Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable peroxisomal acyl-coenzyme A oxidase 1.

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_4 g16336 g16336.t2 TSS g16336.t2 9123182 9123182
chr_4 g16336 g16336.t2 isoform g16336.t2 9123239 9125140
chr_4 g16336 g16336.t2 exon g16336.t2.exon1 9123239 9123347
chr_4 g16336 g16336.t2 cds g16336.t2.CDS1 9123239 9123347
chr_4 g16336 g16336.t2 exon g16336.t2.exon2 9123414 9123567
chr_4 g16336 g16336.t2 cds g16336.t2.CDS2 9123414 9123567
chr_4 g16336 g16336.t2 exon g16336.t2.exon3 9123671 9123726
chr_4 g16336 g16336.t2 cds g16336.t2.CDS3 9123671 9123726
chr_4 g16336 g16336.t2 exon g16336.t2.exon4 9123780 9123902
chr_4 g16336 g16336.t2 cds g16336.t2.CDS4 9123780 9123902
chr_4 g16336 g16336.t2 exon g16336.t2.exon5 9124024 9124121
chr_4 g16336 g16336.t2 cds g16336.t2.CDS5 9124024 9124121
chr_4 g16336 g16336.t2 exon g16336.t2.exon6 9124191 9124338
chr_4 g16336 g16336.t2 cds g16336.t2.CDS6 9124191 9124338
chr_4 g16336 g16336.t2 exon g16336.t2.exon7 9124405 9124426
chr_4 g16336 g16336.t2 cds g16336.t2.CDS7 9124405 9124426
chr_4 g16336 g16336.t2 exon g16336.t2.exon8 9124566 9125140
chr_4 g16336 g16336.t2 cds g16336.t2.CDS8 9124566 9125139
chr_4 g16336 g16336.t2 TTS g16336.t2 9126057 9126057

Sequences

>g16336.t2 Gene=g16336 Length=1285
ATGAATAAAGATTTAGAAATTGAAAGAAGTAAAGTACCATTTAAAATTGAAGAATTGACA
AATTGGTTTTATGGAGGTGAAAAAAATGTCAAAGAAAAAAGATTTTTGGAAAATATTTTC
TACTCTGACCCTGATTTGAAAAGTGACACAAGTTACATGAGTCATGTTGAAAAATATGAA
GAAGCAATTAGAAAAGTCACTGTTATATTGAAAAAATTAAAACACCTTGTAAATCAAGGT
CAATATAACGAAGAAATTTATCCCAAAATTTTGGGAGCGCAATTCTTAAAACATTTAATA
AAGGAAGGCAACCCAACAAGTGTGCATTTTGACATGTTTATACCAGGCATTAAAAGTATG
GGAACACAAGTACAACAAGATGAATGGTTACCTAAAGCATTAACCTTAAAAATCATTGGC
ACTTATGCTCAAACAGAATTAGGTCATGGTACATATGTTCGAGGATTAGAAACTACAGCA
ACCTTTGATGAAAATACAAAAGAATTTGTTCTTAACACACCAACTTTAACAGCATACAAA
TGGTGGCCGGGCAATTTAGGTCATACAGTCAACCATGCTCTTGTTATGGCCCAATTGTAT
ACAAAAGGCAAATGTTATGGCATTCACGCATTCATTGTACCTTTGAGAGACTTAGAAACC
CATAAACCTTTGCCAGGAGTTCATATAGGAGAAATTGGTACAAAATTCGGATACAACACT
GTCAATAATGGCTTTTTAGGATTGAAAAATGTTCGAATTCCCAGAAAAAATATGTTGATG
AAAAATAGTGAAGTAACTGAAAGTGGGGAATTTGTAATTCATAAAAACCCACTTCTAACT
TATGGGACGATGACAATGATTAGAGTTGGAATAATTCAAGAAGTCCAAGTATTTTTAGCG
AAAGCTGTTACTATTGCAACTCGGTATTCATTGGTAAGACGTCAAAGTCCAATAAACCCA
AATGATGAAATAGAACCGCAAATCATTGAACACACGACACAACAGTACAAACTTTTTGTG
CCATTGGCAAAAGTTTTTTCTTTAAAAATTACATCTGACTACCTATGGAATCAATATGAA
GATACAATGAAAAAAATTGACAAGGGTGATTTGACAACATTACCAGAATTACATGCACTT
TCTTGTTGTTTAAAAGCTATATGCACTAACGATGCTGCTGAAGGTACTGAAATTTGCCGA
TTATCTTGCGGAGGTCATGGCTTTCTTAATTCATCTGCACTTCCTGATTGCTATAAAATG
ATAACACCGGCTCAAACATATGAAG

>g16336.t2 Gene=g16336 Length=428
MNKDLEIERSKVPFKIEELTNWFYGGEKNVKEKRFLENIFYSDPDLKSDTSYMSHVEKYE
EAIRKVTVILKKLKHLVNQGQYNEEIYPKILGAQFLKHLIKEGNPTSVHFDMFIPGIKSM
GTQVQQDEWLPKALTLKIIGTYAQTELGHGTYVRGLETTATFDENTKEFVLNTPTLTAYK
WWPGNLGHTVNHALVMAQLYTKGKCYGIHAFIVPLRDLETHKPLPGVHIGEIGTKFGYNT
VNNGFLGLKNVRIPRKNMLMKNSEVTESGEFVIHKNPLLTYGTMTMIRVGIIQEVQVFLA
KAVTIATRYSLVRRQSPINPNDEIEPQIIEHTTQQYKLFVPLAKVFSLKITSDYLWNQYE
DTMKKIDKGDLTTLPELHALSCCLKAICTNDAAEGTEICRLSCGGHGFLNSSALPDCYKM
ITPAQTYE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g16336.t2 Coils Coil Coil 56 76 -
7 g16336.t2 Gene3D G3DSA:1.10.540.10 - 15 139 4.2E-35
8 g16336.t2 Gene3D G3DSA:2.40.110.10 - 140 273 1.1E-57
9 g16336.t2 Gene3D G3DSA:1.20.140.10 - 279 428 7.4E-44
3 g16336.t2 PANTHER PTHR10909:SF250 ACYL-COENZYME A OXIDASE 2 428 4.0E-164
4 g16336.t2 PANTHER PTHR10909 ELECTRON TRANSPORT OXIDOREDUCTASE 2 428 4.0E-164
1 g16336.t2 Pfam PF14749 Acyl-coenzyme A oxidase N-terminal 16 139 2.5E-32
2 g16336.t2 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 142 251 2.2E-12
5 g16336.t2 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 95 263 1.11E-49
6 g16336.t2 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 279 428 1.34E-35

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:0016627 oxidoreductase activity, acting on the CH-CH group of donors MF
GO:0050660 flavin adenine dinucleotide binding MF
GO:0055114 NA NA

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