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.t1 TSS g5631.t1 10732477 10732477
chr_2 g5631 g5631.t1 isoform g5631.t1 10732556 10735708
chr_2 g5631 g5631.t1 exon g5631.t1.exon1 10732556 10732588
chr_2 g5631 g5631.t1 cds g5631.t1.CDS1 10732556 10732588
chr_2 g5631 g5631.t1 exon g5631.t1.exon2 10733142 10734773
chr_2 g5631 g5631.t1 cds g5631.t1.CDS2 10733142 10734773
chr_2 g5631 g5631.t1 exon g5631.t1.exon3 10734940 10735443
chr_2 g5631 g5631.t1 cds g5631.t1.CDS3 10734940 10735443
chr_2 g5631 g5631.t1 exon g5631.t1.exon4 10735517 10735708
chr_2 g5631 g5631.t1 cds g5631.t1.CDS4 10735517 10735708
chr_2 g5631 g5631.t1 TTS g5631.t1 10736088 10736088

Sequences

>g5631.t1 Gene=g5631 Length=2361
ATGGTCCATTATACGAAATTATTAACACAGCAGGCGAAACGAGCGGCTTTGTATGCCGTT
GATGCACAACAAAGATGGTTCCATGCAAGTTGTGCAATGAGCAGCAAAGTTGCTTTGTCA
AAATTCGATGAGAATGTCTACTTGCCATATGAGAAACTCGTTGAACGTCTAAATATTGTC
AAGAAGCGATTGAATCGTCCATTAACAATGTCAGAAAAAGTTTTATATTCACATCTCGAT
GATCCAGCAAATCAAGACATTGAACGTGGTGTTTCTTATTTGCGCTTGAGACCTGATCGA
GTCGCTTGTCAAGATGCCACCGCCCAAATGGCTATGATGCAATTCATTTCCTCCGGATTG
AAACGTGTCGCTGTTCCAACAACAATTCATTGCGATCATTTGATTGAAGCACAAATTGGA
GGCGATCAAGATTTAGCTCGCGCAAAGAAACTCAATGAAGAAGTTTATCGTTTCTTAGAG
ACTGCAAGTGCCAAGTATGGAGTTGGTTTCTGGAAGCCTGGTTCAGGTATTATTCATCAA
ATCATTCTTGAGAATTACGCATTCCCTGGTCTTTTGATGATCGGTACTGACTCTCATACA
CCAAATGGAGGCGGACTTGGTGGCCTTTGCATTGGTGTCGGTGGCGCTGATGCTGTTGAT
GTTATGGCTAATATTCCGTGGGAATTGAAATGTCCAAAAGTTATTGGTGTTCATTTAACG
GGAAAAATTGGTGGTTGGACTTCACCAAAGGATGTTATCTTGAAGGTTGCTGATATTTTG
ACTGTAAAGGGAGGCACTGGTGCAATTGTTGAATATCATGGTAAAGGTGTTGATTCAATT
TCATGCACAGGTATGGCAACAATCTGTAATATGGGTGCTGAAATTGGTGCAACCACTTCA
ACTTTCCCATTCAATTCAAGAATGGCTGCTTATTTGAAATCAACTCTTCGTGATGGCATT
GCTGCCGAAGCTGCCAAATTCCAAACTCAATTGCTCCAAGCAGATGAAGGTGCACAATAT
GACGAGCTCATTGAAATTAATTTGGATACATTGGAACCACATGTAAATGGTCCATTCACT
CCAGATCTTGCTCATCCAATTAGCAAACTTGGTGAAAATTCAAAAAAGAACGGTTATCCA
ATTGATATTAAAGTTGGTTTAATTGGTTCATGTACAAACTCATCATATGAAGATATGGGT
CGATGTGCTTCTATTGTCAAAGATGCTTTGTCTCATGGTCTTAAATCAAAAATTCCATTC
AATGTTACACCCGGCTCTGAGCAAGTTCGTGCTACAATTGAACGTGATGGAATTGCGAAA
ACTCTTCGTGATTTTGGTGGTACTGTCTTAGCTAATGCTTGTGGACCATGTATTGGTCAA
TGGGATCGTCAAGATGTAAAGAAGGGTGACAAAAACACAATTGTAACTTCATACAACCGT
AACTTTACCGGACGTAATGATGCTAATCCAGCAACTCATTGCTTCGTTACTTCACCTGAA
ATGGTTACAGCTTTGTCAATTGCTGGCCGCTTAGATTTCAATCCATTGAAAGACGAATTG
ACTGGTGCTGATGGTAAGAAATTCAAATTGAAGGAACCATTCGGTGATGAATTGCCAGTT
CGTGGCTTTGATCCTGGCCAAGATACTTATCAACATCCACCAGCTGACGGTAGCAACGTA
AAAGTCGATGTTGATCCAAAATCACAACGCTTACAATTACTTGAACCATTTGATAAATGG
GATGGCAAAGATTTAACAGAAATGACAGTTTTGATTAAAGTTAAAGGCAAGTGCACAACC
GATCACATCTCAGCTGCTGGACCTTGGTTGAAATATCGTGGACATTTGGATAATATCTCA
AATAACATGTTTATTGGTGCCACTAATGCTGAAAACAATGAAATGAATAAGATTAAAAAT
CAGGTTACTGGTGAATGGGGCGGAGTTCCAGACGTTGCTCGTTTCTATAAATCAAAGGGC
ATCCGTTGGGTTGCTGTTGGTGATGAAAATTACGGAGAGGGTTCATCTCGCGAGCATGCT
GCTCTTGAACCACGTCATTTGGGAGGTCGCGCTATTATTGTTAAATCTTTTGCTCGTATT
CACGAAACAAACTTGAAGAAGCAAGGCATGTTGCCAGTAACTTTCGCTAATCCAGCTGAC
TACGATAAGATTCAACCAACTGATAAGATTTCAATTCTCGGTTTGAAAGATTTTGCACCA
GGCAAACAATTGACAGCTGAAATTAAACACGCTGATGGTAAGACCGAGCAAATTAAATTG
AACCACAGTTTCAACGATCTTCAGATTTCATGGTTCAAGGCTGGTAGTGCATTAAATCGT
ATGAAGGAAACAGCACACTAA

>g5631.t1 Gene=g5631 Length=786
MVHYTKLLTQQAKRAALYAVDAQQRWFHASCAMSSKVALSKFDENVYLPYEKLVERLNIV
KKRLNRPLTMSEKVLYSHLDDPANQDIERGVSYLRLRPDRVACQDATAQMAMMQFISSGL
KRVAVPTTIHCDHLIEAQIGGDQDLARAKKLNEEVYRFLETASAKYGVGFWKPGSGIIHQ
IILENYAFPGLLMIGTDSHTPNGGGLGGLCIGVGGADAVDVMANIPWELKCPKVIGVHLT
GKIGGWTSPKDVILKVADILTVKGGTGAIVEYHGKGVDSISCTGMATICNMGAEIGATTS
TFPFNSRMAAYLKSTLRDGIAAEAAKFQTQLLQADEGAQYDELIEINLDTLEPHVNGPFT
PDLAHPISKLGENSKKNGYPIDIKVGLIGSCTNSSYEDMGRCASIVKDALSHGLKSKIPF
NVTPGSEQVRATIERDGIAKTLRDFGGTVLANACGPCIGQWDRQDVKKGDKNTIVTSYNR
NFTGRNDANPATHCFVTSPEMVTALSIAGRLDFNPLKDELTGADGKKFKLKEPFGDELPV
RGFDPGQDTYQHPPADGSNVKVDVDPKSQRLQLLEPFDKWDGKDLTEMTVLIKVKGKCTT
DHISAAGPWLKYRGHLDNISNNMFIGATNAENNEMNKIKNQVTGEWGGVPDVARFYKSKG
IRWVAVGDENYGEGSSREHAALEPRHLGGRAIIVKSFARIHETNLKKQGMLPVTFANPAD
YDKIQPTDKISILGLKDFAPGKQLTAEIKHADGKTEQIKLNHSFNDLQISWFKAGSALNR
MKETAH

Protein features from InterProScan

Transcript Database ID Name Start End E.value
20 g5631.t1 CDD cd01584 AcnA_Mitochondrial 100 511 0.0
19 g5631.t1 CDD cd01578 AcnA_Mitochon_Swivel 593 741 1.67123E-108
15 g5631.t1 Gene3D G3DSA:3.30.499.10 Aconitase 34 233 3.7E-91
17 g5631.t1 Gene3D G3DSA:3.40.1060.10 Aconitase 234 351 6.3E-39
16 g5631.t1 Gene3D G3DSA:3.30.499.10 Aconitase 352 523 2.9E-64
18 g5631.t1 Gene3D G3DSA:3.20.19.10 Aconitase 567 786 7.0E-105
3 g5631.t1 PANTHER PTHR43160 ACONITATE HYDRATASE B 23 784 0.0
4 g5631.t1 PANTHER PTHR43160:SF3 ACONITATE HYDRATASE, MITOCHONDRIAL 23 784 0.0
11 g5631.t1 PRINTS PR00415 Aconitase family signature 168 176 2.3E-37
6 g5631.t1 PRINTS PR00415 Aconitase family signature 188 201 2.3E-37
8 g5631.t1 PRINTS PR00415 Aconitase family signature 202 217 2.3E-37
10 g5631.t1 PRINTS PR00415 Aconitase family signature 264 277 2.3E-37
12 g5631.t1 PRINTS PR00415 Aconitase family signature 278 291 2.3E-37
9 g5631.t1 PRINTS PR00415 Aconitase family signature 353 367 2.3E-37
5 g5631.t1 PRINTS PR00415 Aconitase family signature 387 398 2.3E-37
7 g5631.t1 PRINTS PR00415 Aconitase family signature 446 459 2.3E-37
2 g5631.t1 Pfam PF00330 Aconitase family (aconitate hydratase) 72 509 1.6E-150
1 g5631.t1 Pfam PF00694 Aconitase C-terminal domain 588 717 2.0E-43
21 g5631.t1 ProSitePatterns PS00450 Aconitase family signature 1. 383 399 -
22 g5631.t1 ProSitePatterns PS01244 Aconitase family signature 2. 446 459 -
14 g5631.t1 SUPERFAMILY SSF53732 Aconitase iron-sulfur domain 39 557 6.28E-167
13 g5631.t1 SUPERFAMILY SSF52016 LeuD/IlvD-like 563 783 1.51E-65
23 g5631.t1 TIGRFAM TIGR01340 aconitase_mito: aconitate hydratase, mitochondrial 50 781 0.0

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5631/g5631.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5631.t1.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