General information for g9550.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g9550 is located on chr_1: 4035638..4036040 (+ 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 | g9550 | g9550.t1 | isoform | g9550.t1 | 4035638 | 4036040 |
| chr_1 | g9550 | g9550.t1 | exon | g9550.t1.exon1 | 4035638 | 4035660 |
| chr_1 | g9550 | g9550.t1 | cds | g9550.t1.CDS1 | 4035638 | 4035660 |
| chr_1 | g9550 | g9550.t1 | exon | g9550.t1.exon2 | 4035717 | 4035784 |
| chr_1 | g9550 | g9550.t1 | cds | g9550.t1.CDS2 | 4035717 | 4035784 |
| chr_1 | g9550 | g9550.t1 | exon | g9550.t1.exon3 | 4035841 | 4036040 |
| chr_1 | g9550 | g9550.t1 | cds | g9550.t1.CDS3 | 4035841 | 4036040 |
| chr_1 | g9550 | g9550.t1 | TTS | g9550.t1 | 4036077 | 4036077 |
| chr_1 | g9550 | g9550.t1 | TSS | g9550.t1 | NA | NA |
Sequences
>g9550.t1 Gene=g9550 Length=291
ATGGAAATAAAACTTGATTTTGGAGGAGGTGCAGAAGTATTGTTCGACAACATTAAAAAG
AGAGATCTCACATTAGATTCAAGTAAAAAATGGACAATCAGAACATTCCTTCAATACATG
AAAGAGAATCTTTTGACCGATAGAGAAGAGCTTTTTTTACAAGGAGAATGTGTTAGACCT
GGAATACTAGTTCTCATAAACGACACAGATTGGGAGTTATTAGGAGAGCTAGATTATGAA
ATACAGCCAAATGATAACATTTCTTTTATTTCAACACTCCATGGAGGATAA
>g9550.t1 Gene=g9550 Length=96
MEIKLDFGGGAEVLFDNIKKRDLTLDSSKKWTIRTFLQYMKENLLTDREELFLQGECVRP
GILVLINDTDWELLGELDYEIQPNDNISFISTLHGG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 7 | g9550.t1 | CDD | cd01764 | Ubl_Urm1 | 3 | 96 | 0.00000 |
| 5 | g9550.t1 | Gene3D | G3DSA:3.10.20.30 | - | 1 | 96 | 0.00000 |
| 3 | g9550.t1 | Hamap | MF_03048 | Ubiquitin-related modifier 1 [URM1]. | 1 | 96 | 32.42351 |
| 2 | g9550.t1 | PANTHER | PTHR14986 | RURM1 PROTEIN | 1 | 96 | 0.00000 |
| 6 | g9550.t1 | PIRSF | PIRSF037379 | Urm1 | 1 | 96 | 0.00000 |
| 1 | g9550.t1 | Pfam | PF09138 | Urm1 (Ubiquitin related modifier) | 2 | 96 | 0.00000 |
| 4 | g9550.t1 | SUPERFAMILY | SSF54285 | MoaD/ThiS | 1 | 96 | 0.00000 |
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:0034227 | tRNA thio-modification | BP |
| GO:0005737 | cytoplasm | CC |
KEGG
Orthology
- This transcript has been annotated with K12161 (ubiquitin related modifier 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.
