General information for g5732.t20
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t20 | TTS | g5732.t20 | 11445921 | 11445921 |
| chr_2 | g5732 | g5732.t20 | isoform | g5732.t20 | 11446010 | 11447330 |
| chr_2 | g5732 | g5732.t20 | exon | g5732.t20.exon1 | 11446010 | 11446177 |
| chr_2 | g5732 | g5732.t20 | cds | g5732.t20.CDS1 | 11446158 | 11446177 |
| chr_2 | g5732 | g5732.t20 | exon | g5732.t20.exon2 | 11446243 | 11446603 |
| chr_2 | g5732 | g5732.t20 | cds | g5732.t20.CDS2 | 11446243 | 11446603 |
| chr_2 | g5732 | g5732.t20 | exon | g5732.t20.exon3 | 11446663 | 11446861 |
| chr_2 | g5732 | g5732.t20 | cds | g5732.t20.CDS3 | 11446663 | 11446861 |
| chr_2 | g5732 | g5732.t20 | exon | g5732.t20.exon4 | 11446929 | 11447330 |
| chr_2 | g5732 | g5732.t20 | cds | g5732.t20.CDS4 | 11446929 | 11447035 |
| chr_2 | g5732 | g5732.t20 | TSS | g5732.t20 | 11447399 | 11447399 |
Sequences
>g5732.t20 Gene=g5732 Length=1130
ATGCTTTCTCGCGCGGCTTTGTTGTCTACAGGTGAGTTACATTCAGTGTTATTTAGGAAA
CCATGAATCTACAAGCGAGGAGTTTTTAAAATTAATATTTTTTGCTATTTTTTCATGTCA
TAACACGCTAACCAACATCCATATTGCATAACAATCAAAAACTCTAATTAAAGTTCTTAA
ATTAAGGATGTTTAACTTAATAAAATATACAGCTTATTCATTCGACATCTCTTGATAATA
TAAAGTATAAATTTTTAATTGTAATGATATGTTTATAGCCCAAAAGACGTCAGTCATGGC
GCTTGCAACAAGAGGATCAGCCTCATCAACACCAGGCTTTGAACGACCAGTTCGTCTTGA
ACATCCTGGCAAAGTCCGCATGGGATTCATTCCTGATGAATGGTTTAAATTCTTTTATCC
AAAAACAGGTGTCACTGGTCCCTATGTATTCTTAGCTGGTCTCTCAACATACTTGTTTTC
AAAGGAAATCTATGTTATGGAGCACGAATACTATACTGGACTTTCAATTCTTATTGCTGT
CGTTTATGCCACGAAGAAATTTGGTCCATCAGTCGCTAAATCACTCGATAAAGAAGTCGA
TGCTGTTGAAGAAGAATGGAATCAAGGACGCACTGATGAAATTAAAAGTTTAAATGAAGC
CATTGAAGAAGAAAAGAAGGAACAGTGGAGAGCAGAAGGTCAAATGATGCTTATTGATGC
AAAGAAAGAAAATGTTGCACTTCAGCTTGAAGCTGCCTATCGCGAACGTGCTATGCAAGT
CTACCGTGAAGTCAAGAAACGATTGGATTATCAAGTTGAACGTCAAAATATCGATCGTCG
TATTTCACAGAAACATATGGCTCAATGGATAGTCAACAATGTCTTGAAATCTATTACACC
AGATCAAGAAGCACAGACACTCAGTAAATGCATTGCTGATTTGGGTGGATTAGCAGCAGC
TCTGAGAAAGTTCCCGTTATGATAAAAAGTTGTCTCTGAAAAAAAATCTTAACCAACATT
TTTAACGACTTGAATTGTATAAAAAATTGTTTTTCTCCAATTTTCCATCAACAGCATCTA
TTAAAAGTGATTGTCGCGACAAGAAATTGCCACCCAAACGCAAATGTTAA
>g5732.t20 Gene=g5732 Length=228
MALATRGSASSTPGFERPVRLEHPGKVRMGFIPDEWFKFFYPKTGVTGPYVFLAGLSTYL
FSKEIYVMEHEYYTGLSILIAVVYATKKFGPSVAKSLDKEVDAVEEEWNQGRTDEIKSLN
EAIEEEKKEQWRAEGQMMLIDAKKENVALQLEAAYRERAMQVYREVKKRLDYQVERQNID
RRISQKHMAQWIVNNVLKSITPDQEAQTLSKCIADLGGLAAALRKFPL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5732.t20 | Coils | Coil | Coil | 109 | 136 | - |
| 2 | g5732.t20 | PANTHER | PTHR12733:SF3 | ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL | 11 | 222 | 7.6E-90 |
| 3 | g5732.t20 | PANTHER | PTHR12733 | MITOCHONDRIAL ATP SYNTHASE B CHAIN | 11 | 222 | 7.6E-90 |
| 1 | g5732.t20 | Pfam | PF05405 | Mitochondrial ATP synthase B chain precursor (ATP-synt_B) | 57 | 216 | 4.2E-53 |
| 4 | g5732.t20 | SUPERFAMILY | SSF161060 | ATP synthase B chain-like | 95 | 198 | 1.96E-36 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5732/g5732.t20; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5732.t20.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 transcript has been annotated with K02127 (F-type H+-transporting ATPase subunit b)
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. There were no conditions that were differentially expressed