Gene loci information

Transcript annotation

  • This transcript has been annotated as Fumarate hydratase, 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_2 g6704 g6704.t3 TTS g6704.t3 18132833 18132833
chr_2 g6704 g6704.t3 isoform g6704.t3 18132885 18134037
chr_2 g6704 g6704.t3 exon g6704.t3.exon1 18132885 18133562
chr_2 g6704 g6704.t3 cds g6704.t3.CDS1 18132885 18133562
chr_2 g6704 g6704.t3 exon g6704.t3.exon2 18133625 18134037
chr_2 g6704 g6704.t3 cds g6704.t3.CDS2 18133625 18134029
chr_2 g6704 g6704.t3 TSS g6704.t3 18134570 18134570

Sequences

>g6704.t3 Gene=g6704 Length=1091
AATCCAATATGAACGTAAATGAAGTCATTAGCAATCGTGCTATTGAACTTTTAGGTGGAA
CGTTGGGATCTAAAACACCTGTTCATCCAAATGATCATGTTAATAAATCCCAAAGTTCTA
ATGACACCTTTCCCACTGCAATTCATATTTCCGTTGCTCGAGAGCTAAATTCAAATTTAA
AACCAGCTCTTAAAGGTCTTCATGATGCACTAAATGCAAAATCAAATGAATTTAAAGATA
TAATTAAAATTGGTCGTACACATACTCAAGATGCAGTTCCACTTACTTTGGGACAAGAGT
TTAGTGGCTACGTTCAACAAATGAAATTTGCTCTTGATCGTATTGAAGCAGTTTTACCGC
GTGTGTATATGCTTGCTCTTGGAGGATCTGCAGTCGGAACTGGACTTAATACGAGAATCG
GTTTTGCTGAAAAATGTGCGTCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTG
CCCCTAACAAATTTGAAGCATTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCAC
TTAATACCATCAGTTGCAGTTTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCG
GACCACGATGTGGACTTGGTGAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCA
TGCCTGGAAAAGTCAATCCAACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCA
TGGGAAATCATGTTGCAGTTACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTT
TCAAACCGCTAGTCGTCTCGAATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGA
GAGCATTTACAAGCAACTGTGTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAA
TAATGAATGAGTCACTCATGTTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGG
CAGCTAAAATTGCAAAAACCGCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAA
AATTGGGATATTTGACAGAACAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTG
GACCAAAGTAA

>g6704.t3 Gene=g6704 Length=360
MNVNEVISNRAIELLGGTLGSKTPVHPNDHVNKSQSSNDTFPTAIHISVARELNSNLKPA
LKGLHDALNAKSNEFKDIIKIGRTHTQDAVPLTLGQEFSGYVQQMKFALDRIEAVLPRVY
MLALGGSAVGTGLNTRIGFAEKCASKIAELTGLPFVTAPNKFEALAARDSMVEVSGALNT
ISCSLFKIANDIRFLASGPRCGLGELSLPENEPGSSIMPGKVNPTQCEALTMVCAQVMGN
HVAVTVGGASGHFELNVFKPLVVSNVLRSIRLLSDCARAFTSNCVVGIQANRENINKIMN
ESLMLVTALNPHIGYDKAAKIAKTAHKEGTTLKQAALKLGYLTEQQFNDWVKPEEMLGPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6704.t3 CDD cd01362 Fumarase_classII 1 356 0.0
14 g6704.t3 Gene3D G3DSA:1.10.275.10 - 1 35 4.2E-13
16 g6704.t3 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 36 304 1.6E-121
15 g6704.t3 Gene3D G3DSA:1.10.40.30 - 305 360 5.7E-32
5 g6704.t3 Hamap MF_00743 Fumarate hydratase class II [fumC]. 1 359 69.707748
3 g6704.t3 PANTHER PTHR11444:SF1 FUMARATE HYDRATASE, MITOCHONDRIAL 1 359 2.1E-192
4 g6704.t3 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE 1 359 2.1E-192
8 g6704.t3 PRINTS PR00145 Argininosuccinate lyase family signature 30 52 1.5E-5
12 g6704.t3 PRINTS PR00149 Fumarate lyase superfamily signature 31 49 1.0E-35
7 g6704.t3 PRINTS PR00145 Argininosuccinate lyase family signature 72 92 1.5E-5
11 g6704.t3 PRINTS PR00149 Fumarate lyase superfamily signature 77 95 1.0E-35
9 g6704.t3 PRINTS PR00149 Fumarate lyase superfamily signature 168 195 1.0E-35
6 g6704.t3 PRINTS PR00145 Argininosuccinate lyase family signature 214 230 1.5E-5
10 g6704.t3 PRINTS PR00149 Fumarate lyase superfamily signature 214 230 1.0E-35
1 g6704.t3 Pfam PF00206 Lyase 1 239 5.1E-93
2 g6704.t3 Pfam PF10415 Fumarase C C-terminus 305 357 5.0E-27
18 g6704.t3 ProSitePatterns PS00163 Fumarate lyases signature. 214 223 -
13 g6704.t3 SUPERFAMILY SSF48557 L-aspartase-like 1 357 5.65E-127

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.

Raw TPM values