Gene loci information

Transcript annotation

  • This transcript has been annotated as Trifunctional enzyme subunit alpha, 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_1 g9117 g9117.t65 isoform g9117.t65 219159 222072
chr_1 g9117 g9117.t65 exon g9117.t65.exon1 219159 219343
chr_1 g9117 g9117.t65 exon g9117.t65.exon2 219397 219629
chr_1 g9117 g9117.t65 cds g9117.t65.CDS1 219610 219629
chr_1 g9117 g9117.t65 exon g9117.t65.exon3 219766 220005
chr_1 g9117 g9117.t65 cds g9117.t65.CDS2 219766 220005
chr_1 g9117 g9117.t65 exon g9117.t65.exon4 220059 220181
chr_1 g9117 g9117.t65 cds g9117.t65.CDS3 220059 220181
chr_1 g9117 g9117.t65 exon g9117.t65.exon5 220262 220702
chr_1 g9117 g9117.t65 cds g9117.t65.CDS4 220262 220702
chr_1 g9117 g9117.t65 exon g9117.t65.exon6 220766 221309
chr_1 g9117 g9117.t65 cds g9117.t65.CDS5 220766 220994
chr_1 g9117 g9117.t65 exon g9117.t65.exon7 221472 221877
chr_1 g9117 g9117.t65 exon g9117.t65.exon8 222003 222072
chr_1 g9117 g9117.t65 TSS g9117.t65 222169 222169
chr_1 g9117 g9117.t65 TTS g9117.t65 NA NA

Sequences

>g9117.t65 Gene=g9117 Length=2242
ATGGCTAGTTTGCGAGTTAAAGGATTTTTATCTACTATTACACGAGTGAAGAGAATTGGT
CTGCAGAATTCTTCTATCAACCAATTTAATCGTAATTGTTCATCGACGTCGGCAAAAAAT
ATCAAAACGTCCATTGTTGATAATGTACTTGTAATCAAATTAGATCAACCAGGCTCAAAA
GTTAATACTTTAGGAAAACAAATTACTAATGAATTTGAAGCAGTTCTTAAAGAGTTTGAG
ACAAATCCAGCTGTAAAGTCTGCTGTTCTCATATCTGGCAAGCCATCTTGTTTCGTAGCT
GGCGCAGATATAACAATGTTAGAAGAATGTAAAACAGAAAATGATGCCAGGAAGATCAGT
CATGAAGCTCAAATTATGTTTGATCGAATGGAAAAGTCAAATAAGCCCATTGTCTGTGCA
ATTCATGGAACATGTTTTGGAGGCGGATTAGAATTGGCGCTAGCATGCCATTATAGATTT
TAAATAAATTTATATTTCAAATCTATTTGAAAGGTGCTGGAGGAACGCAACGTGTTCAAA
AATTAACATCAATCCCTACCACACTCGATTTGGCACTTACTGGAAAAACTGTAAAGGCTG
ATAAAGCAAAAAAAATTGGCTTAGTTGATTTGCTTGTTGATGAATTGGGTCCAGGCTTGC
ACGATCCTTCAAAAAACACTTTGAAATATCTTGAGGATACAGCAATTAAAGTTGCCAAAG
ATCTTGCAAGTGGTACAATCAAAGTGAATCGTCAAAAGACTGGTGTAATCAATAAGATTA
CAGAAACAGCAATGGGATTTGATTTTGTAAAAGATTTTATTTTTAAAAAAGCACGTCAAC
AAGTTATGAAAATGAGTAATGGTCTCTATCCTGCACCTCTCAAGATTTTGGAAGTAGTTC
GTACTGGTGCAGATAAAGGTTTTGAAGCAGGACTGGAAGCTGAAAGAAATGCTTTTGGAA
CATTATCTCAAACACCACAATCTAAAGGACTGATTTCACTTTTTAGAGGACAAACAGAAT
GCAAGAAAAATCGTTTTGGAAATCCCAGTCGACCTGTAAAAAATGTTGCTGTATTGGGCG
CTGGATTGATGGGGGCTGGTATTGTTCAAGTAACAGTTGATAAAGGCTATAATGTCATAA
TGAAAGATGCAACAGAGGCTGGTTTATCAAGAGGTATTGGACAAATACAAAAAGGTCTTG
ATGGTGCAGTAAAAAGAAAAAAAATTAGCAGTTTGGATAAAGATAAAATAATGAGTAATT
TAACATCGACATTGTCCTACGAACCTTTCAGAAATGCAGATATAGTTATCGAAGCTGTTT
TTGAGAATTTAGACATTAAACATCGTGTAATAAAGGAAATGGAATCTGTCATTCCTGAAC
ATTGCATTATTGCAACAAATACATCAGCTCTTCCCATCACAAAAATTGCAGCCGGTTCAT
CAAGACCAGATAAAGTTATTGTTGATAAGATGCAACTTTTGGAAATTATCACACATCCGG
GCACATCTTTAGAAGCAAAACAAGCAGCAGTTGATTTAGGACTGAAGCAAGGAAAAGTAG
TTATTACAGTTGGTGATGGACCAGGTTTTTATACAACTCGAATTCTTTCAACTATGGTTG
CTGAGGGCATGTTGATAATGCAAGAAGGTGTCGATCCAAAGGACATTGATAAACTCACAA
AACAATTTGGTTTCCCAGTTGGTCTTGCTACTTTAATTGATGAAGTGGGAATTGATGTTG
GTATGCACATTTTCAAAGACTTGCAAGCAGCTTTTGGTGATCGTTTATCAGGCGGTGACG
CAAATATCTCAGTAGATTTGGTTAATGTTTATCATAAAACTTAGGAAAAGGAATTTTCGT
TTATGATGGTCAAACGAAAGGAAGTCGTGAAGTCAATCCTGAGGCATTAGCAATCATTAA
ACAAAAATACGCTTTGGTGTCCAAAGGAGCAAATCAACCAGAAGATTTACAATTGAGAAT
GGTGTCTAGATTTATTAATGAAGCCGTAATGTGTCTTGAAGAAAAGATTTTGCACAGTCC
ATTAGAAGGTGATATTGGTGCCGTATTTGGTCTCGGATTCCCACCTTTTTCCGGTGGTCC
ATTTAAATTTGTTGATACATTCGGAGCTGATAAGCTTGTAAACAAAATGCTATCATATGC
AGAGCTCTATGGAAGACCGTTTCAACCAGCTCAAACATTACTTGATATGGCAAAAGATTC
ATCAAAGAAATTTTATAAATAA

>g9117.t65 Gene=g9117 Length=350
MGFDFVKDFIFKKARQQVMKMSNGLYPAPLKILEVVRTGADKGFEAGLEAERNAFGTLSQ
TPQSKGLISLFRGQTECKKNRFGNPSRPVKNVAVLGAGLMGAGIVQVTVDKGYNVIMKDA
TEAGLSRGIGQIQKGLDGAVKRKKISSLDKDKIMSNLTSTLSYEPFRNADIVIEAVFENL
DIKHRVIKEMESVIPEHCIIATNTSALPITKIAAGSSRPDKVIVDKMQLLEIITHPGTSL
EAKQAAVDLGLKQGKVVITVGDGPGFYTTRILSTMVAEGMLIMQEGVDPKDIDKLTKQFG
FPVGLATLIDEVGIDVGMHIFKDLQAAFGDRLSGGDANISVDLVNVYHKT

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g9117.t65 Gene3D G3DSA:3.90.226.10 - 3 84 0
6 g9117.t65 Gene3D G3DSA:3.40.50.720 - 89 266 0
7 g9117.t65 Gene3D G3DSA:1.10.1040.50 - 267 348 0
3 g9117.t65 PANTHER PTHR43612 TRIFUNCTIONAL ENZYME SUBUNIT ALPHA 3 344 0
2 g9117.t65 Pfam PF02737 3-hydroxyacyl-CoA dehydrogenase, NAD binding domain 91 262 0
1 g9117.t65 Pfam PF00725 3-hydroxyacyl-CoA dehydrogenase, C-terminal domain 265 338 0
4 g9117.t65 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 88 264 0
5 g9117.t65 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 264 330 0

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:0016616 oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor MF
GO:0070403 NAD+ binding MF
GO:0006631 fatty acid metabolic process BP
GO:0055114 NA NA
GO:0016491 oxidoreductase activity MF

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