Gene loci information

Transcript annotation

  • This transcript has been annotated as Lipoyl synthase, 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_3 g4108 g4108.t6 TSS g4108.t6 30664816 30664816
chr_3 g4108 g4108.t6 isoform g4108.t6 30665466 30666197
chr_3 g4108 g4108.t6 exon g4108.t6.exon1 30665466 30666197
chr_3 g4108 g4108.t6 cds g4108.t6.CDS1 30665475 30666197
chr_3 g4108 g4108.t6 TTS g4108.t6 30666225 30666225

Sequences

>g4108.t6 Gene=g4108 Length=732
TTATAGCTTATGGGAGATACTTGCACAAGAGGCTGTCGATTTTGTTCAGTTAAAACTGCT
AGAATTCCTCCACAACTTGATCCAAAAGAACCAATTAATACAGCGACAGCAATTGCATCA
TGGGGTCTTGATTATATTGTACTAACAAGTGTTGATCGAGATGATTTAGCCGATGGTGGA
TCAACACACATTGCAGAAACTATTAAAGAAATTAAACGTCAAAATCCAAGAATTTTCGTT
GAATGTCTTGCACCAGATTTTAAAGGAGATCGTGAATGCATAGAGAGAATAGCAAAATCA
GGAGTTGATGTTTACGCTCATAATATTGAAACTGTTGAAAAATTGACGCCTTATGTGAGA
GACAGAAGAGCAGCTTATCGTCAATCATTGGAATGTTTAAAAACAGCAAAAGAAATCAAT
CCAGAGCTCATTACAAAATCATCAATTATGTTAGGTTTAGGCGAAACAGATTTAGAAATT
GAACAAACGATGAAAGATCTGAAAGAAGCAAAAGTAGATTGTTTAACATTAGGTCAATAT
ATGCAACCAACAAAAAGACATTTGAGTGTAATTGAATATGTTACTCCTGAAAAATTCAAA
TTATGGGAAGATAAAGGAAATGAAATGGGATTTCTATATACTGCATCTGGTCCATTAGTA
AGAAGTTCATATAAAGCTGGTGAATTTTTTATTACGAGTATTTTAAAGAATCGCCGTAAT
TATTCAAATTAA

>g4108.t6 Gene=g4108 Length=240
MGDTCTRGCRFCSVKTARIPPQLDPKEPINTATAIASWGLDYIVLTSVDRDDLADGGSTH
IAETIKEIKRQNPRIFVECLAPDFKGDRECIERIAKSGVDVYAHNIETVEKLTPYVRDRR
AAYRQSLECLKTAKEINPELITKSSIMLGLGETDLEIEQTMKDLKEAKVDCLTLGQYMQP
TKRHLSVIEYVTPEKFKLWEDKGNEMGFLYTASGPLVRSSYKAGEFFITSILKNRRNYSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g4108.t6 CDD cd01335 Radical_SAM 2 198 0.0000001
5 g4108.t6 Gene3D G3DSA:3.20.20.70 Aldolase class I 2 197 0.0000000
3 g4108.t6 Hamap MF_00206 Lipoyl synthase [lipA]. 1 236 112.2835310
2 g4108.t6 PANTHER PTHR10949 LIPOYL SYNTHASE 1 236 0.0000000
6 g4108.t6 PIRSF PIRSF005963 Lipoyl_synth 1 240 0.0000000
1 g4108.t6 Pfam PF04055 Radical SAM superfamily 4 164 0.0000000
10 g4108.t6 SFLD SFLDS00029 Radical SAM 4 164 0.0000000
8 g4108.t6 SMART SM00729 MiaB 1 201 0.0000000
4 g4108.t6 SUPERFAMILY SSF102114 Radical SAM enzymes 2 234 0.0000000
9 g4108.t6 TIGRFAM TIGR00510 lipA: lipoyl synthase 1 234 0.0000000

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:0051539 4 iron, 4 sulfur cluster binding MF
GO:0003824 catalytic activity MF
GO:0051536 iron-sulfur cluster binding MF
GO:0009107 lipoate biosynthetic process BP
GO:0016992 lipoate synthase 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