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.t5 TTS g6704.t5 18132833 18132833
chr_2 g6704 g6704.t5 isoform g6704.t5 18132885 18134570
chr_2 g6704 g6704.t5 exon g6704.t5.exon1 18132885 18133562
chr_2 g6704 g6704.t5 cds g6704.t5.CDS1 18132885 18133562
chr_2 g6704 g6704.t5 exon g6704.t5.exon2 18133625 18134065
chr_2 g6704 g6704.t5 cds g6704.t5.CDS2 18133625 18134065
chr_2 g6704 g6704.t5 exon g6704.t5.exon3 18134128 18134277
chr_2 g6704 g6704.t5 cds g6704.t5.CDS3 18134128 18134277
chr_2 g6704 g6704.t5 exon g6704.t5.exon4 18134338 18134466
chr_2 g6704 g6704.t5 cds g6704.t5.CDS4 18134338 18134466
chr_2 g6704 g6704.t5 exon g6704.t5.exon5 18134518 18134570
chr_2 g6704 g6704.t5 cds g6704.t5.CDS5 18134518 18134523
chr_2 g6704 g6704.t5 TSS g6704.t5 18135078 18135078

Sequences

>g6704.t5 Gene=g6704 Length=1451
AGTTTAATCTTACACTTTGACTTTTCATCAACTCTTCAAGAAAAAAAATGGTTGCTGCAG
GATTTCGAACTGAATCGGATACTTTCGGAGAATTAAAAGTTCCAGATGATAAATACTATG
GAGCTCAAACTGTTAGAAGTACCATGAATTTCCCTATTGGTGGACCAACTGAAAGAATGC
CACAACCAGTTATCACTGCAATGGGTATATTGAAGAAAGCTGCTGCTCTTGTTAACAAAG
AGTATGGTCTTGATCCAAAAATTGCTGATGCAATTTCTGAAGCTGCAGATGATGTTATAT
CTGGAAAACTTTATGATGATCATTTTCCTTTGGTCATTTGGCAAACAGGATCAGGCACAC
AATCCAATATGAACGTAAATGAAGTCATTAGCAATCGTGCTATTGAACTTTTAGGTGGAA
CGTTGGGATCTAAAACACCTGTTCATCCAAATGATCATGTTAATAAATCCCAAAGTTCTA
ATGACACCTTTCCCACTGCAATTCATATTTCCGTTGCTCGAGAGCTAAATTCAAATTTAA
AACCAGCTCTTAAAGGTCTTCATGATGCACTAAATGCAAAATCAAATGAATTTAAAGATA
TAATTAAAATTGGTCGTACACATACTCAAGATGCAGTTCCACTTACTTTGGGACAAGAGT
TTAGTGGCTACGTTCAACAAATGAAATTTGCTCTTGATCGTATTGAAGCAGTTTTACCGC
GTGTGTATATGCTTGCTCTTGGAGGATCTGCAGTCGGAACTGGACTTAATACGAGAATCG
GTTTTGCTGAAAAATGTGCGTCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTG
CCCCTAACAAATTTGAAGCATTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCAC
TTAATACCATCAGTTGCAGTTTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCG
GACCACGATGTGGACTTGGTGAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCA
TGCCTGGAAAAGTCAATCCAACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCA
TGGGAAATCATGTTGCAGTTACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTT
TCAAACCGCTAGTCGTCTCGAATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGA
GAGCATTTACAAGCAACTGTGTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAA
TAATGAATGAGTCACTCATGTTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGG
CAGCTAAAATTGCAAAAACCGCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAA
AATTGGGATATTTGACAGAACAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTG
GACCAAAGTAA

>g6704.t5 Gene=g6704 Length=467
MVAAGFRTESDTFGELKVPDDKYYGAQTVRSTMNFPIGGPTERMPQPVITAMGILKKAAA
LVNKEYGLDPKIADAISEAADDVISGKLYDDHFPLVIWQTGSGTQSNMNVNEVISNRAIE
LLGGTLGSKTPVHPNDHVNKSQSSNDTFPTAIHISVARELNSNLKPALKGLHDALNAKSN
EFKDIIKIGRTHTQDAVPLTLGQEFSGYVQQMKFALDRIEAVLPRVYMLALGGSAVGTGL
NTRIGFAEKCASKIAELTGLPFVTAPNKFEALAARDSMVEVSGALNTISCSLFKIANDIR
FLASGPRCGLGELSLPENEPGSSIMPGKVNPTQCEALTMVCAQVMGNHVAVTVGGASGHF
ELNVFKPLVVSNVLRSIRLLSDCARAFTSNCVVGIQANRENINKIMNESLMLVTALNPHI
GYDKAAKIAKTAHKEGTTLKQAALKLGYLTEQQFNDWVKPEEMLGPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6704.t5 CDD cd01362 Fumarase_classII 7 463 0.0
14 g6704.t5 Gene3D G3DSA:1.10.275.10 - 7 142 4.8E-60
16 g6704.t5 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 143 411 3.5E-121
15 g6704.t5 Gene3D G3DSA:1.10.40.30 - 412 467 8.3E-32
5 g6704.t5 Hamap MF_00743 Fumarate hydratase class II [fumC]. 6 466 88.219086
3 g6704.t5 PANTHER PTHR11444:SF1 FUMARATE HYDRATASE, MITOCHONDRIAL 4 466 6.8E-248
4 g6704.t5 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE 4 466 6.8E-248
7 g6704.t5 PRINTS PR00145 Argininosuccinate lyase family signature 137 159 2.9E-5
11 g6704.t5 PRINTS PR00149 Fumarate lyase superfamily signature 138 156 2.5E-35
8 g6704.t5 PRINTS PR00145 Argininosuccinate lyase family signature 179 199 2.9E-5
12 g6704.t5 PRINTS PR00149 Fumarate lyase superfamily signature 184 202 2.5E-35
10 g6704.t5 PRINTS PR00149 Fumarate lyase superfamily signature 275 302 2.5E-35
6 g6704.t5 PRINTS PR00145 Argininosuccinate lyase family signature 321 337 2.9E-5
9 g6704.t5 PRINTS PR00149 Fumarate lyase superfamily signature 321 337 2.5E-35
1 g6704.t5 Pfam PF00206 Lyase 14 346 2.3E-117
2 g6704.t5 Pfam PF10415 Fumarase C C-terminus 412 464 7.3E-27
18 g6704.t5 ProSitePatterns PS00163 Fumarate lyases signature. 321 330 -
13 g6704.t5 SUPERFAMILY SSF48557 L-aspartase-like 4 460 1.18E-154
19 g6704.t5 TIGRFAM TIGR00979 fumC_II: fumarate hydratase, class II 6 465 1.4E-228

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