Gene loci information

Transcript annotation

  • This transcript has been annotated as Aconitate 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 g5631 g5631.t9 TSS g5631.t9 10732477 10732477
chr_2 g5631 g5631.t9 isoform g5631.t9 10733439 10734995
chr_2 g5631 g5631.t9 exon g5631.t9.exon1 10733439 10734773
chr_2 g5631 g5631.t9 cds g5631.t9.CDS1 10733442 10734773
chr_2 g5631 g5631.t9 exon g5631.t9.exon2 10734940 10734995
chr_2 g5631 g5631.t9 cds g5631.t9.CDS2 10734940 10734993
chr_2 g5631 g5631.t9 TTS g5631.t9 NA NA

Sequences

>g5631.t9 Gene=g5631 Length=1391
GCTATGATGCAATTCATTTCCTCCGGATTGAAACGTGTCGCTGTTCCAACAACAATTCAT
TGCGATCATTTGATTGAAGCACAAATTGGAGGCGATCAAGATTTAGCTCGCGCAAAGAAA
CTCAATGAAGAAGTTTATCGTTTCTTAGAGACTGCAAGTGCCAAGTATGGAGTTGGTTTC
TGGAAGCCTGGTTCAGGTATTATTCATCAAATCATTCTTGAGAATTACGCATTCCCTGGT
CTTTTGATGATCGGTACTGACTCTCATACACCAAATGGAGGCGGACTTGGTGGCCTTTGC
ATTGGTGTCGGTGGCGCTGATGCTGTTGATGTTATGGCTAATATTCCGTGGGAATTGAAA
TGTCCAAAAGTTATTGGTGTTCATTTAACGGGAAAAATTGGTGGTTGGACTTCACCAAAG
GATGTTATCTTGAAGGTTGCTGATATTTTGACTGTAAAGGGAGGCACTGGTGCAATTGTT
GAATATCATGGTAAAGGTGTTGATTCAATTTCATGCACAGGTATGGCAACAATCTGTAAT
ATGGGTGCTGAAATTGGTGCAACCACTTCAACTTTCCCATTCAATTCAAGAATGGCTGCT
TATTTGAAATCAACTCTTCGTGATGGCATTGCTGCCGAAGCTGCCAAATTCCAAACTCAA
TTGCTCCAAGCAGATGAAGGTGCACAATATGACGAGCTCATTGAAATTAATTTGGATACA
TTGGAACCACATGTAAATGGTCCATTCACTCCAGATCTTGCTCATCCAATTAGCAAACTT
GGTGAAAATTCAAAAAAGAACGGTTATCCAATTGATATTAAAGTTGGTTTAATTGGTTCA
TGTACAAACTCATCATATGAAGATATGGGTCGATGTGCTTCTATTGTCAAAGATGCTTTG
TCTCATGGTCTTAAATCAAAAATTCCATTCAATGTTACACCCGGCTCTGAGCAAGTTCGT
GCTACAATTGAACGTGATGGAATTGCGAAAACTCTTCGTGATTTTGGTGGTACTGTCTTA
GCTAATGCTTGTGGACCATGTATTGGTCAATGGGATCGTCAAGATGTAAAGAAGGGTGAC
AAAAACACAATTGTAACTTCATACAACCGTAACTTTACCGGACGTAATGATGCTAATCCA
GCAACTCATTGCTTCGTTACTTCACCTGAAATGGTTACAGCTTTGTCAATTGCTGGCCGC
TTAGATTTCAATCCATTGAAAGACGAATTGACTGGTGCTGATGGTAAGAAATTCAAATTG
AAGGAACCATTCGGTGATGAATTGCCAGTTCGTGGCTTTGATCCTGGCCAAGATACTTAT
CAACATCCACCAGCTGACGGTAGCAACGTAAAAGTCGATGTTGATCCAAAATCACAACGC
TTACAATTACT

>g5631.t9 Gene=g5631 Length=462
MMQFISSGLKRVAVPTTIHCDHLIEAQIGGDQDLARAKKLNEEVYRFLETASAKYGVGFW
KPGSGIIHQIILENYAFPGLLMIGTDSHTPNGGGLGGLCIGVGGADAVDVMANIPWELKC
PKVIGVHLTGKIGGWTSPKDVILKVADILTVKGGTGAIVEYHGKGVDSISCTGMATICNM
GAEIGATTSTFPFNSRMAAYLKSTLRDGIAAEAAKFQTQLLQADEGAQYDELIEINLDTL
EPHVNGPFTPDLAHPISKLGENSKKNGYPIDIKVGLIGSCTNSSYEDMGRCASIVKDALS
HGLKSKIPFNVTPGSEQVRATIERDGIAKTLRDFGGTVLANACGPCIGQWDRQDVKKGDK
NTIVTSYNRNFTGRNDANPATHCFVTSPEMVTALSIAGRLDFNPLKDELTGADGKKFKLK
EPFGDELPVRGFDPGQDTYQHPPADGSNVKVDVDPKSQRLQL

Protein features from InterProScan

Transcript Database ID Name Start End E.value
17 g5631.t9 CDD cd01584 AcnA_Mitochondrial 1 400 0.0
16 g5631.t9 Coils Coil Coil 459 462 -
14 g5631.t9 Gene3D G3DSA:3.30.499.10 Aconitase 1 122 7.1E-58
15 g5631.t9 Gene3D G3DSA:3.40.1060.10 Aconitase 123 240 2.6E-39
13 g5631.t9 Gene3D G3DSA:3.30.499.10 Aconitase 241 412 1.0E-64
20 g5631.t9 MobiDBLite mobidb-lite consensus disorder prediction 426 462 -
2 g5631.t9 PANTHER PTHR43160 ACONITATE HYDRATASE B 1 462 1.9E-257
3 g5631.t9 PANTHER PTHR43160:SF3 ACONITATE HYDRATASE, MITOCHONDRIAL 1 462 1.9E-257
8 g5631.t9 PRINTS PR00415 Aconitase family signature 57 65 5.1E-39
7 g5631.t9 PRINTS PR00415 Aconitase family signature 77 90 5.1E-39
11 g5631.t9 PRINTS PR00415 Aconitase family signature 91 106 5.1E-39
4 g5631.t9 PRINTS PR00415 Aconitase family signature 153 166 5.1E-39
9 g5631.t9 PRINTS PR00415 Aconitase family signature 167 180 5.1E-39
6 g5631.t9 PRINTS PR00415 Aconitase family signature 242 256 5.1E-39
10 g5631.t9 PRINTS PR00415 Aconitase family signature 276 287 5.1E-39
5 g5631.t9 PRINTS PR00415 Aconitase family signature 335 348 5.1E-39
1 g5631.t9 Pfam PF00330 Aconitase family (aconitate hydratase) 12 398 1.4E-143
18 g5631.t9 ProSitePatterns PS00450 Aconitase family signature 1. 272 288 -
19 g5631.t9 ProSitePatterns PS01244 Aconitase family signature 2. 335 348 -
12 g5631.t9 SUPERFAMILY SSF53732 Aconitase iron-sulfur domain 3 446 1.31E-150
21 g5631.t9 TIGRFAM TIGR01340 aconitase_mito: aconitate hydratase, mitochondrial 1 462 3.7E-264

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5631/g5631.t9; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5631.t9.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006099 tricarboxylic acid cycle BP
GO:0003994 aconitate hydratase activity MF
GO:0051539 4 iron, 4 sulfur cluster binding 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