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.t6 TSS g4322.t6 1191585 1191585
chr_2 g4322 g4322.t6 isoform g4322.t6 1191634 1194018
chr_2 g4322 g4322.t6 exon g4322.t6.exon1 1191634 1192084
chr_2 g4322 g4322.t6 exon g4322.t6.exon2 1192234 1192367
chr_2 g4322 g4322.t6 cds g4322.t6.CDS1 1192311 1192367
chr_2 g4322 g4322.t6 exon g4322.t6.exon3 1192618 1194018
chr_2 g4322 g4322.t6 cds g4322.t6.CDS2 1192618 1194018
chr_2 g4322 g4322.t6 TTS g4322.t6 1194175 1194175

Sequences

>g4322.t6 Gene=g4322 Length=1986
ATGTTTCGTGCAATTAATAAAGTCGCAAAAAATTCAAAAGCTCTTAAAAATCAGACAGAA
GTTATTAGGTAAAATTAGAAAATTGCAATTATTTAAATTTGACCTAATTTCATAATACAT
AAATATTTACAACTCACAGTCAACGACTTGTGGACTTTGAACTTTGTTTCATTCAAAAAA
AAATTTTTTTTTTAGATGTTTGTCTGCACAGCCACAAACAAAGTCAAAGCAAACACCAAG
AGCTGAAAAAGCTGCAAAACCTAATTTATCATTCGTTCATAATCTCTTCCGTGGACAAGT
TGAGAGTTCACAAGTTTTTCCATATCCAATTGCACTCAATCAAGAACAAATTGAATATGT
TGGGGCCTTTGTTGATCCAGTTTCAAAATTCTTTTCTGAAGTCAATAATGCTGATCGTAA
TGACATGAATGCTGTAAGTTGACCTTCAATTGTCTACAAGTACCACAAGAACTTGGTGGA
TTAGAATTGAACAATACACAATATGGTAGACTAGCAGAAATCATTGGTATGAATGATTTA
GGTCTTGGTATTGTTATAGGAGCCCATCAGTCCATCGGTTTTAAGGGAATTCTTCTTTAT
GGTACAAAAGAGCAAAAAGAGAAATATTTACCAAAGGTATCATCAGGTGGTGTTTATGCT
GCATTTGCATTGACAGAACCATCATCTGGTAGTGATGCAGCATCAATTAAATGTCGTGCA
GTAAAATCAGCTGATGGCAAACATTACATTTTGAATGGTTCAAAAATTTGGATTTCAAAT
GGTGGCATTGCTGATATTATGACAGTTTTTGCTCAAACAGAAGTTCTCGATGAAGCAACA
GGACAAAAGAAAGACAAAGTAACAGCTTTTATTGTTGAACGTGGATTTGGTGGTGTTTCA
AATGGTCCACCAGAAAAGAAAATGGGAATCAAATGTTCAAATACAGCTGAAGTTTACTTT
GAAGATGTAAAAATTCCAGTTGAAAATGTTTTAGGTAAAGAAGGTGAAGGATTTAAAGTT
GCCATGAATATTCTCAATAATGGTCGTTTTGGTATGGGAATGACACTTGGTGGTACAATG
CGTTATTGTATTCAAAAAGCAACTGATCATGCAACACAAAGAACTCAATTTGGTAAGAAA
TTGGAATCTTATGGTGGCATACAAGAAAAATTAGCAAGAATGTCAGTTTTGCAATATGTA
AATCAATCGATTGCTTACATGATTTCTGGAAATATGGATTTAGGATCAAATGATTATCAT
TTAGAAGCTGCTATTTCAAAAGTCTTCGCATCTGAGGCAGCTTGGTACGTGTGTGATGAA
GCCATTCAAATTTTAGGTGGAATGGGTTTCATGCGAGATACACAGTTAGAACGCTTCATG
CGTGATTTAAGAATCTTTAGAATTTTCGAGGGAACAAATGACATTTTGCGACTTTTTGTT
GCATTGACTGGCATTCAATATGCAGGAAGTCACTTGAAAGAAGTTCAAAAAGCTTTCCAA
AATCCAGCAGCTAATTTGGGATTGATTTTCAAAGAAGCATCGAAGCGTGCAAGTTCATAT
ATTGGTCTAGGTGGTGTAGACATGACTGGTCTTGTTGAGCCATCACTCAAAAATTCTGCC
AAACTTTGTGGTGAAAGTATCGATATGTTTGCACGCACTGTTGAGTCATTATTGATAAAA
TATGGAAAGAAAATTGTTGATGAACAATTTTTACTCAACAGATTAGCTGATTCGGCTATT
GATATTTATGCGATGGCCTCATCACTCTCACGTGCTTCATCTGCACTTAAATCGAATTCA
CCAACAGCTGATTTTGAAAAGCTTATGGTTGAAACTTGGTGTGTTGAAGCAAGCGATAGA
GTAAGAATTAATTTAAGAAAAATTCATAGTGCTGAATTTAATGAAAATTACAAAAGAATG
TCAGTAATATCCAAAAAACTTTGTGAAGCTCACGATATTGTTCATAATAATCCTATTGGA
GTGTAA

>g4322.t6 Gene=g4322 Length=485
MNDLGLGIVIGAHQSIGFKGILLYGTKEQKEKYLPKVSSGGVYAAFALTEPSSGSDAASI
KCRAVKSADGKHYILNGSKIWISNGGIADIMTVFAQTEVLDEATGQKKDKVTAFIVERGF
GGVSNGPPEKKMGIKCSNTAEVYFEDVKIPVENVLGKEGEGFKVAMNILNNGRFGMGMTL
GGTMRYCIQKATDHATQRTQFGKKLESYGGIQEKLARMSVLQYVNQSIAYMISGNMDLGS
NDYHLEAAISKVFASEAAWYVCDEAIQILGGMGFMRDTQLERFMRDLRIFRIFEGTNDIL
RLFVALTGIQYAGSHLKEVQKAFQNPAANLGLIFKEASKRASSYIGLGGVDMTGLVEPSL
KNSAKLCGESIDMFARTVESLLIKYGKKIVDEQFLLNRLADSAIDIYAMASSLSRASSAL
KSNSPTADFEKLMVETWCVEASDRVRINLRKIHSAEFNENYKRMSVISKKLCEAHDIVHN
NPIGV

Protein features from InterProScan

Transcript Database ID Name Start End E.value
11 g4322.t6 Gene3D G3DSA:1.10.540.10 - 2 43 4.9E-138
12 g4322.t6 Gene3D G3DSA:2.40.110.10 - 44 158 4.9E-138
13 g4322.t6 Gene3D G3DSA:1.20.140.10 - 159 305 4.9E-138
14 g4322.t6 Gene3D G3DSA:1.20.140.10 - 348 475 2.8E-43
4 g4322.t6 PANTHER PTHR43884:SF11 VERY LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 1 352 1.9E-202
5 g4322.t6 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 1 352 1.9E-202
3 g4322.t6 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 3 40 2.1E-7
1 g4322.t6 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 45 147 2.1E-25
2 g4322.t6 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 159 305 1.3E-39
10 g4322.t6 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 47 59 -
9 g4322.t6 ProSitePatterns PS00073 Acyl-CoA dehydrogenases signature 2. 267 286 -
6 g4322.t6 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 6 172 4.97E-59
8 g4322.t6 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 157 305 8.05E-45
7 g4322.t6 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 385 453 7.42E-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

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