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.t6 TTS g6704.t6 18132833 18132833
chr_2 g6704 g6704.t6 isoform g6704.t6 18132885 18135022
chr_2 g6704 g6704.t6 exon g6704.t6.exon1 18132885 18133562
chr_2 g6704 g6704.t6 cds g6704.t6.CDS1 18132885 18133562
chr_2 g6704 g6704.t6 exon g6704.t6.exon2 18133625 18134065
chr_2 g6704 g6704.t6 cds g6704.t6.CDS2 18133625 18134065
chr_2 g6704 g6704.t6 exon g6704.t6.exon3 18134128 18134277
chr_2 g6704 g6704.t6 cds g6704.t6.CDS3 18134128 18134277
chr_2 g6704 g6704.t6 exon g6704.t6.exon4 18134338 18134466
chr_2 g6704 g6704.t6 cds g6704.t6.CDS4 18134338 18134376
chr_2 g6704 g6704.t6 exon g6704.t6.exon5 18134674 18135022
chr_2 g6704 g6704.t6 TSS g6704.t6 18135078 18135078

Sequences

>g6704.t6 Gene=g6704 Length=1747
ATGGCTCAAATAACTAATATCAACTTAAGAAAGTTGTCTCAACTAAGCCTCAATGAACTA
GTTCGCCGATCAATATATACAACATCAGCTAGAGTGAGTACATAAAAGAAATATTTAATT
CATCAATTAATAAAAATTGCGTAATCGCAAAATGAATCAAATAATTTAGCAAAAATATTA
TGTACTAAAATGCATTCGCTTTGCTATGATTCAATTGCATTTCACACATTCATTTTAATT
TCTCTCATTTATAAAAACATGTTGTCAAGTTGAAAAAAGAATTGAGAGAGATCGGCGCGA
TCGTTTTACTCTCAAAGTACAGATAAAAAGCAAGAAATAGAATAAACAGGCTGCAGGATT
TCGAACTGAATCGGATACTTTCGGAGAATTAAAAGTTCCAGATGATAAATACTATGGAGC
TCAAACTGTTAGAAGTACCATGAATTTCCCTATTGGTGGACCAACTGAAAGAATGCCACA
ACCAGTTATCACTGCAATGGGTATATTGAAGAAAGCTGCTGCTCTTGTTAACAAAGAGTA
TGGTCTTGATCCAAAAATTGCTGATGCAATTTCTGAAGCTGCAGATGATGTTATATCTGG
AAAACTTTATGATGATCATTTTCCTTTGGTCATTTGGCAAACAGGATCAGGCACACAATC
CAATATGAACGTAAATGAAGTCATTAGCAATCGTGCTATTGAACTTTTAGGTGGAACGTT
GGGATCTAAAACACCTGTTCATCCAAATGATCATGTTAATAAATCCCAAAGTTCTAATGA
CACCTTTCCCACTGCAATTCATATTTCCGTTGCTCGAGAGCTAAATTCAAATTTAAAACC
AGCTCTTAAAGGTCTTCATGATGCACTAAATGCAAAATCAAATGAATTTAAAGATATAAT
TAAAATTGGTCGTACACATACTCAAGATGCAGTTCCACTTACTTTGGGACAAGAGTTTAG
TGGCTACGTTCAACAAATGAAATTTGCTCTTGATCGTATTGAAGCAGTTTTACCGCGTGT
GTATATGCTTGCTCTTGGAGGATCTGCAGTCGGAACTGGACTTAATACGAGAATCGGTTT
TGCTGAAAAATGTGCGTCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTGCCCC
TAACAAATTTGAAGCATTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCACTTAA
TACCATCAGTTGCAGTTTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCGGACC
ACGATGTGGACTTGGTGAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCATGCC
TGGAAAAGTCAATCCAACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCATGGG
AAATCATGTTGCAGTTACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTTTCAA
ACCGCTAGTCGTCTCGAATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGAGAGC
ATTTACAAGCAACTGTGTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAATAAT
GAATGAGTCACTCATGTTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGGCAGC
TAAAATTGCAAAAACCGCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAAAATT
GGGATATTTGACAGAACAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTGGACC
AAAGTAA

>g6704.t6 Gene=g6704 Length=435
MNFPIGGPTERMPQPVITAMGILKKAAALVNKEYGLDPKIADAISEAADDVISGKLYDDH
FPLVIWQTGSGTQSNMNVNEVISNRAIELLGGTLGSKTPVHPNDHVNKSQSSNDTFPTAI
HISVARELNSNLKPALKGLHDALNAKSNEFKDIIKIGRTHTQDAVPLTLGQEFSGYVQQM
KFALDRIEAVLPRVYMLALGGSAVGTGLNTRIGFAEKCASKIAELTGLPFVTAPNKFEAL
AARDSMVEVSGALNTISCSLFKIANDIRFLASGPRCGLGELSLPENEPGSSIMPGKVNPT
QCEALTMVCAQVMGNHVAVTVGGASGHFELNVFKPLVVSNVLRSIRLLSDCARAFTSNCV
VGIQANRENINKIMNESLMLVTALNPHIGYDKAAKIAKTAHKEGTTLKQAALKLGYLTEQ
QFNDWVKPEEMLGPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6704.t6 CDD cd01362 Fumarase_classII 1 431 0.0
14 g6704.t6 Gene3D G3DSA:1.10.275.10 - 1 110 3.6E-45
16 g6704.t6 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 111 379 2.9E-121
15 g6704.t6 Gene3D G3DSA:1.10.40.30 - 380 435 7.5E-32
5 g6704.t6 Hamap MF_00743 Fumarate hydratase class II [fumC]. 1 434 82.927185
3 g6704.t6 PANTHER PTHR11444:SF1 FUMARATE HYDRATASE, MITOCHONDRIAL 2 434 4.3E-233
4 g6704.t6 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE 2 434 4.3E-233
7 g6704.t6 PRINTS PR00145 Argininosuccinate lyase family signature 105 127 2.4E-5
9 g6704.t6 PRINTS PR00149 Fumarate lyase superfamily signature 106 124 2.0E-35
6 g6704.t6 PRINTS PR00145 Argininosuccinate lyase family signature 147 167 2.4E-5
10 g6704.t6 PRINTS PR00149 Fumarate lyase superfamily signature 152 170 2.0E-35
12 g6704.t6 PRINTS PR00149 Fumarate lyase superfamily signature 243 270 2.0E-35
8 g6704.t6 PRINTS PR00145 Argininosuccinate lyase family signature 289 305 2.4E-5
11 g6704.t6 PRINTS PR00149 Fumarate lyase superfamily signature 289 305 2.0E-35
1 g6704.t6 Pfam PF00206 Lyase 14 314 2.2E-111
2 g6704.t6 Pfam PF10415 Fumarase C C-terminus 380 432 6.6E-27
18 g6704.t6 ProSitePatterns PS00163 Fumarate lyases signature. 289 298 -
13 g6704.t6 SUPERFAMILY SSF48557 L-aspartase-like 2 432 4.71E-144
19 g6704.t6 TIGRFAM TIGR00979 fumC_II: fumarate hydratase, class II 2 433 2.9E-214

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