General information for g5570.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Cytoplasmic aconitate hydratase.
Parent gene
- The parent gene g5570 is located on chr_2: 10328995..10331816 (- strand)
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 | g5570 | g5570.t3 | TTS | g5570.t3 | 10328853 | 10328853 |
| chr_2 | g5570 | g5570.t3 | isoform | g5570.t3 | 10328854 | 10329512 |
| chr_2 | g5570 | g5570.t3 | exon | g5570.t3.exon1 | 10328854 | 10329512 |
| chr_2 | g5570 | g5570.t3 | cds | g5570.t3.CDS1 | 10328995 | 10329510 |
| chr_2 | g5570 | g5570.t3 | TSS | g5570.t3 | NA | NA |
Sequences
>g5570.t3 Gene=g5570 Length=659
TTATGGCTCGTGGAACATTCGCAAACATTCGTCTTGTCAACAAATTCATGAAACATGCCG
GTCCTCGTACAATTCATTTCCCATCAAATACTGAGATGGACATTTTCGATTGTGCTGAAC
GTTACAAGAGTGAAAATGTACCTCTTATTATACTTGCTGGCAAAGAATATGGTTCAGGAT
CATCTCGAGATTGGGCAGCTAAAGGACCATATTTATTGGGTATTCGTGCTGTTATTGCTG
AATCTTATGAACGCATTCATCGATCAAATTTGGTTGGAATGGGAATTTGTCCTTTGCAAT
ACTTGCCTGGTCAAAATGCAGAAAGTCTCGGTTTAACTGGTCATGAGACTTTCAATATAC
AAATTCCAGAAGATGTTCATCCATTGCAAAATATTGATGTCACAACAGATACTGGAATTA
AATTCGAAGTTTTGGTTCGCTTCGATACTGATGTTGAAATTTTATATTTCAAGAACGGCG
GAATTTTGAATTTCATGATTAGAAAAATGATCGACTGAATATTCTCCACTCTGAAAACAT
TCTAATATGTATGTTGTTGATTTTTTGACGATAATTATTGATTCGGGTAAAATGTGGTGA
CAGGAACAAAAAATACAATAAAAAAGTTTTTAGAAACTTCTTTTTTATTCATTGTTTTA
>g5570.t3 Gene=g5570 Length=171
MARGTFANIRLVNKFMKHAGPRTIHFPSNTEMDIFDCAERYKSENVPLIILAGKEYGSGS
SRDWAAKGPYLLGIRAVIAESYERIHRSNLVGMGICPLQYLPGQNAESLGLTGHETFNIQ
IPEDVHPLQNIDVTTDTGIKFEVLVRFDTDVEILYFKNGGILNFMIRKMID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5570.t3 | Gene3D | G3DSA:3.20.19.10 | Aconitase | 1 | 171 | 0 |
| 2 | g5570.t3 | PANTHER | PTHR11670 | ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER | 1 | 170 | 0 |
| 3 | g5570.t3 | PANTHER | PTHR11670:SF32 | CYTOPLASMIC ACONITATE HYDRATASE | 1 | 170 | 0 |
| 1 | g5570.t3 | Pfam | PF00694 | Aconitase C-terminal domain | 1 | 100 | 0 |
| 4 | g5570.t3 | SUPERFAMILY | SSF52016 | LeuD/IlvD-like | 1 | 169 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5570/g5570.t3; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5570.t3.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0006879 | cellular iron ion homeostasis | BP |
| GO:0003994 | aconitate hydratase activity | MF |
| GO:0051539 | 4 iron, 4 sulfur cluster binding | MF |
| GO:0010040 | response to iron(II) ion | BP |
KEGG
Orthology
This gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
