General information for g5656.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been not been annotated.
Parent gene
- The parent gene g5656 is located on chr_2: 10943685..10944068 (+ 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 | g5656 | g5656.t1 | TSS | g5656.t1 | 10943550 | 10943550 |
| chr_2 | g5656 | g5656.t1 | isoform | g5656.t1 | 10943685 | 10944068 |
| chr_2 | g5656 | g5656.t1 | exon | g5656.t1.exon1 | 10943685 | 10943702 |
| chr_2 | g5656 | g5656.t1 | cds | g5656.t1.CDS1 | 10943685 | 10943702 |
| chr_2 | g5656 | g5656.t1 | exon | g5656.t1.exon2 | 10943789 | 10943919 |
| chr_2 | g5656 | g5656.t1 | cds | g5656.t1.CDS2 | 10943789 | 10943919 |
| chr_2 | g5656 | g5656.t1 | exon | g5656.t1.exon3 | 10943984 | 10944068 |
| chr_2 | g5656 | g5656.t1 | cds | g5656.t1.CDS3 | 10943984 | 10944068 |
| chr_2 | g5656 | g5656.t1 | TTS | g5656.t1 | 10944206 | 10944206 |
Sequences
>g5656.t1 Gene=g5656 Length=234
ATGCTTATCAAAGTCAAGACACTTACTGGCAAAGAAATTGAAATTGATATCGAGCCAACT
GACAAAGTCGATCGAATCAAAGAACGAGTTGAAGAAAAGGAAGGAATCCCGCCTCAACAA
CAACGTCTAATTTTCTCTGGAAAGCAAATGAATGATGACAAAACAGCTCAAGATTACAAG
GTTCAGGGTGGCTCAGTGCTGCATTTGGTACTCGCGTTAAGAGGTGGAAATTAA
>g5656.t1 Gene=g5656 Length=77
MLIKVKTLTGKEIEIDIEPTDKVDRIKERVEEKEGIPPQQQRLIFSGKQMNDDKTAQDYK
VQGGSVLHLVLALRGGN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 9 | g5656.t1 | CDD | cd01806 | Ubl_NEDD8 | 3 | 76 | 1.20006E-48 |
| 8 | g5656.t1 | Gene3D | G3DSA:3.10.20.90 | - | 1 | 77 | 5.2E-34 |
| 2 | g5656.t1 | PANTHER | PTHR10666 | UBIQUITIN | 1 | 75 | 9.2E-43 |
| 3 | g5656.t1 | PANTHER | PTHR10666:SF319 | NEDD8 | 1 | 75 | 9.2E-43 |
| 6 | g5656.t1 | PRINTS | PR00348 | Ubiquitin signature | 11 | 31 | 7.0E-23 |
| 5 | g5656.t1 | PRINTS | PR00348 | Ubiquitin signature | 32 | 52 | 7.0E-23 |
| 4 | g5656.t1 | PRINTS | PR00348 | Ubiquitin signature | 53 | 74 | 7.0E-23 |
| 1 | g5656.t1 | Pfam | PF00240 | Ubiquitin family | 3 | 74 | 4.5E-28 |
| 10 | g5656.t1 | ProSitePatterns | PS00299 | Ubiquitin domain signature. | 27 | 52 | - |
| 12 | g5656.t1 | ProSiteProfiles | PS50053 | Ubiquitin domain profile. | 1 | 76 | 25.836 |
| 11 | g5656.t1 | SMART | SM00213 | ubq_7 | 1 | 72 | 2.1E-25 |
| 7 | g5656.t1 | SUPERFAMILY | SSF54236 | Ubiquitin-like | 1 | 76 | 3.24E-29 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5656/g5656.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5656.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0005515 | protein binding | MF |
KEGG
Orthology
- This transcript has been annotated with K12158 (ubiquitin-like protein Nedd8)
Pathway
This gene does not belong to any 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.
