Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative ATP synthase subunit d, 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_3 g2383 g2383.t3 TSS g2383.t3 17486241 17486241
chr_3 g2383 g2383.t3 isoform g2383.t3 17486309 17486923
chr_3 g2383 g2383.t3 exon g2383.t3.exon1 17486309 17486454
chr_3 g2383 g2383.t3 cds g2383.t3.CDS1 17486309 17486454
chr_3 g2383 g2383.t3 exon g2383.t3.exon2 17486530 17486923
chr_3 g2383 g2383.t3 cds g2383.t3.CDS2 17486530 17486923
chr_3 g2383 g2383.t3 TTS g2383.t3 17487067 17487067

Sequences

>g2383.t3 Gene=g2383 Length=540
ATGGCTTCACGTCGTATTGCAGCATCTTCAATTAACTGGGCAGCAATTGCCGAACGTGTG
CCAGCAGCGCAGAGAACTAATTTTACTGCTTTCAAGTCGAAGAGCGATAAATATTTGAGA
AGGTTGGTTAAATTTTTAGTGATTAATGTATTGGCTAATCCTGAAAATCCACCAAAAATC
GATTGGGCTGCATACAAGAATTCAGTCCCAATTCCTGGAATGGTTGAAAACTTCCAGAAA
CAGTACGAAGCATTGAAAGTTCCCTATCCATCAGATAATGTTAGCTCACAACTTGATCAA
CAAAAGCAACAAGTTGCAAAGGAAATTGAAGAATTCAAAAGAGATTCATCAGCACGTATT
GCTGAACATGAGAAGGCTGTTGCTCATTTGAAATCATTGCTGCCATACGCTGCTATGACC
ATGGAAGATTTCAATGATGCCTTCCCAGACCAGGCACTTGATGCAATTAATCGTCCAACA
TTCTGGCCTCACGATGCTGCTGAGCAAGAACCAAGAAAAGAACCAGAAGAACATCATTAA

>g2383.t3 Gene=g2383 Length=179
MASRRIAASSINWAAIAERVPAAQRTNFTAFKSKSDKYLRRLVKFLVINVLANPENPPKI
DWAAYKNSVPIPGMVENFQKQYEALKVPYPSDNVSSQLDQQKQQVAKEIEEFKRDSSARI
AEHEKAVAHLKSLLPYAAMTMEDFNDAFPDQALDAINRPTFWPHDAAEQEPRKEPEEHH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g2383.t3 Coils Coil Coil 91 115 -
5 g2383.t3 Gene3D G3DSA:1.20.58.880 - 2 132 9.6E-41
2 g2383.t3 PANTHER PTHR12700:SF12 ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL 1 166 8.5E-41
3 g2383.t3 PANTHER PTHR12700 ATP SYNTHASE SUBUNIT D, MITOCHONDRIAL 1 166 8.5E-41
12 g2383.t3 PIRSF PIRSF005514 Mitoh_ATP-synt_D 1 179 1.8E-59
1 g2383.t3 Pfam PF05873 ATP synthase D chain, mitochondrial (ATP5H) 4 164 6.5E-62
8 g2383.t3 Phobius SIGNAL_PEPTIDE Signal peptide region 1 22 -
9 g2383.t3 Phobius SIGNAL_PEPTIDE_N_REGION N-terminal region of a signal peptide. 1 5 -
10 g2383.t3 Phobius SIGNAL_PEPTIDE_H_REGION Hydrophobic region of a signal peptide. 6 17 -
11 g2383.t3 Phobius SIGNAL_PEPTIDE_C_REGION C-terminal region of a signal peptide. 18 22 -
7 g2383.t3 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 23 179 -
4 g2383.t3 SUPERFAMILY SSF161065 ATP synthase D chain-like 5 132 1.7E-37

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: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.

Raw TPM values