General information for g10899.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Pseudouridine-5’-phosphate glycosidase.
Parent gene
- The parent gene g10899 is located on chr_1: 12530788..12533359 (- 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_1 | g10899 | g10899.t1 | isoform | g10899.t1 | 12530788 | 12533359 |
| chr_1 | g10899 | g10899.t1 | exon | g10899.t1.exon1 | 12530788 | 12531017 |
| chr_1 | g10899 | g10899.t1 | cds | g10899.t1.CDS1 | 12530788 | 12531017 |
| chr_1 | g10899 | g10899.t1 | exon | g10899.t1.exon2 | 12531108 | 12531239 |
| chr_1 | g10899 | g10899.t1 | cds | g10899.t1.CDS2 | 12531108 | 12531239 |
| chr_1 | g10899 | g10899.t1 | exon | g10899.t1.exon3 | 12531366 | 12531930 |
| chr_1 | g10899 | g10899.t1 | cds | g10899.t1.CDS3 | 12531366 | 12531930 |
| chr_1 | g10899 | g10899.t1 | exon | g10899.t1.exon4 | 12533078 | 12533231 |
| chr_1 | g10899 | g10899.t1 | cds | g10899.t1.CDS4 | 12533078 | 12533231 |
| chr_1 | g10899 | g10899.t1 | exon | g10899.t1.exon5 | 12533295 | 12533359 |
| chr_1 | g10899 | g10899.t1 | cds | g10899.t1.CDS5 | 12533295 | 12533359 |
| chr_1 | g10899 | g10899.t1 | TSS | g10899.t1 | NA | NA |
| chr_1 | g10899 | g10899.t1 | TTS | g10899.t1 | NA | NA |
Sequences
>g10899.t1 Gene=g10899 Length=1146
ATGTACAGAACATGTACACTATACTCGACATATCGAAGAAATTTATTCAATTTAAGACAG
CTAAGCTCATTTCTCTTCGACATTAAGCCAGAAGTTCACGATGCCTTATCAAATAATCGA
GCTGTTGTTGCGCTTGAATCTACCATTATAACTCATGGTATGCCTTCACCATATAATTTG
AAAACTGCCATTGAGGTTGAAGAAATTGTTCGTGAACAGGGTGCAATTCCCGCAACTATA
GCTATTCTAAATGGGAAAATTAAAATCGGATTATCTCGTAGTGAGTTAGAAGAACTCGCC
GGTTGTAAAACGAAAGTTATTAAAACATCTCGACGCGATTTAGCATACGTGCTAAGTCAA
AAACTGAATGGTGGCACAACAGTCGCCAGTACACTGATTTGTGCAAATCTATGCGGAATA
AAATTATTCGCAACTGGTGGAATTGGTGGTGTACATAGAAATGGAGAATTCACACTTGAC
ATTTCTGCTGATTTAATTGAAATGGGAAAAAGCTCCGTTGCCGTTGTATCGTCCGGAATA
AAGTCTATACTTGATATACCGAGAACAATGGAGTTTCTCGAAACGCAAGGCGTTTGTGTT
GCAACATTTAAGTGTCCTGATAAAGAGTTTCCTGCATTTTATACACGAGCGAGTGGTACA
AAAGCTCAATATAACTTCAATGATGCTGCTGATGCTGCACAGTGCATTAATAAATCGATT
CAATTGGGATTAAATTCTTCGACCCTCATAGGAGTTCCAGTGCCAAAAGAACACGCGATG
GACGAATTCGTCATCAATAATGCCATTGAAAAGGCTTTAGTAGAAACTGATAAAAAGGGA
ATTAAAGGAAAAGAAGTCACGCCATATTTGCTATCTGCAATTTCTGAGATAACAAAAGGA
AAAAGTCTGCAAACTAACATGGCGTTGATAAAAGAAAATGCAAGAGTTGCTTCAAAAATT
GCAGTTGAGTTAGAAAACCTGCAAAATAACAATGAAAGAGTCTTGAGAAAAAATAAAAAT
AGTGTCGAGTCATCATCTGCACCACTTGTAATCGGTGGAAGTATATTAGACATACACTAT
CGTGTGAATGAAGGAGAAAAGCCTCTAGAGGTGAGTAAATGTAACAAGCTTACATCATTT
TTATAA
>g10899.t1 Gene=g10899 Length=381
MYRTCTLYSTYRRNLFNLRQLSSFLFDIKPEVHDALSNNRAVVALESTIITHGMPSPYNL
KTAIEVEEIVREQGAIPATIAILNGKIKIGLSRSELEELAGCKTKVIKTSRRDLAYVLSQ
KLNGGTTVASTLICANLCGIKLFATGGIGGVHRNGEFTLDISADLIEMGKSSVAVVSSGI
KSILDIPRTMEFLETQGVCVATFKCPDKEFPAFYTRASGTKAQYNFNDAADAAQCINKSI
QLGLNSSTLIGVPVPKEHAMDEFVINNAIEKALVETDKKGIKGKEVTPYLLSAISEITKG
KSLQTNMALIKENARVASKIAVELENLQNNNERVLRKNKNSVESSSAPLVIGGSILDIHY
RVNEGEKPLEVSKCNKLTSFL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g10899.t1 | Coils | Coil | Coil | 317 | 344 | - |
| 6 | g10899.t1 | Gene3D | G3DSA:3.40.1790.10 | Indigoidine synthase domain | 22 | 329 | 7.0E-134 |
| 4 | g10899.t1 | Hamap | MF_01876 | Pseudouridine-5’-phosphate glycosidase [psuG]. | 30 | 326 | 38.168411 |
| 2 | g10899.t1 | PANTHER | PTHR42909 | ZGC:136858 | 19 | 329 | 3.0E-125 |
| 3 | g10899.t1 | PANTHER | PTHR42909:SF1 | ZGC:136858 | 19 | 329 | 3.0E-125 |
| 1 | g10899.t1 | Pfam | PF04227 | Indigoidine synthase A like protein | 31 | 323 | 1.2E-126 |
| 5 | g10899.t1 | SUPERFAMILY | SSF110581 | Indigoidine synthase A-like | 26 | 324 | 1.7E-110 |
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:0016798 | hydrolase activity, acting on glycosyl bonds | MF |
KEGG
Orthology
- This transcript has been annotated with K16330 (pseudouridylate synthase / pseudouridine kinase)
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.
