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.t4 TSS g4108.t4 30664816 30664816
chr_3 g4108 g4108.t4 isoform g4108.t4 30665010 30666197
chr_3 g4108 g4108.t4 exon g4108.t4.exon1 30665010 30665398
chr_3 g4108 g4108.t4 cds g4108.t4.CDS1 30665015 30665398
chr_3 g4108 g4108.t4 exon g4108.t4.exon2 30665472 30666197
chr_3 g4108 g4108.t4 cds g4108.t4.CDS2 30665472 30666197
chr_3 g4108 g4108.t4 TTS g4108.t4 30666225 30666225

Sequences

>g4108.t4 Gene=g4108 Length=1115
AAAAAATGTTACGAAATTCAATAAAAATCAAAACACCAACAAACATTCAAAAGTTTCGCT
ATAAGCATTCATCAGCTGCATTAGAGAAAATTCGTGAGAAGTTAGAGAATGGACCAAATT
TTCAAGATTTTGTTCAAAATCCAAATCATAGTCGTGAAGAAATGGCAAAAGAATTTGAAG
GAAGGTTGAAGAAAGAAAAAGGCGAAAAAGAGAGATTGAGATTGCCACCATGGTTGAAAA
CACAAATTCCAATAGGAAAGAATTATGATAAAATCAAGAATCAGCTACGTGAACTTAAGC
TATCGACAGTGTGTGAAGAGGCAAGATGTCCAAATATCGGTGAATGCTGGGGTGGTGGAA
AGCATGGAACACAAACAGCTACAATTATGCTTATGGGAGATACTTGCACAAGAGGCTGTC
GATTTTGTTCAGTTAAAACTGCTAGAATTCCTCCACAACTTGATCCAAAAGAACCAATTA
ATACAGCGACAGCAATTGCATCATGGGGTCTTGATTATATTGTACTAACAAGTGTTGATC
GAGATGATTTAGCCGATGGTGGATCAACACACATTGCAGAAACTATTAAAGAAATTAAAC
GTCAAAATCCAAGAATTTTCGTTGAATGTCTTGCACCAGATTTTAAAGGAGATCGTGAAT
GCATAGAGAGAATAGCAAAATCAGGAGTTGATGTTTACGCTCATAATATTGAAACTGTTG
AAAAATTGACGCCTTATGTGAGAGACAGAAGAGCAGCTTATCGTCAATCATTGGAATGTT
TAAAAACAGCAAAAGAAATCAATCCAGAGCTCATTACAAAATCATCAATTATGTTAGGTT
TAGGCGAAACAGATTTAGAAATTGAACAAACGATGAAAGATCTGAAAGAAGCAAAAGTAG
ATTGTTTAACATTAGGTCAATATATGCAACCAACAAAAAGACATTTGAGTGTAATTGAAT
ATGTTACTCCTGAAAAATTCAAATTATGGGAAGATAAAGGAAATGAAATGGGATTTCTAT
ATACTGCATCTGGTCCATTAGTAAGAAGTTCATATAAAGCTGGTGAATTTTTTATTACGA
GTATTTTAAAGAATCGCCGTAATTATTCAAATTAA

>g4108.t4 Gene=g4108 Length=369
MLRNSIKIKTPTNIQKFRYKHSSAALEKIREKLENGPNFQDFVQNPNHSREEMAKEFEGR
LKKEKGEKERLRLPPWLKTQIPIGKNYDKIKNQLRELKLSTVCEEARCPNIGECWGGGKH
GTQTATIMLMGDTCTRGCRFCSVKTARIPPQLDPKEPINTATAIASWGLDYIVLTSVDRD
DLADGGSTHIAETIKEIKRQNPRIFVECLAPDFKGDRECIERIAKSGVDVYAHNIETVEK
LTPYVRDRRAAYRQSLECLKTAKEINPELITKSSIMLGLGETDLEIEQTMKDLKEAKVDC
LTLGQYMQPTKRHLSVIEYVTPEKFKLWEDKGNEMGFLYTASGPLVRSSYKAGEFFITSI
LKNRRNYSN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
9 g4108.t4 CDD cd01335 Radical_SAM 131 327 0.0000002
7 g4108.t4 Gene3D G3DSA:3.20.20.70 Aldolase class I 118 326 0.0000000
5 g4108.t4 Hamap MF_00206 Lipoyl synthase [lipA]. 72 365 131.7775120
3 g4108.t4 PANTHER PTHR10949:SF0 LIPOYL SYNTHASE, MITOCHONDRIAL 20 365 0.0000000
4 g4108.t4 PANTHER PTHR10949 LIPOYL SYNTHASE 20 365 0.0000000
8 g4108.t4 PIRSF PIRSF005963 Lipoyl_synth 11 369 0.0000000
2 g4108.t4 Pfam PF16881 N-terminal domain of lipoyl synthase of Radical_SAM family 18 108 0.0000000
1 g4108.t4 Pfam PF04055 Radical SAM superfamily 132 293 0.0000000
12 g4108.t4 SFLD SFLDF00271 lipoyl synthase 61 358 0.0000000
13 g4108.t4 SFLD SFLDS00029 Radical SAM 61 358 0.0000000
10 g4108.t4 SMART SM00729 MiaB 124 330 0.0000000
6 g4108.t4 SUPERFAMILY SSF102114 Radical SAM enzymes 83 363 0.0000000
11 g4108.t4 TIGRFAM TIGR00510 lipA: lipoyl synthase 66 363 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

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