Gene loci information

Transcript annotation

  • This transcript has been annotated as Very long-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_2 g4322 g4322.t1 TSS g4322.t1 1191585 1191585
chr_2 g4322 g4322.t1 isoform g4322.t1 1191634 1194018
chr_2 g4322 g4322.t1 exon g4322.t1.exon1 1191634 1191701
chr_2 g4322 g4322.t1 cds g4322.t1.CDS1 1191634 1191701
chr_2 g4322 g4322.t1 exon g4322.t1.exon2 1191829 1192066
chr_2 g4322 g4322.t1 cds g4322.t1.CDS2 1191829 1192066
chr_2 g4322 g4322.t1 exon g4322.t1.exon3 1192130 1192178
chr_2 g4322 g4322.t1 cds g4322.t1.CDS3 1192130 1192178
chr_2 g4322 g4322.t1 exon g4322.t1.exon4 1192234 1192367
chr_2 g4322 g4322.t1 cds g4322.t1.CDS4 1192234 1192367
chr_2 g4322 g4322.t1 exon g4322.t1.exon5 1192618 1194018
chr_2 g4322 g4322.t1 cds g4322.t1.CDS5 1192618 1194018
chr_2 g4322 g4322.t1 TTS g4322.t1 1194175 1194175

Sequences

>g4322.t1 Gene=g4322 Length=1890
ATGTTTCGTGCAATTAATAAAGTCGCAAAAAATTCAAAAGCTCTTAAAAATCAGACAGAA
GTTATTAGATGTTTGTCTGCACAGCCACAAACAAAGTCAAAGCAAACACCAAGAGCTGAA
AAAGCTGCAAAACCTAATTTATCATTCGTTCATAATCTCTTCCGTGGACAAGTTGAGAGT
TCACAAGTTTTTCCATATCCAATTGCACTCAATCAAGAACAAATTGAATATGTTGGGGCC
TTTGTTGATCCAGTTTCAAAATTCTTTTCTGAAGTCAATAATGCTGATCGTAATGACATG
AATGCTCAAGTTGATGAAGAAACTTTGAAACATCTCTGGGAACTTGGAGCATTTGGTCTA
CAAGTACCACAAGAACTTGGTGGATTAGAATTGAACAATACACAATATGGTAGACTAGCA
GAAATCATTGGTATGAATGATTTAGGTCTTGGTATTGTTATAGGAGCCCATCAGTCCATC
GGTTTTAAGGGAATTCTTCTTTATGGTACAAAAGAGCAAAAAGAGAAATATTTACCAAAG
GTATCATCAGGTGGTGTTTATGCTGCATTTGCATTGACAGAACCATCATCTGGTAGTGAT
GCAGCATCAATTAAATGTCGTGCAGTAAAATCAGCTGATGGCAAACATTACATTTTGAAT
GGTTCAAAAATTTGGATTTCAAATGGTGGCATTGCTGATATTATGACAGTTTTTGCTCAA
ACAGAAGTTCTCGATGAAGCAACAGGACAAAAGAAAGACAAAGTAACAGCTTTTATTGTT
GAACGTGGATTTGGTGGTGTTTCAAATGGTCCACCAGAAAAGAAAATGGGAATCAAATGT
TCAAATACAGCTGAAGTTTACTTTGAAGATGTAAAAATTCCAGTTGAAAATGTTTTAGGT
AAAGAAGGTGAAGGATTTAAAGTTGCCATGAATATTCTCAATAATGGTCGTTTTGGTATG
GGAATGACACTTGGTGGTACAATGCGTTATTGTATTCAAAAAGCAACTGATCATGCAACA
CAAAGAACTCAATTTGGTAAGAAATTGGAATCTTATGGTGGCATACAAGAAAAATTAGCA
AGAATGTCAGTTTTGCAATATGTAAATCAATCGATTGCTTACATGATTTCTGGAAATATG
GATTTAGGATCAAATGATTATCATTTAGAAGCTGCTATTTCAAAAGTCTTCGCATCTGAG
GCAGCTTGGTACGTGTGTGATGAAGCCATTCAAATTTTAGGTGGAATGGGTTTCATGCGA
GATACACAGTTAGAACGCTTCATGCGTGATTTAAGAATCTTTAGAATTTTCGAGGGAACA
AATGACATTTTGCGACTTTTTGTTGCATTGACTGGCATTCAATATGCAGGAAGTCACTTG
AAAGAAGTTCAAAAAGCTTTCCAAAATCCAGCAGCTAATTTGGGATTGATTTTCAAAGAA
GCATCGAAGCGTGCAAGTTCATATATTGGTCTAGGTGGTGTAGACATGACTGGTCTTGTT
GAGCCATCACTCAAAAATTCTGCCAAACTTTGTGGTGAAAGTATCGATATGTTTGCACGC
ACTGTTGAGTCATTATTGATAAAATATGGAAAGAAAATTGTTGATGAACAATTTTTACTC
AACAGATTAGCTGATTCGGCTATTGATATTTATGCGATGGCCTCATCACTCTCACGTGCT
TCATCTGCACTTAAATCGAATTCACCAACAGCTGATTTTGAAAAGCTTATGGTTGAAACT
TGGTGTGTTGAAGCAAGCGATAGAGTAAGAATTAATTTAAGAAAAATTCATAGTGCTGAA
TTTAATGAAAATTACAAAAGAATGTCAGTAATATCCAAAAAACTTTGTGAAGCTCACGAT
ATTGTTCATAATAATCCTATTGGAGTGTAA

>g4322.t1 Gene=g4322 Length=629
MFRAINKVAKNSKALKNQTEVIRCLSAQPQTKSKQTPRAEKAAKPNLSFVHNLFRGQVES
SQVFPYPIALNQEQIEYVGAFVDPVSKFFSEVNNADRNDMNAQVDEETLKHLWELGAFGL
QVPQELGGLELNNTQYGRLAEIIGMNDLGLGIVIGAHQSIGFKGILLYGTKEQKEKYLPK
VSSGGVYAAFALTEPSSGSDAASIKCRAVKSADGKHYILNGSKIWISNGGIADIMTVFAQ
TEVLDEATGQKKDKVTAFIVERGFGGVSNGPPEKKMGIKCSNTAEVYFEDVKIPVENVLG
KEGEGFKVAMNILNNGRFGMGMTLGGTMRYCIQKATDHATQRTQFGKKLESYGGIQEKLA
RMSVLQYVNQSIAYMISGNMDLGSNDYHLEAAISKVFASEAAWYVCDEAIQILGGMGFMR
DTQLERFMRDLRIFRIFEGTNDILRLFVALTGIQYAGSHLKEVQKAFQNPAANLGLIFKE
ASKRASSYIGLGGVDMTGLVEPSLKNSAKLCGESIDMFARTVESLLIKYGKKIVDEQFLL
NRLADSAIDIYAMASSLSRASSALKSNSPTADFEKLMVETWCVEASDRVRINLRKIHSAE
FNENYKRMSVISKKLCEAHDIVHNNPIGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
15 g4322.t1 CDD cd01161 VLCAD 48 457 0.0
11 g4322.t1 Gene3D G3DSA:1.10.540.10 - 72 187 9.4E-163
12 g4322.t1 Gene3D G3DSA:2.40.110.10 - 188 302 9.4E-163
14 g4322.t1 Gene3D G3DSA:1.20.140.10 - 303 449 9.4E-163
13 g4322.t1 Gene3D G3DSA:1.20.140.10 - 492 619 4.3E-43
4 g4322.t1 PANTHER PTHR43884:SF11 VERY LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 27 495 3.4E-247
5 g4322.t1 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 27 495 3.4E-247
3 g4322.t1 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 80 184 9.5E-22
1 g4322.t1 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 189 291 3.2E-25
2 g4322.t1 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 303 449 2.2E-39
10 g4322.t1 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 191 203 -
9 g4322.t1 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 411 430 -
6 g4322.t1 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 64 316 1.01E-71
8 g4322.t1 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 301 449 1.3E-44
7 g4322.t1 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 529 597 9.34E-5

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