General information for g10571.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative U4/U6.U5 small nuclear ribonucleoprotein 27 kDa protein.
Parent gene
- The parent gene g10571 is located on chr_1: 10488870..10489830 (- 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 | g10571 | g10571.t4 | isoform | g10571.t4 | 10487834 | 10489830 |
| chr_1 | g10571 | g10571.t4 | exon | g10571.t4.exon1 | 10487834 | 10488924 |
| chr_1 | g10571 | g10571.t4 | cds | g10571.t4.CDS1 | 10488870 | 10488924 |
| chr_1 | g10571 | g10571.t4 | exon | g10571.t4.exon2 | 10488980 | 10489210 |
| chr_1 | g10571 | g10571.t4 | cds | g10571.t4.CDS2 | 10488980 | 10489210 |
| chr_1 | g10571 | g10571.t4 | exon | g10571.t4.exon3 | 10489383 | 10489632 |
| chr_1 | g10571 | g10571.t4 | cds | g10571.t4.CDS3 | 10489383 | 10489603 |
| chr_1 | g10571 | g10571.t4 | exon | g10571.t4.exon4 | 10489756 | 10489830 |
| chr_1 | g10571 | g10571.t4 | TSS | g10571.t4 | NA | NA |
| chr_1 | g10571 | g10571.t4 | TTS | g10571.t4 | NA | NA |
Sequences
>g10571.t4 Gene=g10571 Length=1647
TACGTTTTTTCTCGATAGAGTTTTGTTTTGTAAATATTTTATTTGATGGTTTTCGGTGAA
TTGTGAGTGCAAAACTTTTCTCAAATAATAGAATTTTCATAATCATGGGACGATCTAGAA
GCAGAAGCAGATCACTGTCACCAGTTCGGCGTAAGCGTGCTAAAGAACGTGATAGATCAA
AGAGGAAGCATAGAAATCGTTCAAAATCACGTGAAAAGAGACGACGCAGTCGTTCACGCT
CAGAAGAATATAGTAGAACTGGAGTAGGCAGCAGTACAGGAAGCTCATTAATGAGACATA
GACGATCTAGTAGATCTCGTTCTAGATCAAGATCTTATGAAAGAAGGCATCGTTCACGTT
CACCATACGCTCCATCAACATCAAAATCCAAAATTTCTTCAGTTAATGTTTCGGAAGCTG
ATTTAGTGGGCAAATCGCCTGATGAAATTGAAATGATGAAAGTGATGGGATTCTGTGGCT
TTGATACAACAAAGGGCAAAAAAGTTGAAGGAAATAATGTAGGAGAAGTTCATGTTATTT
TAAAAAGAAAATATAGACAATATATGAATCGCAAAGGCGGCTTTAATCGACCATTGGACT
TTGTTGCATAAATTGTTAATGCCCACTGACATAATTATGATTTACACCTATCTTATAGCG
TATCTAAGTTAATTCTTCAATAGCTTTTAAGCAATTCATTCTTGAAACAACAGCCAGCAA
ATTTTCTTTTTTATTTTCTCACTTTTATGATGGTATATTTGAAAAATCATCATTTGGATT
TGCAACATAATCAAAAATAACCCTCCACATTTTTTTCACACTCACCACCACATACAGTAC
AATAGTTAAAATTCTTCAGGTTAAACGGGTTAATAATCACTTTCATTTCTTCTTCTACAT
AGATTTCTACTTAATTCTCACTTCTTTTTAACATAATATTTTTAATGGGAAAAAATTGCT
CATTGAGAAAAAATCTGGTATTAGAGTTGAAAGGGAGTGATTTTAACAAAAAAATTTACA
ACATAATATACAATAGTCTTTTCATATACACACAACTCAACTCAATCCACAAATACAAAT
ATGCAATAGTCAGGGAATTATCAAACTTTCGAATTGAGAATTTTAAATCTTAAAAGAGGT
CACCAGTCATCAACATCATCATGCATTCCTTAAAAAATGAAAGAAAAAAGATTCAATTAA
TTCAATTGAAAATATTGTAGTTTTGACATTTTTTAAATAAGAATAACAATTTGCATCAGA
TGATGAATTAGGAATAAAATTTTCGATATGAAAAGTTTGATAATATTATTACACACTTTA
TTTGTTAAACGATTTTTACCATATACAAACAATAGTTCTAAAATTTGCCAATTTTTGAAT
ATACCTCATAACACCATACATTCATACTTATAAAAACGAAACAATTATCTATTGACATAA
GCTCTTTTTCTATAAATTAAATAGTTTTAAGATTATTTCAACCCTTATTTTCATACTACA
CATTTTCTTATTTTTAATTTATTATATTGTATTCTCTATTTCTTTTCTTTTCTGTTCAAG
TCATGTTTGAATCAAGAAATAAATGAATTTTAATTGTGAAATCATTTAATTTATGATAAT
AAACAAATTTAAATTAACATTTGAACT
>g10571.t4 Gene=g10571 Length=168
MGRSRSRSRSLSPVRRKRAKERDRSKRKHRNRSKSREKRRRSRSRSEEYSRTGVGSSTGS
SLMRHRRSSRSRSRSRSYERRHRSRSPYAPSTSKSKISSVNVSEADLVGKSPDEIEMMKV
MGFCGFDTTKGKKVEGNNVGEVHVILKRKYRQYMNRKGGFNRPLDFVA
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 4 | g10571.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 109 | - |
| 7 | g10571.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1 | 40 | - |
| 5 | g10571.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 49 | 64 | - |
| 6 | g10571.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 65 | 81 | - |
| 3 | g10571.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 88 | 105 | - |
| 2 | g10571.t4 | PANTHER | PTHR31077 | U4/U6.U5 SMALL NUCLEAR RIBONUCLEOPROTEIN 27 KDA PROTEIN | 1 | 167 | 6.8E-37 |
| 1 | g10571.t4 | Pfam | PF08648 | U4/U6.U5 small nuclear ribonucleoproteins | 113 | 166 | 1.0E-29 |
| 9 | g10571.t4 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 71 | - |
| 10 | g10571.t4 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 51 | - |
| 11 | g10571.t4 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 52 | 63 | - |
| 12 | g10571.t4 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 64 | 71 | - |
| 8 | g10571.t4 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 72 | 168 | - |
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:0008380 | RNA splicing | BP |
KEGG
Orthology
- This transcript has been annotated with K12846 (U4/U6.U5 tri-snRNP-associated protein 3)
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