Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP synthase subunit b, mitochondrial.

Parent gene

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.t17 TTS g5732.t17 11445921 11445921
chr_2 g5732 g5732.t17 isoform g5732.t17 11446010 11447330
chr_2 g5732 g5732.t17 exon g5732.t17.exon1 11446010 11446603
chr_2 g5732 g5732.t17 cds g5732.t17.CDS1 11446235 11446603
chr_2 g5732 g5732.t17 exon g5732.t17.exon2 11446663 11446861
chr_2 g5732 g5732.t17 cds g5732.t17.CDS2 11446663 11446861
chr_2 g5732 g5732.t17 exon g5732.t17.exon3 11446929 11447052
chr_2 g5732 g5732.t17 cds g5732.t17.CDS3 11446929 11447035
chr_2 g5732 g5732.t17 exon g5732.t17.exon4 11447311 11447330
chr_2 g5732 g5732.t17 TSS g5732.t17 11447399 11447399

Sequences

>g5732.t17 Gene=g5732 Length=937
ATGCTTTCTCGCGCGGCTTTCCCAAAAGACGTCAGTCATGGCGCTTGCAACAAGAGGATC
AGCCTCATCAACACCAGGCTTTGAACGACCAGTTCGTCTTGAACATCCTGGCAAAGTCCG
CATGGGATTCATTCCTGATGAATGGTTTAAATTCTTTTATCCAAAAACAGGTGTCACTGG
TCCCTATGTATTCTTAGCTGGTCTCTCAACATACTTGTTTTCAAAGGAAATCTATGTTAT
GGAGCACGAATACTATACTGGACTTTCAATTCTTATTGCTGTCGTTTATGCCACGAAGAA
ATTTGGTCCATCAGTCGCTAAATCACTCGATAAAGAAGTCGATGCTGTTGAAGAAGAATG
GAATCAAGGACGCACTGATGAAATTAAAAGTTTAAATGAAGCCATTGAAGAAGAAAAGAA
GGAACAGTGGAGAGCAGAAGGTCAAATGATGCTTATTGATGCAAAGAAAGAAAATGTTGC
ACTTCAGCTTGAAGCTGCCTATCGCGAACGTGCTATGCAAGTCTACCGTGAAGTCAAGAA
ACGATTGGATTATCAAGTTGAACGTCAAAATATCGATCGTCGTATTTCACAGAAACATAT
GGCTCAATGGATAGTCAACAATGTCTTGAAATCTATTACACCAGATCAAGAAGCACAGAC
ACTCAGTAAATGCATTGCTGATTTGGGTGGATTAGCAGCAGCTCGTAAGTAAATTTTTCG
CGTGTCTTCGACATATTCCAACAGCAATTATTAAACAACAACACTATAGTGAGAAAGTTC
CCGTTATGATAAAAAGTTGTCTCTGAAAAAAAATCTTAACCAACATTTTTAACGACTTGA
ATTGTATAAAAAATTGTTTTTCTCCAATTTTCCATCAACAGCATCTATTAAAAGTGATTG
TCGCGACAAGAAATTGCCACCCAAACGCAAATGTTAA

>g5732.t17 Gene=g5732 Length=224
MALATRGSASSTPGFERPVRLEHPGKVRMGFIPDEWFKFFYPKTGVTGPYVFLAGLSTYL
FSKEIYVMEHEYYTGLSILIAVVYATKKFGPSVAKSLDKEVDAVEEEWNQGRTDEIKSLN
EAIEEEKKEQWRAEGQMMLIDAKKENVALQLEAAYRERAMQVYREVKKRLDYQVERQNID
RRISQKHMAQWIVNNVLKSITPDQEAQTLSKCIADLGGLAAARK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5732.t17 Coils Coil Coil 109 136 -
2 g5732.t17 PANTHER PTHR12733:SF3 ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL 11 222 5.8E-90
3 g5732.t17 PANTHER PTHR12733 MITOCHONDRIAL ATP SYNTHASE B CHAIN 11 222 5.8E-90
1 g5732.t17 Pfam PF05405 Mitochondrial ATP synthase B chain precursor (ATP-synt_B) 57 216 4.0E-53
4 g5732.t17 SUPERFAMILY SSF161060 ATP synthase B chain-like 95 198 1.83E-36

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5732/g5732.t17; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5732.t17.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

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