General information for g6704.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Fumarate hydratase, mitochondrial.
Parent gene
- The parent gene g6704 is located on chr_2: 18133639..18135022 (- 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_2 | g6704 | g6704.t2 | TTS | g6704.t2 | 18132833 | 18132833 |
| chr_2 | g6704 | g6704.t2 | isoform | g6704.t2 | 18132885 | 18133546 |
| chr_2 | g6704 | g6704.t2 | exon | g6704.t2.exon1 | 18132885 | 18133546 |
| chr_2 | g6704 | g6704.t2 | cds | g6704.t2.CDS1 | 18132885 | 18133457 |
| chr_2 | g6704 | g6704.t2 | TSS | g6704.t2 | 18134570 | 18134570 |
Sequences
>g6704.t2 Gene=g6704 Length=662
AAAAATGTGCGTCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTGCCCCTAACA
AATTTGAAGCATTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCACTTAATACCA
TCAGTTGCAGTTTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCGGACCACGAT
GTGGACTTGGTGAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCATGCCTGGAA
AAGTCAATCCAACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCATGGGAAATC
ATGTTGCAGTTACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTTTCAAACCGC
TAGTCGTCTCGAATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGAGAGCATTTA
CAAGCAACTGTGTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAATAATGAATG
AGTCACTCATGTTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGGCAGCTAAAA
TTGCAAAAACCGCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAAAATTGGGAT
ATTTGACAGAACAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTGGACCAAAGT
AA
>g6704.t2 Gene=g6704 Length=190
MVEVSGALNTISCSLFKIANDIRFLASGPRCGLGELSLPENEPGSSIMPGKVNPTQCEAL
TMVCAQVMGNHVAVTVGGASGHFELNVFKPLVVSNVLRSIRLLSDCARAFTSNCVVGIQA
NRENINKIMNESLMLVTALNPHIGYDKAAKIAKTAHKEGTTLKQAALKLGYLTEQQFNDW
VKPEEMLGPK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g6704.t2 | Gene3D | G3DSA:1.20.200.10 | Fumarase/aspartase (Central domain) | 1 | 134 | 3.0E-60 |
| 7 | g6704.t2 | Gene3D | G3DSA:1.10.40.30 | - | 135 | 190 | 1.9E-32 |
| 3 | g6704.t2 | PANTHER | PTHR11444:SF1 | FUMARATE HYDRATASE, MITOCHONDRIAL | 1 | 189 | 1.1E-100 |
| 4 | g6704.t2 | PANTHER | PTHR11444 | ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE | 1 | 189 | 1.1E-100 |
| 1 | g6704.t2 | Pfam | PF00206 | Lyase | 1 | 69 | 6.5E-30 |
| 2 | g6704.t2 | Pfam | PF10415 | Fumarase C C-terminus | 135 | 187 | 1.7E-27 |
| 6 | g6704.t2 | ProSitePatterns | PS00163 | Fumarate lyases signature. | 44 | 53 | - |
| 5 | g6704.t2 | SUPERFAMILY | SSF48557 | L-aspartase-like | 1 | 187 | 2.51E-63 |
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:0006099 | tricarboxylic acid cycle | BP |
| GO:0016829 | lyase activity | MF |
| GO:0045239 | tricarboxylic acid cycle enzyme complex | CC |
| GO:0003824 | catalytic activity | MF |
| GO:0006106 | fumarate metabolic process | BP |
| GO:0004333 | fumarate hydratase 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.
