General information for g4108.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Lipoyl synthase, mitochondrial.
Parent gene
- The parent gene g4108 is located on chr_3: 30665466..30666197 (+ strand)
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.t1 | isoform | g4108.t1 | 30663730 | 30666197 |
| chr_3 | g4108 | g4108.t1 | exon | g4108.t1.exon1 | 30663730 | 30663909 |
| chr_3 | g4108 | g4108.t1 | cds | g4108.t1.CDS1 | 30663730 | 30663909 |
| chr_3 | g4108 | g4108.t1 | exon | g4108.t1.exon2 | 30664872 | 30664919 |
| chr_3 | g4108 | g4108.t1 | cds | g4108.t1.CDS2 | 30664872 | 30664919 |
| chr_3 | g4108 | g4108.t1 | exon | g4108.t1.exon3 | 30664994 | 30665398 |
| chr_3 | g4108 | g4108.t1 | cds | g4108.t1.CDS3 | 30664994 | 30665398 |
| chr_3 | g4108 | g4108.t1 | exon | g4108.t1.exon4 | 30665472 | 30666197 |
| chr_3 | g4108 | g4108.t1 | cds | g4108.t1.CDS4 | 30665472 | 30666197 |
| chr_3 | g4108 | g4108.t1 | TTS | g4108.t1 | 30666225 | 30666225 |
| chr_3 | g4108 | g4108.t1 | TSS | g4108.t1 | NA | NA |
Sequences
>g4108.t1 Gene=g4108 Length=1359
ATGTCTTTATGTGTGATTATAAATTGTCATAATACTAAGTCAGGAGGTTATACATTATTC
AAATTACCTAATGAAGGAGAAAAATCAAGATCAAAATGGATACAATTTATCAAAATATGT
GGTGTTGATACAGATAATTTGAAAAATGAATTTATTAAAGCTGTGCATGATAACATTATT
AAAAAATATCATTTATTGTTATTTAAAAACACTGTCAATTATTCATTGACAAATTTGCAA
GCACAAAAAATGTTACGAAATTCAATAAAAATCAAAACACCAACAAACATTCAAAAGTTT
CGCTATAAGCATTCATCAGCTGCATTAGAGAAAATTCGTGAGAAGTTAGAGAATGGACCA
AATTTTCAAGATTTTGTTCAAAATCCAAATCATAGTCGTGAAGAAATGGCAAAAGAATTT
GAAGGAAGGTTGAAGAAAGAAAAAGGCGAAAAAGAGAGATTGAGATTGCCACCATGGTTG
AAAACACAAATTCCAATAGGAAAGAATTATGATAAAATCAAGAATCAGCTACGTGAACTT
AAGCTATCGACAGTGTGTGAAGAGGCAAGATGTCCAAATATCGGTGAATGCTGGGGTGGT
GGAAAGCATGGAACACAAACAGCTACAATTATGCTTATGGGAGATACTTGCACAAGAGGC
TGTCGATTTTGTTCAGTTAAAACTGCTAGAATTCCTCCACAACTTGATCCAAAAGAACCA
ATTAATACAGCGACAGCAATTGCATCATGGGGTCTTGATTATATTGTACTAACAAGTGTT
GATCGAGATGATTTAGCCGATGGTGGATCAACACACATTGCAGAAACTATTAAAGAAATT
AAACGTCAAAATCCAAGAATTTTCGTTGAATGTCTTGCACCAGATTTTAAAGGAGATCGT
GAATGCATAGAGAGAATAGCAAAATCAGGAGTTGATGTTTACGCTCATAATATTGAAACT
GTTGAAAAATTGACGCCTTATGTGAGAGACAGAAGAGCAGCTTATCGTCAATCATTGGAA
TGTTTAAAAACAGCAAAAGAAATCAATCCAGAGCTCATTACAAAATCATCAATTATGTTA
GGTTTAGGCGAAACAGATTTAGAAATTGAACAAACGATGAAAGATCTGAAAGAAGCAAAA
GTAGATTGTTTAACATTAGGTCAATATATGCAACCAACAAAAAGACATTTGAGTGTAATT
GAATATGTTACTCCTGAAAAATTCAAATTATGGGAAGATAAAGGAAATGAAATGGGATTT
CTATATACTGCATCTGGTCCATTAGTAAGAAGTTCATATAAAGCTGGTGAATTTTTTATT
ACGAGTATTTTAAAGAATCGCCGTAATTATTCAAATTAA
>g4108.t1 Gene=g4108 Length=452
MSLCVIINCHNTKSGGYTLFKLPNEGEKSRSKWIQFIKICGVDTDNLKNEFIKAVHDNII
KKYHLLLFKNTVNYSLTNLQAQKMLRNSIKIKTPTNIQKFRYKHSSAALEKIREKLENGP
NFQDFVQNPNHSREEMAKEFEGRLKKEKGEKERLRLPPWLKTQIPIGKNYDKIKNQLREL
KLSTVCEEARCPNIGECWGGGKHGTQTATIMLMGDTCTRGCRFCSVKTARIPPQLDPKEP
INTATAIASWGLDYIVLTSVDRDDLADGGSTHIAETIKEIKRQNPRIFVECLAPDFKGDR
ECIERIAKSGVDVYAHNIETVEKLTPYVRDRRAAYRQSLECLKTAKEINPELITKSSIML
GLGETDLEIEQTMKDLKEAKVDCLTLGQYMQPTKRHLSVIEYVTPEKFKLWEDKGNEMGF
LYTASGPLVRSSYKAGEFFITSILKNRRNYSN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g4108.t1 | CDD | cd01335 | Radical_SAM | 214 | 410 | 0.0000002 |
| 7 | g4108.t1 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 201 | 409 | 0.0000000 |
| 5 | g4108.t1 | Hamap | MF_00206 | Lipoyl synthase [lipA]. | 155 | 448 | 131.7775120 |
| 3 | g4108.t1 | PANTHER | PTHR10949:SF0 | LIPOYL SYNTHASE, MITOCHONDRIAL | 103 | 448 | 0.0000000 |
| 4 | g4108.t1 | PANTHER | PTHR10949 | LIPOYL SYNTHASE | 103 | 448 | 0.0000000 |
| 2 | g4108.t1 | Pfam | PF16881 | N-terminal domain of lipoyl synthase of Radical_SAM family | 99 | 191 | 0.0000000 |
| 1 | g4108.t1 | Pfam | PF04055 | Radical SAM superfamily | 215 | 376 | 0.0000000 |
| 11 | g4108.t1 | SFLD | SFLDF00271 | lipoyl synthase | 144 | 441 | 0.0000000 |
| 12 | g4108.t1 | SFLD | SFLDS00029 | Radical SAM | 144 | 441 | 0.0000000 |
| 9 | g4108.t1 | SMART | SM00729 | MiaB | 207 | 413 | 0.0000000 |
| 6 | g4108.t1 | SUPERFAMILY | SSF102114 | Radical SAM enzymes | 166 | 446 | 0.0000000 |
| 10 | g4108.t1 | TIGRFAM | TIGR00510 | lipA: lipoyl synthase | 149 | 446 | 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 transcript has been annotated with K03644 (lipoyl synthase)
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.
