General information for g5570.t1
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.t1 | TTS | g5570.t1 | 10328853 | 10328853 |
| chr_2 | g5570 | g5570.t1 | isoform | g5570.t1 | 10328995 | 10331816 |
| chr_2 | g5570 | g5570.t1 | exon | g5570.t1.exon1 | 10328995 | 10329519 |
| chr_2 | g5570 | g5570.t1 | cds | g5570.t1.CDS1 | 10328995 | 10329519 |
| chr_2 | g5570 | g5570.t1 | exon | g5570.t1.exon2 | 10329580 | 10330034 |
| chr_2 | g5570 | g5570.t1 | cds | g5570.t1.CDS2 | 10329580 | 10330034 |
| chr_2 | g5570 | g5570.t1 | exon | g5570.t1.exon3 | 10330103 | 10330201 |
| chr_2 | g5570 | g5570.t1 | cds | g5570.t1.CDS3 | 10330103 | 10330201 |
| chr_2 | g5570 | g5570.t1 | exon | g5570.t1.exon4 | 10330261 | 10330666 |
| chr_2 | g5570 | g5570.t1 | cds | g5570.t1.CDS4 | 10330261 | 10330666 |
| chr_2 | g5570 | g5570.t1 | exon | g5570.t1.exon5 | 10331781 | 10331816 |
| chr_2 | g5570 | g5570.t1 | cds | g5570.t1.CDS5 | 10331781 | 10331816 |
| chr_2 | g5570 | g5570.t1 | TSS | g5570.t1 | NA | NA |
Sequences
>g5570.t1 Gene=g5570 Length=1521
ATGAAAGAAGATTTTGCTGCCTGCTTAGTTAACAAGATTGGATTCAAAGGCTATGAGTTG
TCACCAAATGATTTAAATAAAAGTGGAACATTCACTTGGGAAGATGGCAAAGAATATACA
CTGCGACATGGATCAGTAATTATTGCTGCAATTACATCATGCACAAATACATCAAATCCA
ACTGTAATTTTGGGTGCAGGATTGCTTGCAAGAAATGCTGTAAAGTTGGGCTTGACTGTT
GCTCCTTATATTAAGACAAGTCTATCACCTGGAAGTGGAGTAGTTACATATTATTTGAAA
GAATCTGACACAATATCAAGTCTTGAGAAGTTAGGCTTTCATATTGTTGGTATGGGCTGC
ATGACTTGCATTGGAAATAGTGGACCAGTTCATGAAAGTGTCGCATCTGTCATTGAAAAG
AATGATCTCGTTTGTTGTGGAGTCCTTTCTGGCAATCGTAATTTTGAGGGTCGTGTACAT
CCATTAACACGCGCCAACTATTTAGCATCACCATTACTCGTTATCGCGTATGCTATTGCA
GGCACTGTTGATATTGATTTTGAGACACAACCGATTGGCAAAGGTTTTGATGGTAGTGAA
GTCTATTTAAGAGATATTTGGCCTAGTCGTAAAGAAATTCAAGAAGTTGAGAAGAAATAT
GTCATTCCAGCAATGTTTAAAGATGTTTATGAGAAAATTCAACAAGGATCACAAAATTGG
CGTGACCTTGTTGCACCAGAAGGAAAATTATATCCATGGGATGATAAATCAACATACATT
AAACATCCACCGTTCTTTGAAAACATGACACGAGAATTGCCTGTTCAAAAGCCAATCTTA
AATGCACGTGTTTTGTTGAATTTCGGTGATAGTGTCACAACTGATCATATTTCACCAGCT
GGTTCGATTGCTCGTAATAGCCCTGCAGCTCGCTATTTAACTGAGCGTAAGATTTTGCCA
AAAGATTTCAATTCTTATGGTTCAAGAAGAGGAAATGACGCAGTTATGGCTCGTGGAACA
TTCGCAAACATTCGTCTTGTCAACAAATTCATGAAACATGCCGGTCCTCGTACAATTCAT
TTCCCATCAAATACTGAGATGGACATTTTCGATTGTGCTGAACGTTACAAGAGTGAAAAT
GTACCTCTTATTATACTTGCTGGCAAAGAATATGGTTCAGGATCATCTCGAGATTGGGCA
GCTAAAGGACCATATTTATTGGGTATTCGTGCTGTTATTGCTGAATCTTATGAACGCATT
CATCGATCAAATTTGGTTGGAATGGGAATTTGTCCTTTGCAATACTTGCCTGGTCAAAAT
GCAGAAAGTCTCGGTTTAACTGGTCATGAGACTTTCAATATACAAATTCCAGAAGATGTT
CATCCATTGCAAAATATTGATGTCACAACAGATACTGGAATTAAATTCGAAGTTTTGGTT
CGCTTCGATACTGATGTTGAAATTTTATATTTCAAGAACGGCGGAATTTTGAATTTCATG
ATTAGAAAAATGATCGACTGA
>g5570.t1 Gene=g5570 Length=506
MKEDFAACLVNKIGFKGYELSPNDLNKSGTFTWEDGKEYTLRHGSVIIAAITSCTNTSNP
TVILGAGLLARNAVKLGLTVAPYIKTSLSPGSGVVTYYLKESDTISSLEKLGFHIVGMGC
MTCIGNSGPVHESVASVIEKNDLVCCGVLSGNRNFEGRVHPLTRANYLASPLLVIAYAIA
GTVDIDFETQPIGKGFDGSEVYLRDIWPSRKEIQEVEKKYVIPAMFKDVYEKIQQGSQNW
RDLVAPEGKLYPWDDKSTYIKHPPFFENMTRELPVQKPILNARVLLNFGDSVTTDHISPA
GSIARNSPAARYLTERKILPKDFNSYGSRRGNDAVMARGTFANIRLVNKFMKHAGPRTIH
FPSNTEMDIFDCAERYKSENVPLIILAGKEYGSGSSRDWAAKGPYLLGIRAVIAESYERI
HRSNLVGMGICPLQYLPGQNAESLGLTGHETFNIQIPEDVHPLQNIDVTTDTGIKFEVLV
RFDTDVEILYFKNGGILNFMIRKMID
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 12 | g5570.t1 | CDD | cd01580 | AcnA_IRP_Swivel | 287 | 454 | 5.59654E-116 |
| 9 | g5570.t1 | Gene3D | G3DSA:3.30.499.10 | Aconitase | 1 | 209 | 1.7E-93 |
| 10 | g5570.t1 | Gene3D | G3DSA:1.10.1440.20 | - | 210 | 271 | 3.5E-28 |
| 11 | g5570.t1 | Gene3D | G3DSA:3.20.19.10 | Aconitase | 272 | 506 | 3.1E-106 |
| 3 | g5570.t1 | PANTHER | PTHR11670 | ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER | 1 | 505 | 1.8E-253 |
| 4 | g5570.t1 | PANTHER | PTHR11670:SF32 | CYTOPLASMIC ACONITATE HYDRATASE | 1 | 505 | 1.8E-253 |
| 2 | g5570.t1 | Pfam | PF00330 | Aconitase family (aconitate hydratase) | 27 | 181 | 8.3E-49 |
| 1 | g5570.t1 | Pfam | PF00694 | Aconitase C-terminal domain | 310 | 435 | 1.1E-41 |
| 7 | g5570.t1 | ProSitePatterns | PS00450 | Aconitase family signature 1. | 46 | 62 | - |
| 8 | g5570.t1 | ProSitePatterns | PS01244 | Aconitase family signature 2. | 112 | 125 | - |
| 6 | g5570.t1 | SUPERFAMILY | SSF53732 | Aconitase iron-sulfur domain | 1 | 244 | 9.29E-76 |
| 5 | g5570.t1 | SUPERFAMILY | SSF52016 | LeuD/IlvD-like | 250 | 504 | 2.55E-83 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5570/g5570.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5570.t1.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 transcript has been annotated with K01681 (aconitate hydratase)
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.
