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.t17 TTS g7327.t17 22965752 22965752
chr_2 g7327 g7327.t17 isoform g7327.t17 22966011 22968336
chr_2 g7327 g7327.t17 exon g7327.t17.exon1 22966011 22966805
chr_2 g7327 g7327.t17 cds g7327.t17.CDS1 22966011 22966805
chr_2 g7327 g7327.t17 exon g7327.t17.exon2 22966871 22967376
chr_2 g7327 g7327.t17 cds g7327.t17.CDS2 22966871 22967376
chr_2 g7327 g7327.t17 exon g7327.t17.exon3 22968291 22968336
chr_2 g7327 g7327.t17 cds g7327.t17.CDS3 22968291 22968336
chr_2 g7327 g7327.t17 TSS g7327.t17 22968351 22968351

Sequences

>g7327.t17 Gene=g7327 Length=1347
ATGTTTACGGCGGTACGAGCTTCGAAATTACTACAGAATATAGCGATCTTGGAAGTCGCT
CAGCATTTGGGAGAAAACACTGTCCGCACAATCGCAATGGACGGTACAGAAGGTTTAGTT
CGTGGACAACGCGTAGCTGACACTGGTTCACCAATTCGTATCCCAGTCGGTGCTGAAACT
TTAGGACGCATTATCAATGTCATTGGCGAGCCAATTGATGAACGTGGTCCAATTGAAACC
GACAAATCAGCTCCAATTCACGCTGAAGCTCCAGAATTTGTTGAAATGAGTGTACAGCAA
GAAATTCTTGTCACTGGTATCAAGGTTGTAGATTTGTTGGCCCCATACGCTAAGGGTGGT
AAAATTGGTCTCTTTGGTGGTGCTGGAGTAGGAAAAACAGTTTTGATTATGGAACTTATT
AACAATGTTGCCAAAGCTCATGGTGGTTATTCAGTCTTTGCTGGTGTCGGAGAACGTACA
CGTGAGGGTAACGATTTGTACAATGAAATGATTGAGTCCGGTGTCATCTCATTGAAGGAC
AAGACTTCAAAGGTAGCACTTGTGTACGGTCAAATGAATGAACCACCAGGTGCTCGTGCT
CGTGTCGCTTTGACTGGTCTCACCGTTGCTGAATATTTCCGTGATCAAGAAGGACAAGAT
GTGTTGCTTTTCATTGACAACATTTTCCGTTTCACACAAGCCGGTTCAGAAGTATCAGCT
TTGCTCGGTCGTATTCCATCAGCTGTCGGTTATCAACCAACATTGGCCACTGACATGGGT
AGTATGCAGGAACGTATCACAACAACAAAGAAGGGTTCAATTACATCTGTACAGGCTATC
TATGTGCCAGCTGATGACTTGACAGATCCTGCTCCAGCCACAACATTCGCTCACTTGGAC
GCTACAACTGTATTGTCACGTGCTATCGCCGAATTGGGTATCTATCCAGCTGTCGATCCA
TTGGATTCAACATCACGTATTATGGACCCTAACATCATCGGACAAGAACATTACAACATT
GCTCGTGGCGTACAAAAGATCTTGCAAGATTACAAATCACTTCAAGATATTATTGCTATC
TTGGGTATGGATGAATTGTCAGAAGAAGATAAATTGACAGTCGCCCGCGCCCGTAAGATC
CAACGTTTCTTGTCACAGCCATTCCAGGTCGCTGAAGTTTTCACTGGTCATGCCGGTAAA
TTAGTACCACTCGCAGAAACAATTAAGGGCTTCACAAAGATTCTCGGAGGTGAACTCGAT
CACTTGCCAGAAGTTGCATTCTACATGGTCGGACCTATCGAGGAAGTTGTCGAAAAGGCC
GAACGTTTGGCTAAGGAAGCAGCATAA

>g7327.t17 Gene=g7327 Length=448
MFTAVRASKLLQNIAILEVAQHLGENTVRTIAMDGTEGLVRGQRVADTGSPIRIPVGAET
LGRIINVIGEPIDERGPIETDKSAPIHAEAPEFVEMSVQQEILVTGIKVVDLLAPYAKGG
KIGLFGGAGVGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYNEMIESGVISLKD
KTSKVALVYGQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSA
LLGRIPSAVGYQPTLATDMGSMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLD
ATTVLSRAIAELGIYPAVDPLDSTSRIMDPNIIGQEHYNIARGVQKILQDYKSLQDIIAI
LGMDELSEEDKLTVARARKIQRFLSQPFQVAEVFTGHAGKLVPLAETIKGFTKILGGELD
HLPEVAFYMVGPIEEVVEKAERLAKEAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g7327.t17 CDD cd01133 F1-ATPase_beta 51 330 0.0
13 g7327.t17 CDD cd18110 ATP-synt_F1_beta_C 332 439 1.62054E-76
11 g7327.t17 Gene3D G3DSA:2.40.10.170 - 3 51 1.1E-15
9 g7327.t17 Gene3D G3DSA:3.40.50.300 - 52 327 4.0E-123
10 g7327.t17 Gene3D G3DSA:1.10.1140.10 - 328 448 1.3E-61
5 g7327.t17 Hamap MF_01347 ATP synthase subunit beta [atpB]. 2 443 53.202972
3 g7327.t17 PANTHER PTHR15184 ATP SYNTHASE 15 448 3.5E-259
4 g7327.t17 PANTHER PTHR15184:SF60 ATP SYNTHASE SUBUNIT BETA-1, MITOCHONDRIAL-RELATED 15 448 3.5E-259
12 g7327.t17 PIRSF PIRSF039072 ATPase_subunit_beta 1 448 2.2E-276
1 g7327.t17 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 16 49 1.5E-11
2 g7327.t17 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 106 325 2.3E-63
15 g7327.t17 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 316 325 -
16 g7327.t17 SMART SM00382 AAA_5 118 302 5.5E-6
6 g7327.t17 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 15 51 4.19E-13
7 g7327.t17 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 53 330 1.8E-91
8 g7327.t17 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 328 444 7.32E-54
17 g7327.t17 TIGRFAM TIGR01039 atpD: ATP synthase F1, beta subunit 13 443 2.1E-241

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:0046034 ATP metabolic process BP
GO:0045261 proton-transporting ATP synthase complex, catalytic core F(1) CC
GO:0015986 ATP synthesis coupled proton transport BP
GO:1902600 proton transmembrane transport BP
GO:0005524 ATP binding MF
GO:0046933 proton-transporting ATP synthase activity, rotational mechanism 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.

Raw TPM values