General information for g5570.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 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.t4 | TTS | g5570.t4 | 10328853 | 10328853 |
| chr_2 | g5570 | g5570.t4 | isoform | g5570.t4 | 10328854 | 10330030 |
| chr_2 | g5570 | g5570.t4 | exon | g5570.t4.exon1 | 10328854 | 10329512 |
| chr_2 | g5570 | g5570.t4 | cds | g5570.t4.CDS1 | 10329462 | 10329512 |
| chr_2 | g5570 | g5570.t4 | exon | g5570.t4.exon2 | 10329580 | 10330030 |
| chr_2 | g5570 | g5570.t4 | cds | g5570.t4.CDS2 | 10329580 | 10329903 |
| chr_2 | g5570 | g5570.t4 | TSS | g5570.t4 | NA | NA |
Sequences
>g5570.t4 Gene=g5570 Length=1110
TGTTGATATTGATTTTGAGACACAACCGATTGGCAAAGGTTTTGATGGTAGTGAAGTCTA
TTTAAGAGATATTTGGCCTAGTCGTAAAGAAATTCAAGAAGTTGAGAAGAAATATGTCAT
TCCAGCAATGTTTAAAGATGTTTATGAGAAAATTCAACAAGGATCACAAAATTGGCGTGA
CCTTGTTGCACCAGAAGGAAAATTATATCCATGGGATGATAAATCAACATACATTAAACA
TCCACCGTTCTTTGAAAACATGACACGAGAATTGCCTGTTCAAAAGCCAATCTTAAATGC
ACGTGTTTTGTTGAATTTCGGTGATAGTGTCACAACTGATCATATTTCACCAGCTGGTTC
GATTGCTCGTAATAGCCCTGCAGCTCGCTATTTAACTGAGCGTAAGATTTTGCCAAAAGA
TTTCAATTCTTATGGTTCAAGAAGAGGAAATTTATGGCTCGTGGAACATTCGCAAACATT
CGTCTTGTCAACAAATTCATGAAACATGCCGGTCCTCGTACAATTCATTTCCCATCAAAT
ACTGAGATGGACATTTTCGATTGTGCTGAACGTTACAAGAGTGAAAATGTACCTCTTATT
ATACTTGCTGGCAAAGAATATGGTTCAGGATCATCTCGAGATTGGGCAGCTAAAGGACCA
TATTTATTGGGTATTCGTGCTGTTATTGCTGAATCTTATGAACGCATTCATCGATCAAAT
TTGGTTGGAATGGGAATTTGTCCTTTGCAATACTTGCCTGGTCAAAATGCAGAAAGTCTC
GGTTTAACTGGTCATGAGACTTTCAATATACAAATTCCAGAAGATGTTCATCCATTGCAA
AATATTGATGTCACAACAGATACTGGAATTAAATTCGAAGTTTTGGTTCGCTTCGATACT
GATGTTGAAATTTTATATTTCAAGAACGGCGGAATTTTGAATTTCATGATTAGAAAAATG
ATCGACTGAATATTCTCCACTCTGAAAACATTCTAATATGTATGTTGTTGATTTTTTGAC
GATAATTATTGATTCGGGTAAAATGTGGTGACAGGAACAAAAAATACAATAAAAAAGTTT
TTAGAAACTTCTTTTTTATTCATTGTTTTA
>g5570.t4 Gene=g5570 Length=124
MFKDVYEKIQQGSQNWRDLVAPEGKLYPWDDKSTYIKHPPFFENMTRELPVQKPILNARV
LLNFGDSVTTDHISPAGSIARNSPAARYLTERKILPKDFNSYGSRRGNLWLVEHSQTFVL
STNS
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 3 | g5570.t4 | Gene3D | G3DSA:1.10.1440.20 | - | 1 | 47 | 0 |
| 4 | g5570.t4 | Gene3D | G3DSA:3.20.19.10 | Aconitase | 48 | 119 | 0 |
| 1 | g5570.t4 | PANTHER | PTHR11670 | ACONITASE/IRON-RESPONSIVE ELEMENT FAMILY MEMBER | 1 | 112 | 0 |
| 2 | g5570.t4 | SUPERFAMILY | SSF52016 | LeuD/IlvD-like | 26 | 110 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5570/g5570.t4; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5570.t4.fa.iupred3.txt does not exist
GO terms from InterProScan
There are no GO annotations for this transcript.
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.
