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.t4 TTS g6704.t4 18132833 18132833
chr_2 g6704 g6704.t4 isoform g6704.t4 18132885 18134273
chr_2 g6704 g6704.t4 exon g6704.t4.exon1 18132885 18133562
chr_2 g6704 g6704.t4 cds g6704.t4.CDS1 18132885 18133562
chr_2 g6704 g6704.t4 exon g6704.t4.exon2 18133625 18134065
chr_2 g6704 g6704.t4 cds g6704.t4.CDS2 18133625 18134065
chr_2 g6704 g6704.t4 exon g6704.t4.exon3 18134128 18134273
chr_2 g6704 g6704.t4 cds g6704.t4.CDS3 18134128 18134259
chr_2 g6704 g6704.t4 TSS g6704.t4 18135078 18135078

Sequences

>g6704.t4 Gene=g6704 Length=1265
CAGTTATCACTGCAATGGGTATATTGAAGAAAGCTGCTGCTCTTGTTAACAAAGAGTATG
GTCTTGATCCAAAAATTGCTGATGCAATTTCTGAAGCTGCAGATGATGTTATATCTGGAA
AACTTTATGATGATCATTTTCCTTTGGTCATTTGGCAAACAGGATCAGGCACACAATCCA
ATATGAACGTAAATGAAGTCATTAGCAATCGTGCTATTGAACTTTTAGGTGGAACGTTGG
GATCTAAAACACCTGTTCATCCAAATGATCATGTTAATAAATCCCAAAGTTCTAATGACA
CCTTTCCCACTGCAATTCATATTTCCGTTGCTCGAGAGCTAAATTCAAATTTAAAACCAG
CTCTTAAAGGTCTTCATGATGCACTAAATGCAAAATCAAATGAATTTAAAGATATAATTA
AAATTGGTCGTACACATACTCAAGATGCAGTTCCACTTACTTTGGGACAAGAGTTTAGTG
GCTACGTTCAACAAATGAAATTTGCTCTTGATCGTATTGAAGCAGTTTTACCGCGTGTGT
ATATGCTTGCTCTTGGAGGATCTGCAGTCGGAACTGGACTTAATACGAGAATCGGTTTTG
CTGAAAAATGTGCGTCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTGCCCCTA
ACAAATTTGAAGCATTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCACTTAATA
CCATCAGTTGCAGTTTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCGGACCAC
GATGTGGACTTGGTGAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCATGCCTG
GAAAAGTCAATCCAACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCATGGGAA
ATCATGTTGCAGTTACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTTTCAAAC
CGCTAGTCGTCTCGAATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGAGAGCAT
TTACAAGCAACTGTGTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAATAATGA
ATGAGTCACTCATGTTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGGCAGCTA
AAATTGCAAAAACCGCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAAAATTGG
GATATTTGACAGAACAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTGGACCAA
AGTAA

>g6704.t4 Gene=g6704 Length=416
MGILKKAAALVNKEYGLDPKIADAISEAADDVISGKLYDDHFPLVIWQTGSGTQSNMNVN
EVISNRAIELLGGTLGSKTPVHPNDHVNKSQSSNDTFPTAIHISVARELNSNLKPALKGL
HDALNAKSNEFKDIIKIGRTHTQDAVPLTLGQEFSGYVQQMKFALDRIEAVLPRVYMLAL
GGSAVGTGLNTRIGFAEKCASKIAELTGLPFVTAPNKFEALAARDSMVEVSGALNTISCS
LFKIANDIRFLASGPRCGLGELSLPENEPGSSIMPGKVNPTQCEALTMVCAQVMGNHVAV
TVGGASGHFELNVFKPLVVSNVLRSIRLLSDCARAFTSNCVVGIQANRENINKIMNESLM
LVTALNPHIGYDKAAKIAKTAHKEGTTLKQAALKLGYLTEQQFNDWVKPEEMLGPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6704.t4 CDD cd01362 Fumarase_classII 1 412 0.0
14 g6704.t4 Gene3D G3DSA:1.10.275.10 - 1 91 3.1E-38
16 g6704.t4 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 92 360 2.5E-121
15 g6704.t4 Gene3D G3DSA:1.10.40.30 - 361 416 7.0E-32
5 g6704.t4 Hamap MF_00743 Fumarate hydratase class II [fumC]. 1 415 80.348282
3 g6704.t4 PANTHER PTHR11444:SF1 FUMARATE HYDRATASE, MITOCHONDRIAL 1 415 6.4E-225
4 g6704.t4 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE 1 415 6.4E-225
8 g6704.t4 PRINTS PR00145 Argininosuccinate lyase family signature 86 108 2.2E-5
11 g6704.t4 PRINTS PR00149 Fumarate lyase superfamily signature 87 105 1.7E-35
7 g6704.t4 PRINTS PR00145 Argininosuccinate lyase family signature 128 148 2.2E-5
12 g6704.t4 PRINTS PR00149 Fumarate lyase superfamily signature 133 151 1.7E-35
10 g6704.t4 PRINTS PR00149 Fumarate lyase superfamily signature 224 251 1.7E-35
6 g6704.t4 PRINTS PR00145 Argininosuccinate lyase family signature 270 286 2.2E-5
9 g6704.t4 PRINTS PR00149 Fumarate lyase superfamily signature 270 286 1.7E-35
1 g6704.t4 Pfam PF00206 Lyase 1 295 5.9E-110
2 g6704.t4 Pfam PF10415 Fumarase C C-terminus 361 413 6.2E-27
18 g6704.t4 ProSitePatterns PS00163 Fumarate lyases signature. 270 279 -
13 g6704.t4 SUPERFAMILY SSF48557 L-aspartase-like 2 413 2.98E-141
19 g6704.t4 TIGRFAM TIGR00979 fumC_II: fumarate hydratase, class II 2 414 2.7E-208

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

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