Gene loci information

Transcript annotation

  • This transcript has been annotated as ATP synthase subunit beta, 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 g7327 g7327.t18 TTS g7327.t18 22965752 22965752
chr_2 g7327 g7327.t18 isoform g7327.t18 22966011 22968336
chr_2 g7327 g7327.t18 exon g7327.t18.exon1 22966011 22966805
chr_2 g7327 g7327.t18 cds g7327.t18.CDS1 22966011 22966805
chr_2 g7327 g7327.t18 exon g7327.t18.exon2 22966871 22967476
chr_2 g7327 g7327.t18 cds g7327.t18.CDS2 22966871 22967326
chr_2 g7327 g7327.t18 exon g7327.t18.exon3 22967534 22967590
chr_2 g7327 g7327.t18 exon g7327.t18.exon4 22968291 22968336
chr_2 g7327 g7327.t18 TSS g7327.t18 22968351 22968351

Sequences

>g7327.t18 Gene=g7327 Length=1504
ATGTTTACGGCGGTACGAGCTTCGAAATTACTACAGAATATAGCGACAAGAAGCTATGCA
GCTAAGGCCGCAAAAGCTGCTGCTGGTGCTCAGGGCAAAGTAAGTTGTTGCTGTCATCGG
TGCCGTTGTGGACGTTCAATTCGATGACAACTTGCCACCAATTTTGAATGCACTCGAGGT
TCAAGATCGCCAGACTCGTTTAGTCTTGGAAGTCGCTCAGCATTTGGGAGAAAACACTGT
CCGCACAATCGCAATGGACGGTACAGAAGGTTTAGTTCGTGGACAACGCGTAGCTGACAC
TGGTTCACCAATTCGTATCCCAGTCGGTGCTGAAACTTTAGGACGCATTATCAATGTCAT
TGGCGAGCCAATTGATGAACGTGGTCCAATTGAAACCGACAAATCAGCTCCAATTCACGC
TGAAGCTCCAGAATTTGTTGAAATGAGTGTACAGCAAGAAATTCTTGTCACTGGTATCAA
GGTTGTAGATTTGTTGGCCCCATACGCTAAGGGTGGTAAAATTGGTCTCTTTGGTGGTGC
TGGAGTAGGAAAAACAGTTTTGATTATGGAACTTATTAACAATGTTGCCAAAGCTCATGG
TGGTTATTCAGTCTTTGCTGGTGTCGGAGAACGTACACGTGAGGGTAACGATTTGTACAA
TGAAATGATTGAGTCCGGTGTCATCTCATTGAAGGACAAGACTTCAAAGGTAGCACTTGT
GTACGGTCAAATGAATGAACCACCAGGTGCTCGTGCTCGTGTCGCTTTGACTGGTCTCAC
CGTTGCTGAATATTTCCGTGATCAAGAAGGACAAGATGTGTTGCTTTTCATTGACAACAT
TTTCCGTTTCACACAAGCCGGTTCAGAAGTATCAGCTTTGCTCGGTCGTATTCCATCAGC
TGTCGGTTATCAACCAACATTGGCCACTGACATGGGTAGTATGCAGGAACGTATCACAAC
AACAAAGAAGGGTTCAATTACATCTGTACAGGCTATCTATGTGCCAGCTGATGACTTGAC
AGATCCTGCTCCAGCCACAACATTCGCTCACTTGGACGCTACAACTGTATTGTCACGTGC
TATCGCCGAATTGGGTATCTATCCAGCTGTCGATCCATTGGATTCAACATCACGTATTAT
GGACCCTAACATCATCGGACAAGAACATTACAACATTGCTCGTGGCGTACAAAAGATCTT
GCAAGATTACAAATCACTTCAAGATATTATTGCTATCTTGGGTATGGATGAATTGTCAGA
AGAAGATAAATTGACAGTCGCCCGCGCCCGTAAGATCCAACGTTTCTTGTCACAGCCATT
CCAGGTCGCTGAAGTTTTCACTGGTCATGCCGGTAAATTAGTACCACTCGCAGAAACAAT
TAAGGGCTTCACAAAGATTCTCGGAGGTGAACTCGATCACTTGCCAGAAGTTGCATTCTA
CATGGTCGGACCTATCGAGGAAGTTGTCGAAAAGGCCGAACGTTTGGCTAAGGAAGCAGC
ATAA

>g7327.t18 Gene=g7327 Length=416
MDGTEGLVRGQRVADTGSPIRIPVGAETLGRIINVIGEPIDERGPIETDKSAPIHAEAPE
FVEMSVQQEILVTGIKVVDLLAPYAKGGKIGLFGGAGVGKTVLIMELINNVAKAHGGYSV
FAGVGERTREGNDLYNEMIESGVISLKDKTSKVALVYGQMNEPPGARARVALTGLTVAEY
FRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAVGYQPTLATDMGSMQERITTTKKG
SITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAIAELGIYPAVDPLDSTSRIMDPNI
IGQEHYNIARGVQKILQDYKSLQDIIAILGMDELSEEDKLTVARARKIQRFLSQPFQVAE
VFTGHAGKLVPLAETIKGFTKILGGELDHLPEVAFYMVGPIEEVVEKAERLAKEAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g7327.t18 CDD cd01133 F1-ATPase_beta 19 298 0.0
10 g7327.t18 CDD cd18110 ATP-synt_F1_beta_C 300 407 6.87421E-77
7 g7327.t18 Gene3D G3DSA:3.40.50.300 - 20 295 3.2E-123
8 g7327.t18 Gene3D G3DSA:1.10.1140.10 - 296 416 1.1E-61
4 g7327.t18 Hamap MF_01347 ATP synthase subunit beta [atpB]. 2 411 49.545055
2 g7327.t18 PANTHER PTHR15184 ATP SYNTHASE 1 416 1.4E-248
3 g7327.t18 PANTHER PTHR15184:SF60 ATP SYNTHASE SUBUNIT BETA-1, MITOCHONDRIAL-RELATED 1 416 1.4E-248
9 g7327.t18 PIRSF PIRSF039072 ATPase_subunit_beta 1 416 8.2E-265
1 g7327.t18 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 74 293 1.9E-63
12 g7327.t18 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 284 293 -
13 g7327.t18 SMART SM00382 AAA_5 86 270 5.5E-6
5 g7327.t18 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 21 298 1.46E-91
6 g7327.t18 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 296 412 6.28E-54
14 g7327.t18 TIGRFAM TIGR01039 atpD: ATP synthase F1, beta subunit 1 411 1.9E-231

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1) CC
GO:0015986 ATP synthesis coupled proton transport BP
GO:0005524 ATP binding MF
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism 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.

Raw TPM values