General information for g1986.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Ribose-5-phosphate isomerase.
Parent gene
- The parent gene g1986 is located on chr_3: 14224935..14227497 (- 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_3 | g1986 | g1986.t3 | isoform | g1986.t3 | 14224885 | 14225703 |
| chr_3 | g1986 | g1986.t3 | exon | g1986.t3.exon1 | 14224885 | 14224981 |
| chr_3 | g1986 | g1986.t3 | TTS | g1986.t3 | 14224886 | 14224886 |
| chr_3 | g1986 | g1986.t3 | cds | g1986.t3.CDS1 | 14224963 | 14224981 |
| chr_3 | g1986 | g1986.t3 | exon | g1986.t3.exon2 | 14225047 | 14225324 |
| chr_3 | g1986 | g1986.t3 | cds | g1986.t3.CDS2 | 14225047 | 14225324 |
| chr_3 | g1986 | g1986.t3 | exon | g1986.t3.exon3 | 14225386 | 14225703 |
| chr_3 | g1986 | g1986.t3 | cds | g1986.t3.CDS3 | 14225386 | 14225703 |
| chr_3 | g1986 | g1986.t3 | TSS | g1986.t3 | 14225873 | 14225873 |
Sequences
>g1986.t3 Gene=g1986 Length=693
ATGTCACTTGAAATGGCAAAGAAAATTGCTGCATATAAAGCAGTTGATGATCATATTACA
GATAATTTAGTTGTTGGAATTGGCAGCGGATCTACAATCGTTTATGGTGTACAGAGACTA
GCAGAGCGTGTAATCAGTGAAAACCTTAATCTAATTTGCATTCCAACAAGTTTTCAAGCC
AAGCAATTGATTCTCGATAATGGATTGATATTAGGTGAATTGGATAGAAATCCTACTATT
GACGTTGCTATTGATGGTGCAGATGAGTGTGATGTTGAGCTTAACTGCATTAAAGGTGGT
GGAGGATGCTTACTTCAGGAAAAAATCGTAGCTTCATGTGCTAAAACTCTCATCATTGTC
GCAGACCATACCAAAAATTCTGAATATTTAACAGAAAAATATAAGAAAATTCCCATCGAA
GTAACACCAATCGCATATATTCCGATTAAAAATAGAATCGAATCACTCTTTGGAGGTGAT
CTGAAATTACGAATGGGGGGTTCTGCCAAAGCTGGACCTATTGTTACAGACAATGGTAAT
TTTATCCTTGATTGGTTTTTTGACGGTTCACCAACAACTGACTTCGATGGAATAAACATA
CTTTGGTATGCCTGATGGTTCAGTTATAGAGAAAGAAATTTAAAATTTATATAACCATAA
TATGTTGATAATAAAATGTGAATTTTACACTCA
>g1986.t3 Gene=g1986 Length=204
MSLEMAKKIAAYKAVDDHITDNLVVGIGSGSTIVYGVQRLAERVISENLNLICIPTSFQA
KQLILDNGLILGELDRNPTIDVAIDGADECDVELNCIKGGGGCLLQEKIVASCAKTLIIV
ADHTKNSEYLTEKYKKIPIEVTPIAYIPIKNRIESLFGGDLKLRMGGSAKAGPIVTDNGN
FILDWFFDGSPTTDFDGINILWYA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1986.t3 | CDD | cd01398 | RPI_A | 6 | 188 | 0 |
| 5 | g1986.t3 | Gene3D | G3DSA:3.40.50.1360 | - | 7 | 128 | 0 |
| 6 | g1986.t3 | Gene3D | G3DSA:3.30.70.260 | - | 129 | 188 | 0 |
| 2 | g1986.t3 | PANTHER | PTHR11934 | RIBOSE-5-PHOSPHATE ISOMERASE | 3 | 188 | 0 |
| 1 | g1986.t3 | Pfam | PF06026 | Ribose 5-phosphate isomerase A (phosphoriboisomerase A) | 53 | 189 | 0 |
| 3 | g1986.t3 | SUPERFAMILY | SSF100950 | NagB/RpiA/CoA transferase-like | 4 | 151 | 0 |
| 4 | g1986.t3 | SUPERFAMILY | SSF75445 | D-ribose-5-phosphate isomerase (RpiA), lid domain | 136 | 190 | 0 |
| 7 | g1986.t3 | TIGRFAM | TIGR00021 | rpiA: ribose 5-phosphate isomerase A | 7 | 189 | 0 |
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:0009052 | pentose-phosphate shunt, non-oxidative branch | BP |
| GO:0004751 | ribose-5-phosphate isomerase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01807 (ribose 5-phosphate isomerase A)
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.
