General information for g1643.t8
Yuki Yoshida
6/2/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Pyrroline-5-carboxylate reductase.
Parent gene
- The parent gene g1643 is located on chr_3: 12273130..12274118 (- 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 | g1643 | g1643.t8 | TTS | g1643.t8 | 12273050 | 12273050 |
| chr_3 | g1643 | g1643.t8 | isoform | g1643.t8 | 12273130 | 12274118 |
| chr_3 | g1643 | g1643.t8 | exon | g1643.t8.exon1 | 12273130 | 12273422 |
| chr_3 | g1643 | g1643.t8 | cds | g1643.t8.CDS1 | 12273130 | 12273422 |
| chr_3 | g1643 | g1643.t8 | exon | g1643.t8.exon2 | 12273482 | 12274118 |
| chr_3 | g1643 | g1643.t8 | cds | g1643.t8.CDS2 | 12273482 | 12273650 |
| chr_3 | g1643 | g1643.t8 | TSS | g1643.t8 | 12274192 | 12274192 |
Sequences
>g1643.t8 Gene=g1643 Length=930
ATGGAGGACATTATAAAATACAAAAATTCATTCTCAACTGAGGCAAAGCTTGGTTTCATA
GGATGTGGCAATATGGCATTTTCAATAGTTAAGGGTTTGCTGCAATCTAAATTATTTGAG
GCAAATGAAATAATAGTTTCTGGTACAAGAGATGAGAGCTTTGAGAGATTGAAGTAAGTT
ATATAGCATTCATTAGTATGTGTATAATAATATTCATATTTTAGGTCATTAGGAAAAATT
AATACAACAAAAAACAATAATGAGGTTGTAAGAGCGGCAGCTATAATTTTTTTGTGTGTC
AAGCCTGCTCATTTGGATGCTGTTGCAATTTCTCTCAAAAAGAATTTCCTTAATCCCGAT
GAAATAGATTTGTCTAATTTAAATAAGACACTTGTTTCTATTCTTGCTGGAACATCATTG
AATACTCTTAGAGAAGCAATTCCAAATTTTGGATCATATATACGTGTTATGCCTAACACT
CCGCTTCAAGTAGGAGCCGGATGTTCTGCAATAACTATTTTTAATGCTTCACTAGATCTT
TTAAATAGTTATAACGCAGTAAAAGCTATTTTTTGCTCACTTGGTCTTGTGGATGTCCTT
GATGAAAGCAAATTTCATGCTATAACTGCTCTTTCAGGAAGTGGGCCAGCTTATGTCTAC
ATAATAATTGATGCCTTAAGTGATGCTGGTGTTAAACAAGGTCTTCCGAGAGATATTGCC
ACTCGTTTTGCAGCACAAACACTTCTTGGTGCCTCAAAAACAGTCTTAGAAAGTTCATTT
CACGTTGGTCAATTAAAAGATCAAGTAACAAGCAGTGGTGGTACAACAATTCATGCCATA
CATGAACTTGAAAAAGGTGGAATACGAAATACACTATTCAATGCAATTGAAGCTGCAACA
AAGCGCTCAAAGGAAATGTCAGAAAATTAA
>g1643.t8 Gene=g1643 Length=153
MPNTPLQVGAGCSAITIFNASLDLLNSYNAVKAIFCSLGLVDVLDESKFHAITALSGSGP
AYVYIIIDALSDAGVKQGLPRDIATRFAAQTLLGASKTVLESSFHVGQLKDQVTSSGGTT
IHAIHELEKGGIRNTLFNAIEAATKRSKEMSEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g1643.t8 | Gene3D | G3DSA:1.10.3730.10 | - | 43 | 153 | 0 |
| 2 | g1643.t8 | PANTHER | PTHR11645 | PYRROLINE-5-CARBOXYLATE REDUCTASE | 1 | 151 | 0 |
| 3 | g1643.t8 | PANTHER | PTHR11645:SF0 | PYRROLINE-5-CARBOXYLATE REDUCTASE 2 | 1 | 151 | 0 |
| 1 | g1643.t8 | Pfam | PF14748 | Pyrroline-5-carboxylate reductase dimerisation | 46 | 150 | 0 |
| 4 | g1643.t8 | SUPERFAMILY | SSF48179 | 6-phosphogluconate dehydrogenase C-terminal domain-like | 45 | 152 | 0 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
GO terms from InterProScan
## [1] "No matching GO terms"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.
