General information for g6936.t40
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.t40 | isoform | g6936.t40 | 20044082 | 20045161 |
| chr_2 | g6936 | g6936.t40 | exon | g6936.t40.exon1 | 20044082 | 20044109 |
| chr_2 | g6936 | g6936.t40 | exon | g6936.t40.exon2 | 20044235 | 20044376 |
| chr_2 | g6936 | g6936.t40 | cds | g6936.t40.CDS1 | 20044266 | 20044376 |
| chr_2 | g6936 | g6936.t40 | exon | g6936.t40.exon3 | 20044463 | 20044540 |
| chr_2 | g6936 | g6936.t40 | cds | g6936.t40.CDS2 | 20044463 | 20044540 |
| chr_2 | g6936 | g6936.t40 | exon | g6936.t40.exon4 | 20044607 | 20045161 |
| chr_2 | g6936 | g6936.t40 | cds | g6936.t40.CDS3 | 20044607 | 20045161 |
| chr_2 | g6936 | g6936.t40 | TTS | g6936.t40 | 20045299 | 20045299 |
| chr_2 | g6936 | g6936.t40 | TSS | g6936.t40 | NA | NA |
Sequences
>g6936.t40 Gene=g6936 Length=803
ATTGAAAGGTCAACAGATTTTCGCAAATTTGATTAAATAGCAAAAAAGACAGCAACAAAA
TGGGTCGCAAATTTTGTGTTGGTGGAAATTGGAAAATGAATGGATCTAAGGATTCTATCA
CAGAATTGGCCAAAATCCTTTCTGCTGGACCATTAGATCCAAATACTGAAGTCGTTGTTG
GATGCCCAAGCGTTTATATCTCATTCGCTCGAGGACTTCTTCCTTCCTCAATTGGTGTTG
CTGGCCAGAATTGCTATAAAGTCAAATCAGGAGCTTTCACAGGAGAAATCGCACCATCAA
TGTTAAAAGATGTTGGTGCTGATTGGGTTATTCTTGGACACTCAGAGAGACGTGCAATTT
TCGGCGAAAGTGATGAATTAATCGCAGATAAAGTTGAATTTGCCCTTTCAGAAGGATTGA
AAGTCATTGCTTGCATTGGTGAAACTCTTCAAGAACGTGAGGCTGGTCAAACTGAAGCAG
TATGCTTCCGTCAAACGAAGGCAATAGCTTCTGTTGTCAAAGACTGGTCAAATGTTGTTA
TCGCTTATGAACCGGTTTGGGCAATTGGAACTGGCAAAACTGCAACTCCAGCTCAAGCCC
AAGAGGTTCATGCTGCTCTCCGTAAATGGTTCGCCGAGAACGTTTCTCAAGCCGTTTCTG
ATTCAATTCGTATTCAATATGGTGGCTCAGTTACTGCTGCTAATGCTCGTGAATTAGCTT
CACAACCAGATATCGATGGATTTTTAGTTGGAGGTGCATCATTAAAACCCGAATTCGTAC
AAATTGTCAATGCTAGGCAGTAA
>g6936.t40 Gene=g6936 Length=247
MGRKFCVGGNWKMNGSKDSITELAKILSAGPLDPNTEVVVGCPSVYISFARGLLPSSIGV
AGQNCYKVKSGAFTGEIAPSMLKDVGADWVILGHSERRAIFGESDELIADKVEFALSEGL
KVIACIGETLQEREAGQTEAVCFRQTKAIASVVKDWSNVVIAYEPVWAIGTGKTATPAQA
QEVHAALRKWFAENVSQAVSDSIRIQYGGSVTAANARELASQPDIDGFLVGGASLKPEFV
QIVNARQ
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g6936.t40 | CDD | cd00311 | TIM | 5 | 244 | 2.16332E-133 |
| 6 | g6936.t40 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 1 | 247 | 2.8E-106 |
| 4 | g6936.t40 | Hamap | MF_00147_B | Triosephosphate isomerase [tpiA]. | 3 | 245 | 59.511757 |
| 2 | g6936.t40 | PANTHER | PTHR21139:SF17 | TRIOSEPHOSPHATE ISOMERASE A | 3 | 246 | 5.6E-116 |
| 3 | g6936.t40 | PANTHER | PTHR21139 | TRIOSEPHOSPHATE ISOMERASE | 3 | 246 | 5.6E-116 |
| 1 | g6936.t40 | Pfam | PF00121 | Triosephosphate isomerase | 6 | 243 | 3.3E-89 |
| 8 | g6936.t40 | ProSitePatterns | PS00171 | Triosephosphate isomerase active site. | 162 | 172 | - |
| 10 | g6936.t40 | ProSiteProfiles | PS51440 | Triosephosphate isomerase (TIM) family profile. | 4 | 245 | 83.436 |
| 5 | g6936.t40 | SUPERFAMILY | SSF51351 | Triosephosphate isomerase (TIM) | 3 | 245 | 1.31E-96 |
| 9 | g6936.t40 | TIGRFAM | TIGR00419 | tim: triose-phosphate isomerase | 7 | 238 | 3.4E-74 |
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:0006096 | glycolytic process | BP |
| GO:0004807 | triose-phosphate isomerase activity | MF |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01803 (triosephosphate isomerase (TIM))
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.
