General information for g7608.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Peroxiredoxin-4.
Parent gene
- The parent gene g7608 is located on chr_2: 24910250..24911301 (- 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 | g7608 | g7608.t11 | TTS | g7608.t11 | 24908670 | 24908670 |
| chr_2 | g7608 | g7608.t11 | isoform | g7608.t11 | 24908768 | 24911201 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon1 | 24908768 | 24908853 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon2 | 24909633 | 24910056 |
| chr_2 | g7608 | g7608.t11 | cds | g7608.t11.CDS1 | 24909944 | 24910056 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon3 | 24910238 | 24910599 |
| chr_2 | g7608 | g7608.t11 | cds | g7608.t11.CDS2 | 24910238 | 24910599 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon4 | 24910658 | 24910850 |
| chr_2 | g7608 | g7608.t11 | cds | g7608.t11.CDS3 | 24910658 | 24910850 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon5 | 24910934 | 24911032 |
| chr_2 | g7608 | g7608.t11 | cds | g7608.t11.CDS4 | 24910934 | 24911021 |
| chr_2 | g7608 | g7608.t11 | exon | g7608.t11.exon6 | 24911185 | 24911201 |
| chr_2 | g7608 | g7608.t11 | TSS | g7608.t11 | 24911300 | 24911300 |
Sequences
>g7608.t11 Gene=g7608 Length=1181
GCTACCTCAATAAAAAATTGGCGCAAAAATGCTGAAGCATTTTGTTATTTTCTCCTTCGT
ACTCTTTGGATTAGCTTTTGCAAATGACGATGGTTCATGCTTTGCAGCCCCAAAAGATGT
GTACCCAACTGATAAAAGTTCTAATAAAATTGAACACAGTTTGCAATATACTAAGGCAGT
GATCTCAAAGCCTGCACCTCAATTTTCTGGCACAGCTGTTATGAATGGAGAATTTAAAAC
AATAAGTTTGAATGATTATCTTGGAAAATATGTAGTTTTCTTCTTCTATCCTTTGGATTT
CACATTTGTATGCCCAACAGAAATTTTGGCATTTAGCGATAGAATTGATGAATTTAAAAA
GATTAACACGGAAGTTATTGCTGCTTCAGTTGATTCTCATTTTACACATCTATCATGGAC
AAAGACACCAAGAAAAGAAGGTGGTTTAGGAAATGTGAAAATTCCTTTGCTGAGCGATTT
ATCGCATAAAATATCTAAAGATTATGGAGTTTATTTGGAGGATCTTGGCCATACACTTAG
AGGACTTTTCATTATTGATGCAAAAGGTGTTTTACGTCAGATTACAATGAATGATTTGCC
AGTTGGACGTAGTGTCGATGAAACTCTTCGTTTGGTACAAGCTTTTCAATATACTGATAC
TCATGGTGAAGTGGAAAAAATTTTTTTTGGTCCATGTGATGGATATGCATCACATGTGCG
GTACATGCATTACTTGTGTCAAAATGGCTCAAAAACCACTTCAGACATGTTTTGTCGACG
TTAAAATTGTCGCACAACATTTTTATTTTCAAACACGACAAAATGTGAAGTGATCGCAGC
GTTACATAAATGCACCATTTTCACCATTTTCACATAAAGTTGATCGGTTCGTCTAATTGT
GTCATTGATTACAAATAATCAAGAATTTTGGTGAAAAATGAAAACTGCGAGCTGTAGAGT
GGATACTGCCGCACGGACACGGGACAAGGGTTTTTTTTGCAAATATCTCTGGACTGGAGT
GATCATTCTTTTATGCAAAAGGTCTTGTTCGATCGGAAATTACGAGGCCCACCTAAAAAT
ACTAGGTGTATACAGTGTGTCCTAGTGGCTGGATGCCGGGATCTAGAACCATCATCCCTG
ATCCTGAGGAGAAGCTAAAATACTTTGAGAAAGAGTTATGA
>g7608.t11 Gene=g7608 Length=251
MLKHFVIFSFVLFGLAFANDDGSCFAAPKDVYPTDKSSNKIEHSLQYTKAVISKPAPQFS
GTAVMNGEFKTISLNDYLGKYVVFFFYPLDFTFVCPTEILAFSDRIDEFKKINTEVIAAS
VDSHFTHLSWTKTPRKEGGLGNVKIPLLSDLSHKISKDYGVYLEDLGHTLRGLFIIDAKG
VLRQITMNDLPVGRSVDETLRLVQAFQYTDTHGEVEKIFFGPCDGYASHVRYMHYLCQNG
SKTTSDMFCRR
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 13 | g7608.t11 | CDD | cd03015 | PRX_Typ2cys | 52 | 215 | 3.62792E-107 |
| 7 | g7608.t11 | Gene3D | G3DSA:3.40.30.10 | Glutaredoxin | 46 | 230 | 9.9E-80 |
| 2 | g7608.t11 | PANTHER | PTHR10681 | THIOREDOXIN PEROXIDASE | 24 | 215 | 2.8E-109 |
| 3 | g7608.t11 | PANTHER | PTHR10681:SF157 | PEROXIREDOXIN-4 | 24 | 215 | 2.8E-109 |
| 1 | g7608.t11 | Pfam | PF00578 | AhpC/TSA family | 52 | 184 | 2.4E-36 |
| 9 | g7608.t11 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 26 | - |
| 10 | g7608.t11 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 5 | - |
| 11 | g7608.t11 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 6 | 17 | - |
| 12 | g7608.t11 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 18 | 26 | - |
| 8 | g7608.t11 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 27 | 251 | - |
| 15 | g7608.t11 | ProSiteProfiles | PS51352 | Thioredoxin domain profile. | 50 | 208 | 17.029 |
| 4 | g7608.t11 | SUPERFAMILY | SSF52833 | Thioredoxin-like | 52 | 215 | 3.86E-59 |
| 6 | g7608.t11 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 14 | g7608.t11 | SignalP_GRAM_NEGATIVE | SignalP-noTM | SignalP-noTM | 1 | 18 | - |
| 5 | g7608.t11 | SignalP_GRAM_POSITIVE | SignalP-TM | SignalP-TM | 1 | 26 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016209 | antioxidant activity | MF |
| GO:0055114 | NA | NA |
| GO:0016491 | oxidoreductase activity | MF |
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. There were no conditions that were differentially expressed