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.t1 TTS g6704.t1 18132833 18132833
chr_2 g6704 g6704.t1 isoform g6704.t1 18132885 18135022
chr_2 g6704 g6704.t1 exon g6704.t1.exon1 18132885 18133562
chr_2 g6704 g6704.t1 cds g6704.t1.CDS1 18132885 18133562
chr_2 g6704 g6704.t1 exon g6704.t1.exon2 18133625 18134065
chr_2 g6704 g6704.t1 cds g6704.t1.CDS2 18133625 18134065
chr_2 g6704 g6704.t1 exon g6704.t1.exon3 18134128 18134277
chr_2 g6704 g6704.t1 cds g6704.t1.CDS3 18134128 18134277
chr_2 g6704 g6704.t1 exon g6704.t1.exon4 18134338 18134466
chr_2 g6704 g6704.t1 cds g6704.t1.CDS4 18134338 18134466
chr_2 g6704 g6704.t1 exon g6704.t1.exon5 18134930 18135022
chr_2 g6704 g6704.t1 cds g6704.t1.CDS5 18134930 18135022
chr_2 g6704 g6704.t1 TSS g6704.t1 18135078 18135078

Sequences

>g6704.t1 Gene=g6704 Length=1491
ATGGCTCAAATAACTAATATCAACTTAAGAAAGTTGTCTCAACTAAGCCTCAATGAACTA
GTTCGCCGATCAATATATACAACATCAGCTAGAGCTGCAGGATTTCGAACTGAATCGGAT
ACTTTCGGAGAATTAAAAGTTCCAGATGATAAATACTATGGAGCTCAAACTGTTAGAAGT
ACCATGAATTTCCCTATTGGTGGACCAACTGAAAGAATGCCACAACCAGTTATCACTGCA
ATGGGTATATTGAAGAAAGCTGCTGCTCTTGTTAACAAAGAGTATGGTCTTGATCCAAAA
ATTGCTGATGCAATTTCTGAAGCTGCAGATGATGTTATATCTGGAAAACTTTATGATGAT
CATTTTCCTTTGGTCATTTGGCAAACAGGATCAGGCACACAATCCAATATGAACGTAAAT
GAAGTCATTAGCAATCGTGCTATTGAACTTTTAGGTGGAACGTTGGGATCTAAAACACCT
GTTCATCCAAATGATCATGTTAATAAATCCCAAAGTTCTAATGACACCTTTCCCACTGCA
ATTCATATTTCCGTTGCTCGAGAGCTAAATTCAAATTTAAAACCAGCTCTTAAAGGTCTT
CATGATGCACTAAATGCAAAATCAAATGAATTTAAAGATATAATTAAAATTGGTCGTACA
CATACTCAAGATGCAGTTCCACTTACTTTGGGACAAGAGTTTAGTGGCTACGTTCAACAA
ATGAAATTTGCTCTTGATCGTATTGAAGCAGTTTTACCGCGTGTGTATATGCTTGCTCTT
GGAGGATCTGCAGTCGGAACTGGACTTAATACGAGAATCGGTTTTGCTGAAAAATGTGCG
TCTAAAATTGCCGAGTTGACAGGATTACCATTTGTAACTGCCCCTAACAAATTTGAAGCA
TTAGCTGCTCGTGATTCAATGGTAGAAGTGTCTGGTGCACTTAATACCATCAGTTGCAGT
TTATTTAAGATTGCCAATGATATTCGTTTCTTAGCATCCGGACCACGATGTGGACTTGGT
GAATTAAGTCTTCCTGAAAACGAACCAGGCTCTTCAATCATGCCTGGAAAAGTCAATCCA
ACGCAATGTGAAGCTTTGACAATGGTTTGCGCTCAGGTCATGGGAAATCATGTTGCAGTT
ACAGTTGGTGGTGCAAGCGGTCATTTTGAGTTAAATGTTTTCAAACCGCTAGTCGTCTCG
AATGTTTTACGTTCAATTCGTTTACTTTCTGATTGTGCGAGAGCATTTACAAGCAACTGT
GTTGTTGGCATTCAAGCCAATCGTGAGAATATAAATAAAATAATGAATGAGTCACTCATG
TTGGTAACTGCCCTTAATCCACACATTGGTTATGATAAGGCAGCTAAAATTGCAAAAACC
GCACATAAAGAGGGAACTACACTTAAACAAGCTGCATTAAAATTGGGATATTTGACAGAA
CAGCAATTCAACGACTGGGTAAAACCAGAAGAAATGCTTGGACCAAAGTAA

>g6704.t1 Gene=g6704 Length=496
MAQITNINLRKLSQLSLNELVRRSIYTTSARAAGFRTESDTFGELKVPDDKYYGAQTVRS
TMNFPIGGPTERMPQPVITAMGILKKAAALVNKEYGLDPKIADAISEAADDVISGKLYDD
HFPLVIWQTGSGTQSNMNVNEVISNRAIELLGGTLGSKTPVHPNDHVNKSQSSNDTFPTA
IHISVARELNSNLKPALKGLHDALNAKSNEFKDIIKIGRTHTQDAVPLTLGQEFSGYVQQ
MKFALDRIEAVLPRVYMLALGGSAVGTGLNTRIGFAEKCASKIAELTGLPFVTAPNKFEA
LAARDSMVEVSGALNTISCSLFKIANDIRFLASGPRCGLGELSLPENEPGSSIMPGKVNP
TQCEALTMVCAQVMGNHVAVTVGGASGHFELNVFKPLVVSNVLRSIRLLSDCARAFTSNC
VVGIQANRENINKIMNESLMLVTALNPHIGYDKAAKIAKTAHKEGTTLKQAALKLGYLTE
QQFNDWVKPEEMLGPK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g6704.t1 CDD cd01362 Fumarase_classII 36 492 0.0
14 g6704.t1 Gene3D G3DSA:1.10.275.10 - 36 171 5.4E-60
16 g6704.t1 Gene3D G3DSA:1.20.200.10 Fumarase/aspartase (Central domain) 172 440 4.1E-121
15 g6704.t1 Gene3D G3DSA:1.10.40.30 - 441 496 9.0E-32
5 g6704.t1 Hamap MF_00743 Fumarate hydratase class II [fumC]. 35 495 88.219086
3 g6704.t1 PANTHER PTHR11444:SF1 FUMARATE HYDRATASE, MITOCHONDRIAL 30 495 4.1E-248
4 g6704.t1 PANTHER PTHR11444 ASPARTATEAMMONIA/ARGININOSUCCINATE/ADENYLOSUCCINATE LYASE 30 495 4.1E-248
8 g6704.t1 PRINTS PR00145 Argininosuccinate lyase family signature 166 188 3.4E-5
11 g6704.t1 PRINTS PR00149 Fumarate lyase superfamily signature 167 185 3.1E-35
6 g6704.t1 PRINTS PR00145 Argininosuccinate lyase family signature 208 228 3.4E-5
10 g6704.t1 PRINTS PR00149 Fumarate lyase superfamily signature 213 231 3.1E-35
9 g6704.t1 PRINTS PR00149 Fumarate lyase superfamily signature 304 331 3.1E-35
7 g6704.t1 PRINTS PR00145 Argininosuccinate lyase family signature 350 366 3.4E-5
12 g6704.t1 PRINTS PR00149 Fumarate lyase superfamily signature 350 366 3.1E-35
1 g6704.t1 Pfam PF00206 Lyase 43 375 2.8E-117
2 g6704.t1 Pfam PF10415 Fumarase C C-terminus 441 493 7.9E-27
18 g6704.t1 ProSitePatterns PS00163 Fumarate lyases signature. 350 359 -
13 g6704.t1 SUPERFAMILY SSF48557 L-aspartase-like 34 489 1.73E-154
19 g6704.t1 TIGRFAM TIGR00979 fumC_II: fumarate hydratase, class II 35 494 1.8E-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