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.t6 TTS g14410.t6 355402 355402
chr_4 g14410 g14410.t6 isoform g14410.t6 355467 356959
chr_4 g14410 g14410.t6 exon g14410.t6.exon1 355467 355528
chr_4 g14410 g14410.t6 cds g14410.t6.CDS1 355467 355528
chr_4 g14410 g14410.t6 exon g14410.t6.exon2 355589 355679
chr_4 g14410 g14410.t6 cds g14410.t6.CDS2 355589 355679
chr_4 g14410 g14410.t6 exon g14410.t6.exon3 355738 356471
chr_4 g14410 g14410.t6 cds g14410.t6.CDS3 355738 356471
chr_4 g14410 g14410.t6 exon g14410.t6.exon4 356526 356819
chr_4 g14410 g14410.t6 cds g14410.t6.CDS4 356526 356819
chr_4 g14410 g14410.t6 exon g14410.t6.exon5 356938 356959
chr_4 g14410 g14410.t6 cds g14410.t6.CDS5 356938 356959
chr_4 g14410 g14410.t6 TSS g14410.t6 357084 357084

Sequences

>g14410.t6 Gene=g14410 Length=1203
ATGTTTACTATTAGACAATCATCTTCATCAATCAATGCTCGTTCAATTGTGTCCCTCTCG
CATCTTCCTGAGACTCATCAAATGTTGTATAAGACATGTCGTGATTTTGCTGATAATGAG
TTAGCACCAATTGCTAAACAAATTGATAAAGAACATCGATATCCATCGGAGCAAGTTAAG
AAAATGGGTGAACTTGGTTTACTTGCGATTGCTATTCCTGAAAAATATGGAGGAACAGGG
CTTGATTATCTTGCTTATGCTATTGGCATGGAAGAAATTTCTCGAGGTTGTGCTACTTGT
GGTGTCATTATGACTGTCAACAACACTTTATATTTGGGACCAGTTAAAAATTTTGGTAAC
GAAGCTCAAAAAAAAGAATTTTTAACTCCTTACACTGATGGTGACAAGATTGGATGTTTT
GCATTATCTGAGCCTGGAAATGGAAGTGATGCTGCAGCTGCTTCTACTACAGCAAAACTT
GTTGGTGATAAATGGGTTTTAAATGGTACCAAAAATTGGATAACAAATGGTCCTGATGCT
TCAGCTGCAATTGTTTTTGCTACCACTGATAAAAAATTAAAACACAAAGGTATTTCAGCT
TTTATTGTAGAGCGTGGTATACCAGGATTTAGTTATGGCAAGAAAGAAGATAAATTGGGT
ATAAGAGGTAGTTCAACATGCTCTTTGATTTTTGATGACTGTGCTATACCTAAAGAAAAT
ATTCTCGGTGAAGAAGGATTTGGATTTAAAATTGCAATGAAAACATTAGATGAGGGCCGA
ATTGGAATAGCAGGGCAAGCATTAGGCATTGCTCAAGCATCATTAGAATGTGCAGTTGAT
TATGCAAATAAGAGAATCGCATTTGGAAATCCTATAAGCAAAATGCAAACAATACAAAAT
AAAATAGCCGATATGGCAATGAGAATTGAAGCAGCAAGATTACTAACCTGGAGAGCTGCT
GTGTTGAAAGATGAAGGTAAATCAATAACAAAAGAAGCTGCTATGGCAAAATTAGCTGCT
AGTGAAACTGCAACTTTCTGTTCCCATCAAGCAATACAAATTCTTGGTGGTATGGGATAC
GTAACAGATATGCCAGCAGAACGTCATTATAGAGATGCAAGAATAACTGAAATTTATGAA
GGAACATCCGAAATTCAAAGACTTGTAATTGCTGGTCAAATACTTAAACAAATGTCACAA
TAA

>g14410.t6 Gene=g14410 Length=400
MFTIRQSSSSINARSIVSLSHLPETHQMLYKTCRDFADNELAPIAKQIDKEHRYPSEQVK
KMGELGLLAIAIPEKYGGTGLDYLAYAIGMEEISRGCATCGVIMTVNNTLYLGPVKNFGN
EAQKKEFLTPYTDGDKIGCFALSEPGNGSDAAAASTTAKLVGDKWVLNGTKNWITNGPDA
SAAIVFATTDKKLKHKGISAFIVERGIPGFSYGKKEDKLGIRGSSTCSLIFDDCAIPKEN
ILGEEGFGFKIAMKTLDEGRIGIAGQALGIAQASLECAVDYANKRIAFGNPISKMQTIQN
KIADMAMRIEAARLLTWRAAVLKDEGKSITKEAAMAKLAASETATFCSHQAIQILGGMGY
VTDMPAERHYRDARITEIYEGTSEIQRLVIAGQILKQMSQ

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g14410.t6 CDD cd01158 SCAD_SBCAD 24 396 0.0
10 g14410.t6 Gene3D G3DSA:1.10.540.10 - 15 137 4.7E-40
11 g14410.t6 Gene3D G3DSA:2.40.110.10 - 138 251 2.3E-44
12 g14410.t6 Gene3D G3DSA:1.20.140.10 - 252 400 9.7E-55
4 g14410.t6 PANTHER PTHR43884:SF26 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED 16 398 2.5E-155
5 g14410.t6 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 16 398 2.5E-155
13 g14410.t6 PIRSF PIRSF016578 PIGM 13 129 7.2E-7
14 g14410.t6 PIRSF PIRSF016578 PIGM 146 397 4.3E-13
3 g14410.t6 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 24 135 2.3E-33
1 g14410.t6 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 139 234 1.8E-28
2 g14410.t6 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 248 394 1.4E-49
9 g14410.t6 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 141 153 -
8 g14410.t6 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 353 372 -
6 g14410.t6 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 21 259 5.63E-86
7 g14410.t6 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 244 397 1.58E-59

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:0003995 acyl-CoA dehydrogenase activity MF
GO:0055114 NA NA

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