Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative 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_2 g5005 g5005.t3 TSS g5005.t3 6398234 6398234
chr_2 g5005 g5005.t3 isoform g5005.t3 6398315 6399819
chr_2 g5005 g5005.t3 exon g5005.t3.exon1 6398315 6398756
chr_2 g5005 g5005.t3 exon g5005.t3.exon2 6398921 6399701
chr_2 g5005 g5005.t3 cds g5005.t3.CDS1 6399206 6399701
chr_2 g5005 g5005.t3 exon g5005.t3.exon3 6399767 6399819
chr_2 g5005 g5005.t3 cds g5005.t3.CDS2 6399767 6399819
chr_2 g5005 g5005.t3 TTS g5005.t3 6399985 6399985

Sequences

>g5005.t3 Gene=g5005 Length=1276
ATGTCTATAAGAAATAAATATTTGTTACATAGTTCTAAGAATATAATCTCAAGATTTTTC
ACTACGAATCTTCCAAATGATGTGATAGTGTTACAAGAATTATGTAGAAAGTTTGCCGAT
ACTGAATTAAAACCTGTTGCAAGTCATCATGATAAAGAAAGTAAATATCCAACTGAACAA
ATTAAGCAGCTTGGTGAAATGGGATTTATGGGAGTAAATGCATCCGTTGAATTCGGTGGT
TCTGGCTTAAAAACTCTTGCACTCTCTGTTATTGTTGAAGAGCTTTCTAGAGGCGATGCA
TCAGTAGGGTCTATTGTATCTATTCATAATTGTCTTTATGCAAATTTAATTGATAGAGTA
GCTAATCAGGCACAAAAAGAACAATGGTTAAGAGAATTTACACAAGGAAAGAAAATTGGA
GCTTTTGCATTAAGTGAAAGTGATGCCGGTTCGGATGTTGCAAATATTTCAACAAAAGCT
GTTAAAGATGGTGATTATTATATTTTAAATGGTACAAAAGCATGGGTAAGCTAGAATGAA
TTATGTTAAAAATTTTTTTTATTTTAGAATATAAATTTATTATTCTTAACAGGTCACAAG
TGCGGAACAAGCTTCTGCAGCTATAATTTTTGCTACTGTCGATAGAGATAAAAAACATAA
AGGCATAGCTGCATTTCTAGTCAGTTTAGATCAACCAGGTGTAGTTGTAGGAAAAAATGA
ACGAAAAATGAGCATTAAAGCTACCTCAACGTGTACTATCACATTAAATGATGTTCATGT
TCATTCCAGTCAACTTTTGTGTAAACCAGGTGAAGGTTTCAGAGTAGCTATGGAGCAACT
TGATGTTGCTCGAATTGGAATTGCTTCACAAGCATTAGGTATCGCTCAAGCTTCTTTGGA
TACTGCCATTGCATATGCAGCTCAACGTATAGCTTTTGATAATCCCATACTAAGATTATC
GTCTGTTAAACAAAGACTTGCAGAAATGGCAACATCAATTGAATCGTCAAGACTTTTAGT
ACGACAAGCAGCTCAGAAAAAAGACGAGCATCTACGCTCAACAAAATACACATCAATGGC
AAAATGGCAAGCTAGTCAAACTGCAACATTCTGTGCACATAATTGTATCCAAATCATGGG
TGGGATGGGAATTGTTGAGTCATCTGATGCTGAACGTTACTATCGAGACGCAAGAATAAC
TGAAATATATGGAGGAGTTACAGATGTACAAATAATGATTATTGCTGAGCAGTTACAAAA
GGAATATGGGCTATGA

>g5005.t3 Gene=g5005 Length=182
MSIKATSTCTITLNDVHVHSSQLLCKPGEGFRVAMEQLDVARIGIASQALGIAQASLDTA
IAYAAQRIAFDNPILRLSSVKQRLAEMATSIESSRLLVRQAAQKKDEHLRSTKYTSMAKW
QASQTATFCAHNCIQIMGGMGIVESSDAERYYRDARITEIYGGVTDVQIMIIAEQLQKEY
GL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
6 g5005.t3 Gene3D G3DSA:1.20.140.10 - 6 181 0.0e+00
2 g5005.t3 PANTHER PTHR43884:SF26 MEDIUM-CHAIN SPECIFIC ACYL-COA DEHYDROGENASE, MITOCHONDRIAL-LIKE PROTEIN-RELATED 2 180 0.0e+00
3 g5005.t3 PANTHER PTHR43884 ACYL-COA DEHYDROGENASE 2 180 0.0e+00
1 g5005.t3 Pfam PF00441 Acyl-CoA dehydrogenase, C-terminal domain 28 176 0.0e+00
4 g5005.t3 SUPERFAMILY SSF56645 Acyl-CoA dehydrogenase NM domain-like 1 39 8.7e-05
5 g5005.t3 SUPERFAMILY SSF47203 Acyl-CoA dehydrogenase C-terminal domain-like 27 180 0.0e+00

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5005/g5005.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5005.t3.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0016627 oxidoreductase activity, acting on the CH-CH group of donors 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