General information for g1643.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as 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.t1 | TTS | g1643.t1 | 12273050 | 12273050 |
| chr_3 | g1643 | g1643.t1 | isoform | g1643.t1 | 12273130 | 12274118 |
| chr_3 | g1643 | g1643.t1 | exon | g1643.t1.exon1 | 12273130 | 12273422 |
| chr_3 | g1643 | g1643.t1 | cds | g1643.t1.CDS1 | 12273130 | 12273422 |
| chr_3 | g1643 | g1643.t1 | exon | g1643.t1.exon2 | 12273482 | 12273894 |
| chr_3 | g1643 | g1643.t1 | cds | g1643.t1.CDS2 | 12273482 | 12273894 |
| chr_3 | g1643 | g1643.t1 | exon | g1643.t1.exon3 | 12273946 | 12274118 |
| chr_3 | g1643 | g1643.t1 | cds | g1643.t1.CDS3 | 12273946 | 12274118 |
| chr_3 | g1643 | g1643.t1 | TSS | g1643.t1 | 12274192 | 12274192 |
Sequences
>g1643.t1 Gene=g1643 Length=879
ATGGAGGACATTATAAAATACAAAAATTCATTCTCAACTGAGGCAAAGCTTGGTTTCATA
GGATGTGGCAATATGGCATTTTCAATAGTTAAGGGTTTGCTGCAATCTAAATTATTTGAG
GCAAATGAAATAATAGTTTCTGGTACAAGAGATGAGAGCTTTGAGAGATTGAAGTCATTA
GGAAAAATTAATACAACAAAAAACAATAATGAGGTTGTAAGAGCGGCAGCTATAATTTTT
TTGTGTGTCAAGCCTGCTCATTTGGATGCTGTTGCAATTTCTCTCAAAAAGAATTTCCTT
AATCCCGATGAAATAGATTTGTCTAATTTAAATAAGACACTTGTTTCTATTCTTGCTGGA
ACATCATTGAATACTCTTAGAGAAGCAATTCCAAATTTTGGATCATATATACGTGTTATG
CCTAACACTCCGCTTCAAGTAGGAGCCGGATGTTCTGCAATAACTATTTTTAATGCTTCA
CTAGATCTTTTAAATAGTTATAACGCAGTAAAAGCTATTTTTTGCTCACTTGGTCTTGTG
GATGTCCTTGATGAAAGCAAATTTCATGCTATAACTGCTCTTTCAGGAAGTGGGCCAGCT
TATGTCTACATAATAATTGATGCCTTAAGTGATGCTGGTGTTAAACAAGGTCTTCCGAGA
GATATTGCCACTCGTTTTGCAGCACAAACACTTCTTGGTGCCTCAAAAACAGTCTTAGAA
AGTTCATTTCACGTTGGTCAATTAAAAGATCAAGTAACAAGCAGTGGTGGTACAACAATT
CATGCCATACATGAACTTGAAAAAGGTGGAATACGAAATACACTATTCAATGCAATTGAA
GCTGCAACAAAGCGCTCAAAGGAAATGTCAGAAAATTAA
>g1643.t1 Gene=g1643 Length=292
MEDIIKYKNSFSTEAKLGFIGCGNMAFSIVKGLLQSKLFEANEIIVSGTRDESFERLKSL
GKINTTKNNNEVVRAAAIIFLCVKPAHLDAVAISLKKNFLNPDEIDLSNLNKTLVSILAG
TSLNTLREAIPNFGSYIRVMPNTPLQVGAGCSAITIFNASLDLLNSYNAVKAIFCSLGLV
DVLDESKFHAITALSGSGPAYVYIIIDALSDAGVKQGLPRDIATRFAAQTLLGASKTVLE
SSFHVGQLKDQVTSSGGTTIHAIHELEKGGIRNTLFNAIEAATKRSKEMSEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g1643.t1 | Gene3D | G3DSA:3.40.50.720 | - | 4 | 186 | 0.00000 |
| 9 | g1643.t1 | Gene3D | G3DSA:1.10.3730.10 | - | 187 | 292 | 0.00000 |
| 5 | g1643.t1 | Hamap | MF_01925 | Pyrroline-5-carboxylate reductase [proC]. | 15 | 289 | 25.63316 |
| 3 | g1643.t1 | PANTHER | PTHR11645 | PYRROLINE-5-CARBOXYLATE REDUCTASE | 14 | 290 | 0.00000 |
| 4 | g1643.t1 | PANTHER | PTHR11645:SF0 | PYRROLINE-5-CARBOXYLATE REDUCTASE 2 | 14 | 290 | 0.00000 |
| 11 | g1643.t1 | PIRSF | PIRSF000193 | P5CR | 14 | 292 | 0.00000 |
| 1 | g1643.t1 | Pfam | PF03807 | NADP oxidoreductase coenzyme F420-dependent | 16 | 97 | 0.00000 |
| 2 | g1643.t1 | Pfam | PF14748 | Pyrroline-5-carboxylate reductase dimerisation | 185 | 289 | 0.00000 |
| 6 | g1643.t1 | SUPERFAMILY | SSF51735 | NAD(P)-binding Rossmann-fold domains | 16 | 159 | 0.00000 |
| 7 | g1643.t1 | SUPERFAMILY | SSF48179 | 6-phosphogluconate dehydrogenase C-terminal domain-like | 184 | 291 | 0.00000 |
| 10 | g1643.t1 | TIGRFAM | TIGR00112 | proC: pyrroline-5-carboxylate reductase | 17 | 289 | 0.00000 |
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:0006561 | proline biosynthetic process | BP |
| GO:0055114 | NA | NA |
| GO:0004735 | pyrroline-5-carboxylate reductase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00286 (pyrroline-5-carboxylate reductase)
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.
