Gene loci information

Transcript annotation

  • This transcript has been annotated as Short-chain specific acyl-CoA dehydrogenase, 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_4 g14410 g14410.t5 TTS g14410.t5 355402 355402
chr_4 g14410 g14410.t5 isoform g14410.t5 355467 356959
chr_4 g14410 g14410.t5 exon g14410.t5.exon1 355467 355528
chr_4 g14410 g14410.t5 cds g14410.t5.CDS1 355467 355528
chr_4 g14410 g14410.t5 exon g14410.t5.exon2 355589 355679
chr_4 g14410 g14410.t5 cds g14410.t5.CDS2 355589 355679
chr_4 g14410 g14410.t5 exon g14410.t5.exon3 355738 356355
chr_4 g14410 g14410.t5 cds g14410.t5.CDS3 355738 356031
chr_4 g14410 g14410.t5 exon g14410.t5.exon4 356526 356819
chr_4 g14410 g14410.t5 exon g14410.t5.exon5 356929 356959
chr_4 g14410 g14410.t5 TSS g14410.t5 357084 357084

Sequences

>g14410.t5 Gene=g14410 Length=1096
ATGTTTACTATTAGACAATCATTCAAATTTGCTTCATCAATCAATGCTCGTTCAATTGTG
TCCCTCTCGCATCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCGTGATTTTGCT
GATAATGAGTTAGCACCAATTGCTAAACAAATTGATAAAGAACATCGATATCCATCGGAG
CAAGTTAAGAAAATGGGTGAACTTGGTTTACTTGCGATTGCTATTCCTGAAAAATATGGA
GGAACAGGGCTTGATTATCTTGCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGT
GCTACTTGTGGTGTCATTATGACTGCCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTAC
TACAGCAAAACTTGTTGGTGATAAATGGGTTTTAAATGGTACCAAAAATTGGATAACAAA
TGGTCCTGATGCTTCAGCTGCAATTGTTTTTGCTACCACTGATAAAAAATTAAAACACAA
AGGTATTTCAGCTTTTATTGTAGAGCGTGGTATACCAGGATTTAGTTATGGCAAGAAAGA
AGATAAATTGGGTATAAGAGGTAGTTCAACATGCTCTTTGATTTTTGATGACTGTGCTAT
ACCTAAAGAAAATATTCTCGGTGAAGAAGGATTTGGATTTAAAATTGCAATGAAAACATT
AGATGAGGGCCGAATTGGAATAGCAGGGCAAGCATTAGGCATTGCTCAAGCATCATTAGA
ATGTGCAGTTGATTATGCAAATAAGAGAATCGCATTTGGAAATCCTATAAGCAAAATGCA
AACAATACAAAATAAAATAGCCGATATGGCAATGAGAATTGAAGCAGCAAGATTACTAAC
CTGGAGAGCTGCTGTGTTGAAAGATGAAGGTAAATCAATAACAAAAGAAGCTGCTATGGC
AAAATTAGCTGCTAGTGAAACTGCAACTTTCTGTTCCCATCAAGCAATACAAATTCTTGG
TGGTATGGGATACGTAACAGATATGCCAGCAGAACGTCATTATAGAGATGCAAGAATAAC
TGAAATTTATGAAGGAACATCCGAAATTCAAAGACTTGTAATTGCTGGTCAAATACTTAA
ACAAATGTCACAATAA

>g14410.t5 Gene=g14410 Length=148
MKTLDEGRIGIAGQALGIAQASLECAVDYANKRIAFGNPISKMQTIQNKIADMAMRIEAA
RLLTWRAAVLKDEGKSITKEAAMAKLAASETATFCSHQAIQILGGMGYVTDMPAERHYRD
ARITEIYEGTSEIQRLVIAGQILKQMSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g14410.t5 Gene3D G3DSA:1.20.140.10 - 1 148 3.4E-55
2 g14410.t5 PANTHER PTHR43884:SF26 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED 1 146 2.7E-59
3 g14410.t5 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 146 2.7E-59
1 g14410.t5 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 1 142 7.2E-48
5 g14410.t5 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 101 120 -
4 g14410.t5 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 1 145 1.21E-56

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:0003995 acyl-CoA dehydrogenase activity 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. There were no conditions that were differentially expressed