Gene loci information

Transcript annotation

  • This transcript has been annotated as Pyrroline-5-carboxylate reductase.

Parent gene

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 g1164 g1164.t1 TTS g1164.t1 8449137 8449137
chr_3 g1164 g1164.t1 isoform g1164.t1 8449273 8450228
chr_3 g1164 g1164.t1 exon g1164.t1.exon1 8449273 8449554
chr_3 g1164 g1164.t1 cds g1164.t1.CDS1 8449273 8449554
chr_3 g1164 g1164.t1 exon g1164.t1.exon2 8449612 8450078
chr_3 g1164 g1164.t1 cds g1164.t1.CDS2 8449612 8450078
chr_3 g1164 g1164.t1 exon g1164.t1.exon3 8450147 8450228
chr_3 g1164 g1164.t1 cds g1164.t1.CDS3 8450147 8450228
chr_3 g1164 g1164.t1 TSS g1164.t1 8450294 8450294

Sequences

>g1164.t1 Gene=g1164 Length=831
ATGACGAATAGAATCTTAAAAATCGGATTTTTAGGAGCTGGAAAAATGGCGCAAGCATTG
AGCAAGGGCTTTATAAAATCAGGCTTATTAAGTAGTCAGCATTTAATTGCAAGCGCACAT
CCATCAGATGAGGCCTCATTAAAAGCTTTTCGAGATGATTTAAAAGCAGAAGCAGTGACA
CAAAATCAATTGGTTGTTGAGAAATCTGAAATTATTTTTATATCAACGAAGCCAAATGTA
GTCAAAACTGTTTTGCACGATGTTAAAGCTCTAAGTTCGGGCAAACTTTTTATTTCAATC
GCTATGGGAACAACGTTAGATGAGATTCAGAAAATATTAGCACATGATTCGAGAATTATT
AGAGTAATGCCAAATATACCTGCAACTGTTCTTGAATCGTGCTCTGTTTTTGTTCGAGGT
AAAAATGCGACAGACGACGATGCCAATATAGTTCAAAAGTTATTAAAATCGATTGGAACA
TGTGAAGAATTGACGACAGAATCTTTGATGGATGTCTGTACTGGACTTTCTGGAAGTGGA
CCAGCTTATGTTTTTTTATTAATTGAAAGTCTTGCAGATGGGGGTGTGAAATGCGGTCTT
CCTAGAGATTTAGCTTATAGATTGGCAGCTCAAACAGTTTTAGGTTCGGGTAAATTAGTT
ATTGATTCGAATATTCATCCGGCTATATTAAAAGATAATGTGATGAGCCCTCTTGGAAGC
ACAGCTTATGGGGTGCATTATTTAGAGAAAAACAATTTTAGAAATACTATAATTGGTGCA
GTTGAAGCTGCAACAAATCGATGCCGAGAGATTTCTGGCATCTCAAAATAA

>g1164.t1 Gene=g1164 Length=276
MTNRILKIGFLGAGKMAQALSKGFIKSGLLSSQHLIASAHPSDEASLKAFRDDLKAEAVT
QNQLVVEKSEIIFISTKPNVVKTVLHDVKALSSGKLFISIAMGTTLDEIQKILAHDSRII
RVMPNIPATVLESCSVFVRGKNATDDDANIVQKLLKSIGTCEELTTESLMDVCTGLSGSG
PAYVFLLIESLADGGVKCGLPRDLAYRLAAQTVLGSGKLVIDSNIHPAILKDNVMSPLGS
TAYGVHYLEKNNFRNTIIGAVEAATNRCREISGISK

Protein features from InterProScan

Transcript Database ID Name Start End E.value
8 g1164.t1 Gene3D G3DSA:3.40.50.720 - 4 169 0.0000
9 g1164.t1 Gene3D G3DSA:1.10.3730.10 - 170 273 0.0000
5 g1164.t1 Hamap MF_01925 Pyrroline-5-carboxylate reductase [proC]. 6 271 25.3545
3 g1164.t1 PANTHER PTHR11645 PYRROLINE-5-CARBOXYLATE REDUCTASE 6 272 0.0000
4 g1164.t1 PANTHER PTHR11645:SF0 PYRROLINE-5-CARBOXYLATE REDUCTASE 2 6 272 0.0000
11 g1164.t1 PIRSF PIRSF000193 P5CR 6 273 0.0000
1 g1164.t1 Pfam PF03807 NADP oxidoreductase coenzyme F420-dependent 7 102 0.0000
2 g1164.t1 Pfam PF14748 Pyrroline-5-carboxylate reductase dimerisation 167 270 0.0000
6 g1164.t1 SUPERFAMILY SSF51735 NAD(P)-binding Rossmann-fold domains 7 163 0.0000
7 g1164.t1 SUPERFAMILY SSF48179 6-phosphogluconate dehydrogenase C-terminal domain-like 167 272 0.0000
10 g1164.t1 TIGRFAM TIGR00112 proC: pyrroline-5-carboxylate reductase 8 271 0.0000

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

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. There were no conditions that were differentially expressed