MLSRAALLSTAQKTSVMALATRGSASSTPGFERPVRLEHPGKVRMGFIPDEWFKFFYPKT
GVTGPYVFLAGLSTYLFSKEIYVMEHEYYTGLSILIAVVYATKKFGPSVAKSLDKEVD
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 2 | g5732.t30 | PANTHER | PTHR12733:SF3 | ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL | 1 | 117 | 4.8E-38 |
| 3 | g5732.t30 | PANTHER | PTHR12733 | MITOCHONDRIAL ATP SYNTHASE B CHAIN | 1 | 117 | 4.8E-38 |
| 1 | g5732.t30 | Pfam | PF05405 | Mitochondrial ATP synthase B chain precursor (ATP-synt_B) | 73 | 118 | 7.8E-11 |
| 6 | g5732.t30 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 25 | - |
| 7 | g5732.t30 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 4 | - |
| 8 | g5732.t30 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 5 | 16 | - |
| 9 | g5732.t30 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 17 | 25 | - |
| 5 | g5732.t30 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 26 | 118 | - |
| 4 | g5732.t30 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 20 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5732/g5732.t30; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5732.t30.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0015986 | ATP synthesis coupled proton transport | BP |
| GO:0000276 | mitochondrial proton-transporting ATP synthase complex, coupling factor F(o) | CC |
| GO:0015078 | proton transmembrane transporter activity | 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.
