General information for g12055.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g12055 is located on chr_1: 20678484..20679349 (+ 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 | g12055 | g12055.t1 | TSS | g12055.t1 | 20678387 | 20678387 |
| chr_1 | g12055 | g12055.t1 | isoform | g12055.t1 | 20678484 | 20679349 |
| chr_1 | g12055 | g12055.t1 | exon | g12055.t1.exon1 | 20678484 | 20678501 |
| chr_1 | g12055 | g12055.t1 | cds | g12055.t1.CDS1 | 20678484 | 20678501 |
| chr_1 | g12055 | g12055.t1 | exon | g12055.t1.exon2 | 20679028 | 20679147 |
| chr_1 | g12055 | g12055.t1 | cds | g12055.t1.CDS2 | 20679028 | 20679147 |
| chr_1 | g12055 | g12055.t1 | exon | g12055.t1.exon3 | 20679212 | 20679349 |
| chr_1 | g12055 | g12055.t1 | cds | g12055.t1.CDS3 | 20679212 | 20679349 |
| chr_1 | g12055 | g12055.t1 | TTS | g12055.t1 | 20679791 | 20679791 |
Sequences
>g12055.t1 Gene=g12055 Length=276
ATGGCAGATGAAAAGAAAGGCAGTGAAAGTGAACACATCAATTTGAAAGTCTTGGGTCAA
GATAACGCCGTAGTACAGTTCAAAATCAAACGCCACACTCCGTTACGGAAATTGATGAAC
GCGTACTGCGATAGAGCTGGTTTGAGTATGCAAGTTGTGCGATTCCGATTTGATGGTTCA
CCAATTAATGAAAATGACACTCCAACTTCACTTGAAATGGAAGAAGGAGATACAATTGAA
GTCTATCAGCAGCAAACCGGTGGTAGAGCTAATTAA
>g12055.t1 Gene=g12055 Length=91
MADEKKGSESEHINLKVLGQDNAVVQFKIKRHTPLRKLMNAYCDRAGLSMQVVRFRFDGS
PINENDTPTSLEMEEGDTIEVYQQQTGGRAN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g12055.t1 | CDD | cd16115 | Ubl_SUMO2_3_4 | 12 | 83 | 0.000 |
| 6 | g12055.t1 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 88 | 0.000 |
| 2 | g12055.t1 | PANTHER | PTHR10562 | SMALL UBIQUITIN-RELATED MODIFIER | 4 | 89 | 0.000 |
| 3 | g12055.t1 | PANTHER | PTHR10562:SF56 | SMALL UBIQUITIN-RELATED MODIFIER | 4 | 89 | 0.000 |
| 1 | g12055.t1 | Pfam | PF11976 | Ubiquitin-2 like Rad60 SUMO-like | 13 | 82 | 0.000 |
| 7 | g12055.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 11 | 88 | 13.489 |
| 5 | g12055.t1 | SMART | SM00213 | ubq_7 | 13 | 84 | 0.000 |
| 4 | g12055.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 8 | 88 | 0.000 |
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:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12160 (small ubiquitin-related modifier)
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.
