Gene loci information

Transcript annotation

  • This transcript has been annotated as Probable 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.t4 TSS g5631.t4 10732477 10732477
chr_2 g5631 g5631.t4 isoform g5631.t4 10732556 10734995
chr_2 g5631 g5631.t4 exon g5631.t4.exon1 10732556 10732588
chr_2 g5631 g5631.t4 exon g5631.t4.exon2 10733152 10734773
chr_2 g5631 g5631.t4 cds g5631.t4.CDS1 10733205 10734773
chr_2 g5631 g5631.t4 exon g5631.t4.exon3 10734940 10734995
chr_2 g5631 g5631.t4 cds g5631.t4.CDS2 10734940 10734993
chr_2 g5631 g5631.t4 TTS g5631.t4 NA NA

Sequences

>g5631.t4 Gene=g5631 Length=1711
ATGGTCCATTATACGAAATTATTAACACAGCAGCGGCTTTGTATGCCGTTGATGCACAAC
AAAGATGGTTCCATGCAAGTTGTGCAATGAGCAGCAAAGTTGCTTTGTCAAAATTCGATG
AGAATGTCTACTTGCCATATGAGAAACTCGTTGAACGTCTAAATATTGTCAAGAAGCGAT
TGAATCGTCCATTAACAATGTCAGAAAAAGTTTTATATTCACATCTCGATGATCCAGCAA
ATCAAGACATTGAACGTGGTGTTTCTTATTTGCGCTTGAGACCTGATCGAGTCGCTTGTC
AAGATGCCACCGCCCAAATGGCTATGATGCAATTCATTTCCTCCGGATTGAAACGTGTCG
CTGTTCCAACAACAATTCATTGCGATCATTTGATTGAAGCACAAATTGGAGGCGATCAAG
ATTTAGCTCGCGCAAAGAAACTCAATGAAGAAGTTTATCGTTTCTTAGAGACTGCAAGTG
CCAAGTATGGAGTTGGTTTCTGGAAGCCTGGTTCAGGTATTATTCATCAAATCATTCTTG
AGAATTACGCATTCCCTGGTCTTTTGATGATCGGTACTGACTCTCATACACCAAATGGAG
GCGGACTTGGTGGCCTTTGCATTGGTGTCGGTGGCGCTGATGCTGTTGATGTTATGGCTA
ATATTCCGTGGGAATTGAAATGTCCAAAAGTTATTGGTGTTCATTTAACGGGAAAAATTG
GTGGTTGGACTTCACCAAAGGATGTTATCTTGAAGGTTGCTGATATTTTGACTGTAAAGG
GAGGCACTGGTGCAATTGTTGAATATCATGGTAAAGGTGTTGATTCAATTTCATGCACAG
GTATGGCAACAATCTGTAATATGGGTGCTGAAATTGGTGCAACCACTTCAACTTTCCCAT
TCAATTCAAGAATGGCTGCTTATTTGAAATCAACTCTTCGTGATGGCATTGCTGCCGAAG
CTGCCAAATTCCAAACTCAATTGCTCCAAGCAGATGAAGGTGCACAATATGACGAGCTCA
TTGAAATTAATTTGGATACATTGGAACCACATGTAAATGGTCCATTCACTCCAGATCTTG
CTCATCCAATTAGCAAACTTGGTGAAAATTCAAAAAAGAACGGTTATCCAATTGATATTA
AAGTTGGTTTAATTGGTTCATGTACAAACTCATCATATGAAGATATGGGTCGATGTGCTT
CTATTGTCAAAGATGCTTTGTCTCATGGTCTTAAATCAAAAATTCCATTCAATGTTACAC
CCGGCTCTGAGCAAGTTCGTGCTACAATTGAACGTGATGGAATTGCGAAAACTCTTCGTG
ATTTTGGTGGTACTGTCTTAGCTAATGCTTGTGGACCATGTATTGGTCAATGGGATCGTC
AAGATGTAAAGAAGGGTGACAAAAACACAATTGTAACTTCATACAACCGTAACTTTACCG
GACGTAATGATGCTAATCCAGCAACTCATTGCTTCGTTACTTCACCTGAAATGGTTACAG
CTTTGTCAATTGCTGGCCGCTTAGATTTCAATCCATTGAAAGACGAATTGACTGGTGCTG
ATGGTAAGAAATTCAAATTGAAGGAACCATTCGGTGATGAATTGCCAGTTCGTGGCTTTG
ATCCTGGCCAAGATACTTATCAACATCCACCAGCTGACGGTAGCAACGTAAAAGTCGATG
TTGATCCAAAATCACAACGCTTACAATTACT

>g5631.t4 Gene=g5631 Length=541
MSSKVALSKFDENVYLPYEKLVERLNIVKKRLNRPLTMSEKVLYSHLDDPANQDIERGVS
YLRLRPDRVACQDATAQMAMMQFISSGLKRVAVPTTIHCDHLIEAQIGGDQDLARAKKLN
EEVYRFLETASAKYGVGFWKPGSGIIHQIILENYAFPGLLMIGTDSHTPNGGGLGGLCIG
VGGADAVDVMANIPWELKCPKVIGVHLTGKIGGWTSPKDVILKVADILTVKGGTGAIVEY
HGKGVDSISCTGMATICNMGAEIGATTSTFPFNSRMAAYLKSTLRDGIAAEAAKFQTQLL
QADEGAQYDELIEINLDTLEPHVNGPFTPDLAHPISKLGENSKKNGYPIDIKVGLIGSCT
NSSYEDMGRCASIVKDALSHGLKSKIPFNVTPGSEQVRATIERDGIAKTLRDFGGTVLAN
ACGPCIGQWDRQDVKKGDKNTIVTSYNRNFTGRNDANPATHCFVTSPEMVTALSIAGRLD
FNPLKDELTGADGKKFKLKEPFGDELPVRGFDPGQDTYQHPPADGSNVKVDVDPKSQRLQ
L

Protein features from InterProScan

Transcript Database ID Name Start End E.value
16 g5631.t4 CDD cd01584 AcnA_Mitochondrial 68 479 0.0
13 g5631.t4 Gene3D G3DSA:3.30.499.10 Aconitase 2 201 1.8E-91
15 g5631.t4 Gene3D G3DSA:3.40.1060.10 Aconitase 202 319 3.5E-39
14 g5631.t4 Gene3D G3DSA:3.30.499.10 Aconitase 320 491 1.4E-64
19 g5631.t4 MobiDBLite mobidb-lite consensus disorder prediction 505 541 -
2 g5631.t4 PANTHER PTHR43160 ACONITATE HYDRATASE B 2 541 5.2E-296
3 g5631.t4 PANTHER PTHR43160:SF3 ACONITATE HYDRATASE, MITOCHONDRIAL 2 541 5.2E-296
11 g5631.t4 PRINTS PR00415 Aconitase family signature 136 144 1.5E-38
5 g5631.t4 PRINTS PR00415 Aconitase family signature 156 169 1.5E-38
10 g5631.t4 PRINTS PR00415 Aconitase family signature 170 185 1.5E-38
8 g5631.t4 PRINTS PR00415 Aconitase family signature 232 245 1.5E-38
6 g5631.t4 PRINTS PR00415 Aconitase family signature 246 259 1.5E-38
9 g5631.t4 PRINTS PR00415 Aconitase family signature 321 335 1.5E-38
7 g5631.t4 PRINTS PR00415 Aconitase family signature 355 366 1.5E-38
4 g5631.t4 PRINTS PR00415 Aconitase family signature 414 427 1.5E-38
1 g5631.t4 Pfam PF00330 Aconitase family (aconitate hydratase) 40 477 5.1E-151
17 g5631.t4 ProSitePatterns PS00450 Aconitase family signature 1. 351 367 -
18 g5631.t4 ProSitePatterns PS01244 Aconitase family signature 2. 414 427 -
12 g5631.t4 SUPERFAMILY SSF53732 Aconitase iron-sulfur domain 7 525 1.7E-167
20 g5631.t4 TIGRFAM TIGR01340 aconitase_mito: aconitate hydratase, mitochondrial 18 541 9.6E-296

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5631/g5631.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5631.t4.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