General information for g15885.t2
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Uridine 5’-monophosphate synthase.
Parent gene
- The parent gene g15885 is located on chr_4: 7172902..7174282 (+ 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_4 | g15885 | g15885.t2 | TSS | g15885.t2 | 7172658 | 7172658 |
| chr_4 | g15885 | g15885.t2 | isoform | g15885.t2 | 7172902 | 7174282 |
| chr_4 | g15885 | g15885.t2 | exon | g15885.t2.exon1 | 7172902 | 7174282 |
| chr_4 | g15885 | g15885.t2 | cds | g15885.t2.CDS1 | 7172969 | 7174252 |
| chr_4 | g15885 | g15885.t2 | TTS | g15885.t2 | 7174308 | 7174308 |
Sequences
>g15885.t2 Gene=g15885 Length=1381
TTTAAAATCAGGAGAAATAAGTCCAGTTTATTTTGATCTTCGTGTGATTATTTCACATCC
AGATGTAATGGAAAATTTGACTAATTTAATGTTGTTGTTTATAAAAGAAAAAGAAATTCA
ATGTGATCAATTATGTGGTGTTCCATATACAGCATTACCACTTGCAACTCTTTTATCTGT
CAAAATGAAACAACCAATGTTGATTAGAAGAAAAGAAGCAAAAACTTATGGAACTAAAAA
GTTGATTGAAGGAAAATTTCAAGATCAAGAGACATGTTTGATTATTGAGGATGTTGTTAC
AACAGGAAGCAGCATAATTGAAACAACAAATGATTTAAGAAATGAAAATCTCGAAGTTGA
AGATGCAATTGTTGTTGTTGATCGTGAGCAAGGTGGAAAAGATAATTTGACAAAAAATGG
AATTCGAATGCATTCACTTTTTACACTGCCATATTTTCTTGAAATTCTCAAAGATGAAGG
AAAAATTGAAGACGATATGATTAAAACTATAAAAGACTACATTTCAAAATCAACTGAAAA
AAAGGAAGTTAAAAAATCTGCAACAAGACTTCAAATGACTTTTTCATCTCGTGCTGAAAT
TGCTAAAAATGAAGCTGCAAAAGAACTTTTTAAAATTATGGAAGCTAAAAAATCAAATCT
ATGTCTCGCAGCTGATGTCACAAAGAGTGATGAAATTTTAAATTTGGCAGAATCTTTGGG
ACCTTTTATTTGTGTTTTAAAAACTCATGTTGACATTGTTGAAGATTTCAGTGAAAATTT
TGTCAATTCCCTTAAAGCACTTGCTAAAAAGCACAATTTTATGATAATGGAAGACAGAAA
ATTTGCAGATATTGGCAACACAGTTGCATTACAATTCAGTAAAGGAATTTATAAGATTTC
TGAATGGTGTGATCTTGTGACTGCACATTCATTGCCTGGTGATGGACTTTTAAAAGGACT
GAAAGAAGTCATTAAAAATAAGGAAAAAATTGGAATTTTTATGCTTACTGAAATGTCATC
AGATGGACATTTAATGTCACAAGATTACAGCAACAAAACAATGCAAATGATTGCAAATTA
TTCAGACATTGTTGCTGGAATTGTCGCTCAAAGTTCTCAATTTACTGAAAATCAACCAGA
ACTTATTCAATTGACACCAGGTTGCAAATTGGATGAAACTGGAGACAATTTAGGTCAGAA
ATATAACACACCGGAATTTTTAGTAAAAGAAAAAGGTGCTGACATTGCTGTAGTTGGAAG
AGGCATTATTGAAAGCAAAAATCCTGTTGAGGTTGCTAAAACTTATCGTGAACGTTTATG
GAATTCTTATGAAGAAAGAATAAAATATTAAAATTTTCGTTTTTATAAAATTTTATTTCA
A
>g15885.t2 Gene=g15885 Length=427
MENLTNLMLLFIKEKEIQCDQLCGVPYTALPLATLLSVKMKQPMLIRRKEAKTYGTKKLI
EGKFQDQETCLIIEDVVTTGSSIIETTNDLRNENLEVEDAIVVVDREQGGKDNLTKNGIR
MHSLFTLPYFLEILKDEGKIEDDMIKTIKDYISKSTEKKEVKKSATRLQMTFSSRAEIAK
NEAAKELFKIMEAKKSNLCLAADVTKSDEILNLAESLGPFICVLKTHVDIVEDFSENFVN
SLKALAKKHNFMIMEDRKFADIGNTVALQFSKGIYKISEWCDLVTAHSLPGDGLLKGLKE
VIKNKEKIGIFMLTEMSSDGHLMSQDYSNKTMQMIANYSDIVAGIVAQSSQFTENQPELI
QLTPGCKLDETGDNLGQKYNTPEFLVKEKGADIAVVGRGIIESKNPVEVAKTYRERLWNS
YEERIKY
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g15885.t2 | CDD | cd06223 | PRTases_typeI | 4 | 126 | 4.26337E-19 |
| 10 | g15885.t2 | CDD | cd04725 | OMP_decarboxylase_like | 198 | 413 | 9.76354E-53 |
| 7 | g15885.t2 | Gene3D | G3DSA:3.40.50.2020 | - | 1 | 160 | 4.9E-46 |
| 8 | g15885.t2 | Gene3D | G3DSA:3.20.20.70 | Aldolase class I | 167 | 427 | 1.1E-92 |
| 3 | g15885.t2 | PANTHER | PTHR19278 | OROTATE PHOSPHORIBOSYLTRANSFERASE | 5 | 424 | 2.8E-166 |
| 4 | g15885.t2 | PANTHER | PTHR19278:SF9 | URIDINE 5’-MONOPHOSPHATE SYNTHASE | 5 | 424 | 2.8E-166 |
| 1 | g15885.t2 | Pfam | PF00156 | Phosphoribosyl transferase domain | 20 | 112 | 6.6E-7 |
| 2 | g15885.t2 | Pfam | PF00215 | Orotidine 5’-phosphate decarboxylase / HUMPS family | 196 | 413 | 1.0E-70 |
| 11 | g15885.t2 | ProSitePatterns | PS00156 | Orotidine 5’-phosphate decarboxylase active site. | 253 | 266 | - |
| 12 | g15885.t2 | SMART | SM00934 | OMPdecase_2 | 197 | 413 | 1.0E-38 |
| 5 | g15885.t2 | SUPERFAMILY | SSF53271 | PRTase-like | 4 | 148 | 1.42E-29 |
| 6 | g15885.t2 | SUPERFAMILY | SSF51366 | Ribulose-phoshate binding barrel | 169 | 425 | 5.3E-60 |
| 13 | g15885.t2 | TIGRFAM | TIGR01740 | pyrF: orotidine 5’-phosphate decarboxylase | 198 | 414 | 5.3E-58 |
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:0044205 | ‘de novo’ UMP biosynthetic process | BP |
| GO:0009116 | nucleoside metabolic process | BP |
| GO:0004590 | orotidine-5’-phosphate decarboxylase activity | MF |
| GO:0006207 | ‘de novo’ pyrimidine nucleobase biosynthetic process | BP |
| GO:0003824 | catalytic activity | MF |
KEGG
Orthology
- This transcript has been annotated with K01591 (orotidine-5’-phosphate decarboxylase)
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.
