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.t28 TTS g5732.t28 11445921 11445921
chr_2 g5732 g5732.t28 isoform g5732.t28 11446010 11447330
chr_2 g5732 g5732.t28 exon g5732.t28.exon1 11446010 11446603
chr_2 g5732 g5732.t28 cds g5732.t28.CDS1 11446235 11446603
chr_2 g5732 g5732.t28 exon g5732.t28.exon2 11446663 11446861
chr_2 g5732 g5732.t28 cds g5732.t28.CDS2 11446663 11446767
chr_2 g5732 g5732.t28 exon g5732.t28.exon3 11446943 11447052
chr_2 g5732 g5732.t28 exon g5732.t28.exon4 11447300 11447330
chr_2 g5732 g5732.t28 TSS g5732.t28 11447399 11447399

Sequences

>g5732.t28 Gene=g5732 Length=934
ATGCTTTCTCGCGCGGCTTTGTTGTCTACAGCCCAAAAGACGTCAGTCATGGCGCTTGCA
ACAAGAGGATCAGCCTCATCAACACCAGGCTTTGAACGACCAGTTCGTCTTGAACATCCT
GGCAAAGTCCGCATGGGATTCGTTTAAATTCTTTTATCCAAAAACAGGTGTCACTGGTCC
CTATGTATTCTTAGCTGGTCTCTCAACATACTTGTTTTCAAAGGAAATCTATGTTATGGA
GCACGAATACTATACTGGACTTTCAATTCTTATTGCTGTCGTTTATGCCACGAAGAAATT
TGGTCCATCAGTCGCTAAATCACTCGATAAAGAAGTCGATGCTGTTGAAGAAGAATGGAA
TCAAGGACGCACTGATGAAATTAAAAGTTTAAATGAAGCCATTGAAGAAGAAAAGAAGGA
ACAGTGGAGAGCAGAAGGTCAAATGATGCTTATTGATGCAAAGAAAGAAAATGTTGCACT
TCAGCTTGAAGCTGCCTATCGCGAACGTGCTATGCAAGTCTACCGTGAAGTCAAGAAACG
ATTGGATTATCAAGTTGAACGTCAAAATATCGATCGTCGTATTTCACAGAAACATATGGC
TCAATGGATAGTCAACAATGTCTTGAAATCTATTACACCAGATCAAGAAGCACAGACACT
CAGTAAATGCATTGCTGATTTGGGTGGATTAGCAGCAGCTCGTAAGTAAATTTTTCGCGT
GTCTTCGACATATTCCAACAGCAATTATTAAACAACAACACTATAGTGAGAAAGTTCCCG
TTATGATAAAAAGTTGTCTCTGAAAAAAAATCTTAACCAACATTTTTAACGACTTGAATT
GTATAAAAAATTGTTTTTCTCCAATTTTCCATCAACAGCATCTATTAAAAGTGATTGTCG
CGACAAGAAATTGCCACCCAAACGCAAATGTTAA

>g5732.t28 Gene=g5732 Length=157
MEHEYYTGLSILIAVVYATKKFGPSVAKSLDKEVDAVEEEWNQGRTDEIKSLNEAIEEEK
KEQWRAEGQMMLIDAKKENVALQLEAAYRERAMQVYREVKKRLDYQVERQNIDRRISQKH
MAQWIVNNVLKSITPDQEAQTLSKCIADLGGLAAARK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
5 g5732.t28 Coils Coil Coil 42 69 -
2 g5732.t28 PANTHER PTHR12733:SF3 ATP SYNTHASE F(0) COMPLEX SUBUNIT B1, MITOCHONDRIAL 1 155 4.3E-57
3 g5732.t28 PANTHER PTHR12733 MITOCHONDRIAL ATP SYNTHASE B CHAIN 1 155 4.3E-57
1 g5732.t28 Pfam PF05405 Mitochondrial ATP synthase B chain precursor (ATP-synt_B) 1 149 8.1E-47
4 g5732.t28 SUPERFAMILY SSF161060 ATP synthase B chain-like 28 131 7.06E-37

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5732/g5732.t28; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5732.t28.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. There were no conditions that were differentially expressed