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.t4 TTS g5732.t4 11445921 11445921
chr_2 g5732 g5732.t4 isoform g5732.t4 11446010 11447051
chr_2 g5732 g5732.t4 exon g5732.t4.exon1 11446010 11446603
chr_2 g5732 g5732.t4 cds g5732.t4.CDS1 11446235 11446603
chr_2 g5732 g5732.t4 exon g5732.t4.exon2 11446669 11446861
chr_2 g5732 g5732.t4 cds g5732.t4.CDS2 11446669 11446861
chr_2 g5732 g5732.t4 exon g5732.t4.exon3 11446929 11447051
chr_2 g5732 g5732.t4 cds g5732.t4.CDS3 11446929 11447035
chr_2 g5732 g5732.t4 TSS g5732.t4 11447399 11447399

Sequences

>g5732.t4 Gene=g5732 Length=910
CCAAAAGACGTCAGTCATGGCGCTTGCAACAAGAGGATCAGCCTCATCAACACCAGGCTT
TGAACGACCAGTTCGTCTTGAACATCCTGGCAAAGTCCGCATGGGATTCATTCCTGATGA
ATGGTTTAAATTCTTTTATCCAAAAACAGGTGTCACTGGTCCCTATGTATTCTTAGCTGG
TCTCTCAACATACTTGTTTTCAAAGGAAATCTATGTTATGGAGCACGAATACTATACTGG
ACTTTCAATTCTTATTGCTGTCGTTTATGCCACGAAGAAATTTGGTCCATCAGTCGCTAA
ATCACTCGATAAAGAAGCTGTTGAAGAAGAATGGAATCAAGGACGCACTGATGAAATTAA
AAGTTTAAATGAAGCCATTGAAGAAGAAAAGAAGGAACAGTGGAGAGCAGAAGGTCAAAT
GATGCTTATTGATGCAAAGAAAGAAAATGTTGCACTTCAGCTTGAAGCTGCCTATCGCGA
ACGTGCTATGCAAGTCTACCGTGAAGTCAAGAAACGATTGGATTATCAAGTTGAACGTCA
AAATATCGATCGTCGTATTTCACAGAAACATATGGCTCAATGGATAGTCAACAATGTCTT
GAAATCTATTACACCAGATCAAGAAGCACAGACACTCAGTAAATGCATTGCTGATTTGGG
TGGATTAGCAGCAGCTCGTAAGTAAATTTTTCGCGTGTCTTCGACATATTCCAACAGCAA
TTATTAAACAACAACACTATAGTGAGAAAGTTCCCGTTATGATAAAAAGTTGTCTCTGAA
AAAAAATCTTAACCAACATTTTTAACGACTTGAATTGTATAAAAAATTGTTTTTCTCCAA
TTTTCCATCAACAGCATCTATTAAAAGTGATTGTCGCGACAAGAAATTGCCACCCAAACG
CAAATGTTAA

>g5732.t4 Gene=g5732 Length=222
MALATRGSASSTPGFERPVRLEHPGKVRMGFIPDEWFKFFYPKTGVTGPYVFLAGLSTYL
FSKEIYVMEHEYYTGLSILIAVVYATKKFGPSVAKSLDKEAVEEEWNQGRTDEIKSLNEA
IEEEKKEQWRAEGQMMLIDAKKENVALQLEAAYRERAMQVYREVKKRLDYQVERQNIDRR
ISQKHMAQWIVNNVLKSITPDQEAQTLSKCIADLGGLAAARK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5732.t4 Coils Coil Coil 107 134 -
2 g5732.t4 PANTHER PTHR12733:SF3 ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL 11 220 8.0E-88
3 g5732.t4 PANTHER PTHR12733 MITOCHONDRIAL ATP SYNTHASE B CHAIN 11 220 8.0E-88
1 g5732.t4 Pfam PF05405 Mitochondrial ATP synthase B chain precursor (ATP-synt_B) 57 214 6.3E-50
4 g5732.t4 SUPERFAMILY SSF161060 ATP synthase B chain-like 100 196 1.16E-34

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5732/g5732.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5732.t4.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