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.t1 TTS g7327.t1 22965752 22965752
chr_2 g7327 g7327.t1 isoform g7327.t1 22966011 22968336
chr_2 g7327 g7327.t1 exon g7327.t1.exon1 22966011 22966805
chr_2 g7327 g7327.t1 cds g7327.t1.CDS1 22966011 22966805
chr_2 g7327 g7327.t1 exon g7327.t1.exon2 22966871 22967476
chr_2 g7327 g7327.t1 cds g7327.t1.CDS2 22966871 22967476
chr_2 g7327 g7327.t1 exon g7327.t1.exon3 22967538 22967590
chr_2 g7327 g7327.t1 cds g7327.t1.CDS3 22967538 22967590
chr_2 g7327 g7327.t1 exon g7327.t1.exon4 22968291 22968336
chr_2 g7327 g7327.t1 cds g7327.t1.CDS4 22968291 22968336
chr_2 g7327 g7327.t1 TSS g7327.t1 22968351 22968351

Sequences

>g7327.t1 Gene=g7327 Length=1500
ATGTTTACGGCGGTACGAGCTTCGAAATTACTACAGAATATAGCGACAAGAAGCTATGCA
GCTAAGGCCGCAAAAGCTGCTGCTGGTGCTCAGGGCAAAGTTGTTGCTGTCATCGGTGCC
GTTGTGGACGTTCAATTCGATGACAACTTGCCACCAATTTTGAATGCACTCGAGGTTCAA
GATCGCCAGACTCGTTTAGTCTTGGAAGTCGCTCAGCATTTGGGAGAAAACACTGTCCGC
ACAATCGCAATGGACGGTACAGAAGGTTTAGTTCGTGGACAACGCGTAGCTGACACTGGT
TCACCAATTCGTATCCCAGTCGGTGCTGAAACTTTAGGACGCATTATCAATGTCATTGGC
GAGCCAATTGATGAACGTGGTCCAATTGAAACCGACAAATCAGCTCCAATTCACGCTGAA
GCTCCAGAATTTGTTGAAATGAGTGTACAGCAAGAAATTCTTGTCACTGGTATCAAGGTT
GTAGATTTGTTGGCCCCATACGCTAAGGGTGGTAAAATTGGTCTCTTTGGTGGTGCTGGA
GTAGGAAAAACAGTTTTGATTATGGAACTTATTAACAATGTTGCCAAAGCTCATGGTGGT
TATTCAGTCTTTGCTGGTGTCGGAGAACGTACACGTGAGGGTAACGATTTGTACAATGAA
ATGATTGAGTCCGGTGTCATCTCATTGAAGGACAAGACTTCAAAGGTAGCACTTGTGTAC
GGTCAAATGAATGAACCACCAGGTGCTCGTGCTCGTGTCGCTTTGACTGGTCTCACCGTT
GCTGAATATTTCCGTGATCAAGAAGGACAAGATGTGTTGCTTTTCATTGACAACATTTTC
CGTTTCACACAAGCCGGTTCAGAAGTATCAGCTTTGCTCGGTCGTATTCCATCAGCTGTC
GGTTATCAACCAACATTGGCCACTGACATGGGTAGTATGCAGGAACGTATCACAACAACA
AAGAAGGGTTCAATTACATCTGTACAGGCTATCTATGTGCCAGCTGATGACTTGACAGAT
CCTGCTCCAGCCACAACATTCGCTCACTTGGACGCTACAACTGTATTGTCACGTGCTATC
GCCGAATTGGGTATCTATCCAGCTGTCGATCCATTGGATTCAACATCACGTATTATGGAC
CCTAACATCATCGGACAAGAACATTACAACATTGCTCGTGGCGTACAAAAGATCTTGCAA
GATTACAAATCACTTCAAGATATTATTGCTATCTTGGGTATGGATGAATTGTCAGAAGAA
GATAAATTGACAGTCGCCCGCGCCCGTAAGATCCAACGTTTCTTGTCACAGCCATTCCAG
GTCGCTGAAGTTTTCACTGGTCATGCCGGTAAATTAGTACCACTCGCAGAAACAATTAAG
GGCTTCACAAAGATTCTCGGAGGTGAACTCGATCACTTGCCAGAAGTTGCATTCTACATG
GTCGGACCTATCGAGGAAGTTGTCGAAAAGGCCGAACGTTTGGCTAAGGAAGCAGCATAA

>g7327.t1 Gene=g7327 Length=499
MFTAVRASKLLQNIATRSYAAKAAKAAAGAQGKVVAVIGAVVDVQFDDNLPPILNALEVQ
DRQTRLVLEVAQHLGENTVRTIAMDGTEGLVRGQRVADTGSPIRIPVGAETLGRIINVIG
EPIDERGPIETDKSAPIHAEAPEFVEMSVQQEILVTGIKVVDLLAPYAKGGKIGLFGGAG
VGKTVLIMELINNVAKAHGGYSVFAGVGERTREGNDLYNEMIESGVISLKDKTSKVALVY
GQMNEPPGARARVALTGLTVAEYFRDQEGQDVLLFIDNIFRFTQAGSEVSALLGRIPSAV
GYQPTLATDMGSMQERITTTKKGSITSVQAIYVPADDLTDPAPATTFAHLDATTVLSRAI
AELGIYPAVDPLDSTSRIMDPNIIGQEHYNIARGVQKILQDYKSLQDIIAILGMDELSEE
DKLTVARARKIQRFLSQPFQVAEVFTGHAGKLVPLAETIKGFTKILGGELDHLPEVAFYM
VGPIEEVVEKAERLAKEAA

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g7327.t1 CDD cd18115 ATP-synt_F1_beta_N 34 103 1.22936E-34
15 g7327.t1 CDD cd01133 F1-ATPase_beta 102 381 0.0
13 g7327.t1 CDD cd18110 ATP-synt_F1_beta_C 383 490 5.70386E-76
11 g7327.t1 Gene3D G3DSA:2.40.10.170 - 19 102 1.4E-37
9 g7327.t1 Gene3D G3DSA:3.40.50.300 - 103 378 5.4E-123
10 g7327.t1 Gene3D G3DSA:1.10.1140.10 - 379 499 1.6E-61
5 g7327.t1 Hamap MF_01347 ATP synthase subunit beta [atpB]. 29 494 57.271595
3 g7327.t1 PANTHER PTHR15184 ATP SYNTHASE 22 499 3.2E-279
4 g7327.t1 PANTHER PTHR15184:SF60 ATP SYNTHASE SUBUNIT BETA-1, MITOCHONDRIAL-RELATED 22 499 3.2E-279
12 g7327.t1 PIRSF PIRSF039072 ATPase_subunit_beta 3 499 2.9E-294
1 g7327.t1 Pfam PF02874 ATP synthase alpha/beta family, beta-barrel domain 34 100 2.0E-21
2 g7327.t1 Pfam PF00006 ATP synthase alpha/beta family, nucleotide-binding domain 157 376 3.0E-63
16 g7327.t1 ProSitePatterns PS00152 ATP synthase alpha and beta subunits signature. 367 376 -
17 g7327.t1 SMART SM00382 AAA_5 169 353 5.5E-6
6 g7327.t1 SUPERFAMILY SSF50615 N-terminal domain of alpha and beta subunits of F1 ATP synthase 30 102 3.92E-26
7 g7327.t1 SUPERFAMILY SSF52540 P-loop containing nucleoside triphosphate hydrolases 104 381 2.47E-91
8 g7327.t1 SUPERFAMILY SSF47917 C-terminal domain of alpha and beta subunits of F1 ATP synthase 379 495 8.89E-54
18 g7327.t1 TIGRFAM TIGR01039 atpD: ATP synthase F1, beta subunit 31 494 4.4E-253

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