General information for g5341.t18
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative Probable H/ACA ribonucleoprotein complex subunit 1.
Parent gene
- The parent gene g5341 is located on chr_2: 9018041..9018845 (- 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_2 | g5341 | g5341.t18 | TTS | g5341.t18 | 9017475 | 9017475 |
| chr_2 | g5341 | g5341.t18 | isoform | g5341.t18 | 9017585 | 9018740 |
| chr_2 | g5341 | g5341.t18 | exon | g5341.t18.exon1 | 9017585 | 9017616 |
| chr_2 | g5341 | g5341.t18 | exon | g5341.t18.exon2 | 9017978 | 9018409 |
| chr_2 | g5341 | g5341.t18 | cds | g5341.t18.CDS1 | 9018003 | 9018409 |
| chr_2 | g5341 | g5341.t18 | exon | g5341.t18.exon3 | 9018473 | 9018565 |
| chr_2 | g5341 | g5341.t18 | cds | g5341.t18.CDS2 | 9018473 | 9018565 |
| chr_2 | g5341 | g5341.t18 | exon | g5341.t18.exon4 | 9018704 | 9018740 |
| chr_2 | g5341 | g5341.t18 | cds | g5341.t18.CDS3 | 9018704 | 9018740 |
| chr_2 | g5341 | g5341.t18 | TSS | g5341.t18 | 9018838 | 9018838 |
Sequences
>g5341.t18 Gene=g5341 Length=594
ATGGGATTTGGAGGTCGAGGAGGTGGTAATCGTGGAGAAGGCGGCAATCGAGGTGGAGGA
GGAGGACGAGGCGGCTTTGGAAATAAAGGAAAATTTGACCAAGGGCCGCCGGCAAGAGTT
GTTCCATTTGGATATTTTGATTACACATGTCAAGATGATCTTGTTCTTAAAGCAGAAATT
GAAGACGTTCCCTATTTCAATGCACCAATTTTTCTTGAAAACAAATCACAAATCGGAAAA
ATTGATGAGATTTTTGGAACATTACGTGATTATTCAGTGTCAGTGAAATTGGGTGAAAAT
ATGAAAGCATCAAGTTTTGTGCCGAAACAGAAACTTTTTATTGATCCAGCCAAGTTACTT
CCATTACAAAGATTTTTACCGCAACCACCAAAGCCGAAAGGAATTGGAAAGAAAAAGAAA
GGAGACAAGTCACAAGCTGGTGCAGCTGGTGGAAACAATTCATTTGGAGCAAAACGTGGA
GGATTTGGCGGAAGAGGTAGTGGTGGTGGTCGAGGAAGTAAGTTCGATCAATTTTAAAAG
GCAGAATCTGATTGGTAAACAAATCGTGGAGGAGGTGGTGGTAAAAGATGGTAG
>g5341.t18 Gene=g5341 Length=178
MGFGGRGGGNRGEGGNRGGGGGRGGFGNKGKFDQGPPARVVPFGYFDYTCQDDLVLKAEI
EDVPYFNAPIFLENKSQIGKIDEIFGTLRDYSVSVKLGENMKASSFVPKQKLFIDPAKLL
PLQRFLPQPPKPKGIGKKKKGDKSQAGAAGGNNSFGAKRGGFGGRGSGGGRGSKFDQF
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g5341.t18 | Gene3D | G3DSA:2.40.10.230 | Probable tRNA pseudouridine synthase domain | 36 | 127 | 5.3E-36 |
| 6 | g5341.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 22 | - |
| 5 | g5341.t18 | MobiDBLite | mobidb-lite | consensus disorder prediction | 125 | 178 | - |
| 2 | g5341.t18 | PANTHER | PTHR23237 | NUCLEOLAR PROTEIN FAMILY A MEMBER 1 SNORNP PROTEIN GAR1 | 4 | 173 | 1.5E-47 |
| 3 | g5341.t18 | PANTHER | PTHR23237:SF6 | H/ACA RIBONUCLEOPROTEIN COMPLEX SUBUNIT 1 | 4 | 173 | 1.5E-47 |
| 1 | g5341.t18 | Pfam | PF04410 | Gar1/Naf1 RNA binding region | 28 | 128 | 1.5E-31 |
| 4 | g5341.t18 | SUPERFAMILY | SSF50447 | Translation proteins | 41 | 115 | 5.65E-13 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5341/g5341.t18; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5341.t18.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0042254 | ribosome biogenesis | BP |
| GO:0001522 | pseudouridine synthesis | BP |
KEGG
Orthology
- This transcript has been annotated with K11128 (H/ACA ribonucleoprotein complex subunit 1)
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.
