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_4 g14888 g14888.t1 isoform g14888.t1 2846858 2851533
chr_4 g14888 g14888.t1 exon g14888.t1.exon1 2846858 2848368
chr_4 g14888 g14888.t1 cds g14888.t1.CDS1 2846858 2848368
chr_4 g14888 g14888.t1 exon g14888.t1.exon2 2848606 2849013
chr_4 g14888 g14888.t1 cds g14888.t1.CDS2 2848606 2849013
chr_4 g14888 g14888.t1 exon g14888.t1.exon3 2849461 2850033
chr_4 g14888 g14888.t1 cds g14888.t1.CDS3 2849461 2850033
chr_4 g14888 g14888.t1 exon g14888.t1.exon4 2850114 2850939
chr_4 g14888 g14888.t1 cds g14888.t1.CDS4 2850114 2850939
chr_4 g14888 g14888.t1 exon g14888.t1.exon5 2850996 2851178
chr_4 g14888 g14888.t1 cds g14888.t1.CDS5 2850996 2851178
chr_4 g14888 g14888.t1 exon g14888.t1.exon6 2851231 2851533
chr_4 g14888 g14888.t1 cds g14888.t1.CDS6 2851231 2851533
chr_4 g14888 g14888.t1 TSS g14888.t1 2851575 2851575
chr_4 g14888 g14888.t1 TTS g14888.t1 NA NA

Sequences

>g14888.t1 Gene=g14888 Length=3804
ATGTTCCGTGTGACTAGAATTGGTGTTTTATCAAAATTCAAAAAATGTAATTCTAATGTA
CATCAAAAATGCTCTCTTTATACAACAATAAAAGTTCATCAATCTGAAACCAATAAGAAT
ACTGTAGAGAAAAATTCTTCATTTGTTCATAACATATTTCGTGGTCAAATTGAAAGTTCA
CAAGTTTTTCCATTTCCGATGGCACTTAATGAGGAACAACTTGAAAATACAAGCGCATTT
ATTGATCCAATGACGAAATTTTTTACTCAAGTTAACAATGCTGATAAAAATGATGCAAAT
GAAATTATAGATCCAGAAGTTGTAAAACATCTTTCTGAGACAGGTGCATTTGGTTTACAA
GTTCCACTAGAATATGGAGGATTAGGACTGAACAACACTCAGTATGGTAGAATGGGTGAA
ATTATTGGAATGTATGATTTAGGTCTTTCAATTTTCATTGGTGCACATCAGTCAATTGGT
TTTAAAGGAATTTTATTGTATGGAACAAAAGAGCAAAAAGCAAAATATTTACCAAAATTA
TCATCAGGAGAAAATATAACAGCATTTGCATTAACAGAACCGTCAGCTGGTAGTGATGCA
GCATCAATTAAAAGTCGAGCTGTTAAATCAGCTGATGGCAAGCATTACATTTTGAATGGA
TCTAAAATTTGGATCAGTAACGGTGGCATAGCTGAAATCATGACAGTATTTGCAAGGACT
GAAGTTGTTGATGAAAAAACAGGACAAAAAAAAGATAAAATTACAGCATTTATTGTTGAA
CGAGCATTTGGTGGTGTTTCAAATGGTCCACCAGAGAAAAAACTAGGAATTAAATGCTCA
AATACAGCAGAAGTTTATTTTGAAGATGTAAAAATTCCAATTGAAAATGTTTTAGGTGGT
GAAGGAAATGGATTTAAAGTTGCAATGAATATATTAAATAATGGAAGATTTGGGATGGGA
ATGGCACTTGGTGGAACAATGAGAATGTCAATACAAAAAGCAACAGAGCATGCAACACAA
AGAGTACAATTTGGTAGAAAACTAGAAACTTATGGCAGCATACAAGAGAAACTTGCACGA
ATGAGCACAGTTCATTATGTCAATCAGTCAATTGCTTATATGATTTCATCAAATATGGAC
TTGGGCTCAAATGATTATCATCTTGAAGCTGCAATATCTAAAGTCTTTGCATCTGAAGGT
GCTTGGTATGTTTGTGACGAAGCAATTCAAATTTTAGGTGGAATGGGTTTCATGAGAAGC
ACCGGATTGGAAAGATTTTTACGAGATTTGAGAATTTTTAGGATTTTTGAAGGTGCGAAT
GATATTTTAAGACTCTTCATAGCACTCACTGGCATTCAATATGCTGGCTCACATTTAAAA
CAAGTTCAAAAAGCATTAAAAAATCCAATCGGAAACTTTGGTATAATTTTGAAAGAAGCA
TCAAAAAGAGCAGGATCATTCATAAATTTAGGCAGTGATGGCATGACAATAACAAATTAT
GTTGACGCATCACTTTTACCATCAGCAAAACTTTGTGGTGAAAGCATCGATATGTTTTCA
CGTTCAGTTGATAAACTTTTAATTAAATATGGAAAAGGAATTATTGATGAGCAATTTTTA
TTAAATCGTTTAGCAGATTCAGCAATTGACATTTATGCAATGGCTTGTGCATTATCAAGA
TGTTCACGTTCGATGAAATTTAAATTACCTTCAGTTGAGATTGAAAAATTAATGACTGAA
AGTTGGTGCCTTGAAGCAAGCGACAGAGTAAGAGTTAATTTAAGAAAAATTCATAGTTCT
GATTTTCATGAAAATTATAAAAGAATGACAAAAATTTCTGAAAATGTTTGTAAAGTTAAA
GATATTGTTCATAATAATCCAATAGAATTTTTCAACTTTGATTTTACAAATAATCAAAAT
TTTGATGCAATAGAAATTTTTGATTGTGAAAATTCATCAAAAACTCTTGAAATAATTCAA
AATGAAAAATTTCAAAACGATTTTAAAGAATTAAAAAAAGTCACAACTTTTTTGTTTAAT
ATTCATGGTGATTTAGACAAAATCAAAGGAGGAAAATTTAATACAAATATTTTGAATTTT
CAAAGGCCTCTCGTTGTTGCTTTCGTTCAAGAAAATAACAAAGTTTTTGAGATCTTTTGG
AAAACAAAAAATTCAAATTTTCATAACATTTCTATTTCTAACAGTTTTCGAAATTGGAGT
GCAATTAATTTTATGAATGTTATTGAGTTTTTTATAAAGTTCTTGAAGAATGAAGTATCT
AACAGTCGATCAGCAATTTCACCATACTATGCCTCTGAAACAGACGATACAATCACTCAT
TGTTTGACAGAACTTGTTGACTCATTTAATGACAATTTGTTACTTGTATCCATCAAGTAT
GATAATATGGATGCTTATAATTTCTTAAAAACGCCATCATTTGATGAATTAATGGTTTAT
AAGAAAGGCAAAGCTGTCACAACGTCGACAATTGACCTTGCATTCAGTAAAGAAAACGTA
AAATTATTTCATGACCTTCTTCAAAAAGAAATGAAATTTCCAAAATTATTTAAGCAAAAA
AGAGAAATTTTTGAGGAACAATGTCCAGAACTGAAAGAATTGGTTGAAAATTTTGAACAA
ATGCATAAATTTGTTGATGAAATTAATGACGAAGAAGACTGTGAAAAATTGTGGAATTTA
TTAATTGGAAAAAATGATGATAAAATTTCATCTGATGATCCTTTAAGAATTTTTTATGGT
CTATTAAAGAAGCATTATGGAAAGAAATATTGTTATAATACCAAAAATATTTCTCTTCTC
AAACATGCAAAAAATCTTAGAAAGGAAAAACTTTACAACTTACTCATTGAACTAAAAATG
AAGTACAGTTCAAATGATGATGAAAACAATAATATCAAAGCTGAACATGTTGATTCTAAT
TTTTCTTCAGCAATGAAACTCAAGGGTGATCACATAACTCAACTTTTGAATTCTTCGCGT
CTTAAAATTGATGAAAATGCTCTGACATGTGAACACCGAAAAACTTTGAGGAAAATTTTT
GATTATTTGGATACAATTGAATTCATCAAACCTATTCTTATGATTATAGCTGCGTGTTCA
AATTTTTTAATTCTTTTTGATACTGACAGTGATGATGTTACAAGAACATTAATGGAAGGA
TTTCAAGGTACACTTGGAGCTGCTTTCTTTAAAAAAGGTCGATTGATTGTTGGTGCTAAA
AGTTTATTTAATTCTGAAACAATGAAAGTAATTTGTGATAAGAAATTCAATTTTGAGACT
TTAAAAGTTGAAGTTGCAAGAAGCATTGGAACTTTGGTGCATGAACTTTGCCATTATGCA
ATGTATTTGATTTTTAAAAATGATTGTCGACCTTATCTTGGTGATTTCAACAGTAAATTT
GATGGTATTGTTAAAAACTTAAATACAAGTAGAATTAACCTTAAAAATGATGACGAAAAA
AGAATTATTGGAGCTGTATTTACTCATTATAAAAATACTGCGTGGCATGCTGAAGCAATT
GTTCGTGTTCCACAAATTTATGCTGAGTTTTCTCATATAAATGTACGTTTGAATGAATTA
AGGGAAACATTTAAGGAACTTTTTGAATTCTATGAAAAAAATCTTTTAGAAATAGTAAAA
GTTTCAGTTGAAACTATTGAGAAAGTCAACAAGAAAAGTGTAAAATTTTCTGACCTTGAT
GAACATTGGAAAGAAGTAACAAGAAAATCAGAAATAAATTTTCATGAAAATGATTTGAAA
TTATCTTACTTGATAAGAGAGTAG

>g14888.t1 Gene=g14888 Length=1267
MFRVTRIGVLSKFKKCNSNVHQKCSLYTTIKVHQSETNKNTVEKNSSFVHNIFRGQIESS
QVFPFPMALNEEQLENTSAFIDPMTKFFTQVNNADKNDANEIIDPEVVKHLSETGAFGLQ
VPLEYGGLGLNNTQYGRMGEIIGMYDLGLSIFIGAHQSIGFKGILLYGTKEQKAKYLPKL
SSGENITAFALTEPSAGSDAASIKSRAVKSADGKHYILNGSKIWISNGGIAEIMTVFART
EVVDEKTGQKKDKITAFIVERAFGGVSNGPPEKKLGIKCSNTAEVYFEDVKIPIENVLGG
EGNGFKVAMNILNNGRFGMGMALGGTMRMSIQKATEHATQRVQFGRKLETYGSIQEKLAR
MSTVHYVNQSIAYMISSNMDLGSNDYHLEAAISKVFASEGAWYVCDEAIQILGGMGFMRS
TGLERFLRDLRIFRIFEGANDILRLFIALTGIQYAGSHLKQVQKALKNPIGNFGIILKEA
SKRAGSFINLGSDGMTITNYVDASLLPSAKLCGESIDMFSRSVDKLLIKYGKGIIDEQFL
LNRLADSAIDIYAMACALSRCSRSMKFKLPSVEIEKLMTESWCLEASDRVRVNLRKIHSS
DFHENYKRMTKISENVCKVKDIVHNNPIEFFNFDFTNNQNFDAIEIFDCENSSKTLEIIQ
NEKFQNDFKELKKVTTFLFNIHGDLDKIKGGKFNTNILNFQRPLVVAFVQENNKVFEIFW
KTKNSNFHNISISNSFRNWSAINFMNVIEFFIKFLKNEVSNSRSAISPYYASETDDTITH
CLTELVDSFNDNLLLVSIKYDNMDAYNFLKTPSFDELMVYKKGKAVTTSTIDLAFSKENV
KLFHDLLQKEMKFPKLFKQKREIFEEQCPELKELVENFEQMHKFVDEINDEEDCEKLWNL
LIGKNDDKISSDDPLRIFYGLLKKHYGKKYCYNTKNISLLKHAKNLRKEKLYNLLIELKM
KYSSNDDENNNIKAEHVDSNFSSAMKLKGDHITQLLNSSRLKIDENALTCEHRKTLRKIF
DYLDTIEFIKPILMIIAACSNFLILFDTDSDDVTRTLMEGFQGTLGAAFFKKGRLIVGAK
SLFNSETMKVICDKKFNFETLKVEVARSIGTLVHELCHYAMYLIFKNDCRPYLGDFNSKF
DGIVKNLNTSRINLKNDDEKRIIGAVFTHYKNTAWHAEAIVRVPQIYAEFSHINVRLNEL
RETFKELFEFYEKNLLEIVKVSVETIEKVNKKSVKFSDLDEHWKEVTRKSEINFHENDLK
LSYLIRE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
14 g14888.t1 CDD cd01161 VLCAD 47 456 0.0
13 g14888.t1 Coils Coil Coil 861 881 -
9 g14888.t1 Gene3D G3DSA:1.10.540.10 - 71 186 4.5E-160
10 g14888.t1 Gene3D G3DSA:2.40.110.10 - 187 301 4.5E-160
12 g14888.t1 Gene3D G3DSA:1.20.140.10 - 302 448 4.5E-160
11 g14888.t1 Gene3D G3DSA:1.20.140.10 - 493 620 5.5E-40
4 g14888.t1 PANTHER PTHR43884:SF11 VERY LONG-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL 41 510 8.3E-238
5 g14888.t1 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 41 510 8.3E-238
3 g14888.t1 Pfam PF02771 Acyl-CoA dehydrogenase, N-terminal domain 79 184 7.6E-21
1 g14888.t1 Pfam PF02770 Acyl-CoA dehydrogenase, middle domain 188 290 7.7E-26
2 g14888.t1 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 302 448 3.3E-35
8 g14888.t1 ProSitePatterns PS00072 Acyl-CoA dehydrogenases signature 1. 190 202 -
6 g14888.t1 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 61 315 1.1E-71
7 g14888.t1 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 300 448 1.08E-41

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