General information for g6936.t56
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Triosephosphate isomerase.
Parent gene
- The parent gene g6936 is located on chr_2: 20044463..20045782 (+ 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 | g6936 | g6936.t56 | isoform | g6936.t56 | 20044092 | 20045161 |
| chr_2 | g6936 | g6936.t56 | exon | g6936.t56.exon1 | 20044092 | 20044117 |
| chr_2 | g6936 | g6936.t56 | exon | g6936.t56.exon2 | 20044235 | 20044416 |
| chr_2 | g6936 | g6936.t56 | exon | g6936.t56.exon3 | 20044607 | 20045161 |
| chr_2 | g6936 | g6936.t56 | cds | g6936.t56.CDS1 | 20044658 | 20045161 |
| chr_2 | g6936 | g6936.t56 | TTS | g6936.t56 | 20045299 | 20045299 |
| chr_2 | g6936 | g6936.t56 | TSS | g6936.t56 | NA | NA |
Sequences
>g6936.t56 Gene=g6936 Length=763
CAACAGATTTTCGCAAATTTCATCCGTTGATTAAATAGCAAAAAAGACAGCAACAAAATG
GGTCGCAAATTTTGTGTTGGTGGAAATTGGAAAATGAATGGATCTAAGGATTCTATCACA
GAATTGGCCAAAATCCTTTCTGCTGGACCATTAGATCCAAATACTGAAGTGAGTTTCTTT
AAGCTGTCACAATATTTTTGAGTTTTATAATTGCTATAAAGTCAAATCAGGAGCTTTCAC
AGGAGAAATCGCACCATCAATGTTAAAAGATGTTGGTGCTGATTGGGTTATTCTTGGACA
CTCAGAGAGACGTGCAATTTTCGGCGAAAGTGATGAATTAATCGCAGATAAAGTTGAATT
TGCCCTTTCAGAAGGATTGAAAGTCATTGCTTGCATTGGTGAAACTCTTCAAGAACGTGA
GGCTGGTCAAACTGAAGCAGTATGCTTCCGTCAAACGAAGGCAATAGCTTCTGTTGTCAA
AGACTGGTCAAATGTTGTTATCGCTTATGAACCGGTTTGGGCAATTGGAACTGGCAAAAC
TGCAACTCCAGCTCAAGCCCAAGAGGTTCATGCTGCTCTCCGTAAATGGTTCGCCGAGAA
CGTTTCTCAAGCCGTTTCTGATTCAATTCGTATTCAATATGGTGGCTCAGTTACTGCTGC
TAATGCTCGTGAATTAGCTTCACAACCAGATATCGATGGATTTTTAGTTGGAGGTGCATC
ATTAAAACCCGAATTCGTACAAATTGTCAATGCTAGGCAGTAA
>g6936.t56 Gene=g6936 Length=167
MLKDVGADWVILGHSERRAIFGESDELIADKVEFALSEGLKVIACIGETLQEREAGQTEA
VCFRQTKAIASVVKDWSNVVIAYEPVWAIGTGKTATPAQAQEVHAALRKWFAENVSQAVS
DSIRIQYGGSVTAANARELASQPDIDGFLVGGASLKPEFVQIVNARQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g6936.t56 | CDD | cd00311 | TIM | 1 | 164 | 4.66132E-99 |
| 4 | g6936.t56 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 167 | 9.4E-79 |
| 2 | g6936.t56 | PANTHER | PTHR21139 | TRIOSEPHOSPHATE ISOMERASE | 1 | 165 | 5.9E-84 |
| 1 | g6936.t56 | Pfam | PF00121 | Triosephosphate isomerase | 1 | 163 | 5.2E-69 |
| 6 | g6936.t56 | ProSitePatterns | PS00171 | Triosephosphate isomerase active site. | 82 | 92 | - |
| 7 | g6936.t56 | ProSiteProfiles | PS51440 | Triosephosphate isomerase (TIM) family profile. | 1 | 165 | 64.007 |
| 3 | g6936.t56 | SUPERFAMILY | SSF51351 | Triosephosphate isomerase (TIM) | 1 | 165 | 1.44E-70 |
| 8 | g6936.t56 | TIGRFAM | TIGR00419 | tim: triose-phosphate isomerase | 1 | 158 | 4.1E-58 |
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:0004807 | triose-phosphate isomerase activity | MF |
| GO:0003824 | catalytic 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