General information for g16268.t3
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as GATOR complex protein Wdr59.
Parent gene
- The parent gene g16268 is located on chr_4: 8926269..8930024 (+ 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_4 | g16268 | g16268.t3 | TSS | g16268.t3 | 8926139 | 8926139 |
| chr_4 | g16268 | g16268.t3 | isoform | g16268.t3 | 8926269 | 8927045 |
| chr_4 | g16268 | g16268.t3 | exon | g16268.t3.exon1 | 8926269 | 8927045 |
| chr_4 | g16268 | g16268.t3 | cds | g16268.t3.CDS1 | 8926269 | 8927045 |
| chr_4 | g16268 | g16268.t3 | TTS | g16268.t3 | NA | NA |
Sequences
>g16268.t3 Gene=g16268 Length=777
ATGGAAATTGAAATAGAAGAGAAAAGTCCGGTAATAAGAACAGCAGAATATTGTATGAAC
CTCGAAGATTTACAAGCAACAGCTTTGTCAATAAATTACACTGGACAATATTTGTTACTT
GCTGGTCGTCGTCATCTTGCCTTAAAAAATCTTTATGATTACACAGAGCCATTAAAGCTT
TTTAATAGAAATAGCAAATTTGAAGTTTCATGTGCAGAATTTGCAATTTGTAACAATTCA
TCAGCATTTTGTGCCATTGCAACTTCACAACTCATTGAAGTTCTAAAATGGACAGAATCA
AGTCCAGTGCTGGAATATTCATTACGTGCTCATACTCGAGTTGTTACTGATATTGATTGG
CACAGTAAACATCCTTATATGCTCGCTACATGCAGCATAGACACTTATACACATCTTTGG
GACTTGCGAGATCCAAAAAGACCAATTTTATCACTTTCTGCTGTTTGTATGTCTGGTGCC
ACTCAAGTTGGCTTTAATAGAGTTAGTGGAAATTTCATAGCAACAGCACATGATGGAGAT
TTAAGAATTTGGGATATTCGAAAAGGTTCAAGACCTGTGCAGTACATTACAGCACATTTG
AATCGAATTCATGGAATTAATTGGAGTCATACAGAAGAAAGTAATTTAATAACAGCAAGT
CAAGATGGAAGTGTGAAATTTTTTGATATCAATAATCCAAGGAGAGCTGAAAGAATTATT
ACGACCCCAACGCCATCACCTGTATGGAGGGCTAGATATACTCCACCTGCTTTTAAG
>g16268.t3 Gene=g16268 Length=259
MEIEIEEKSPVIRTAEYCMNLEDLQATALSINYTGQYLLLAGRRHLALKNLYDYTEPLKL
FNRNSKFEVSCAEFAICNNSSAFCAIATSQLIEVLKWTESSPVLEYSLRAHTRVVTDIDW
HSKHPYMLATCSIDTYTHLWDLRDPKRPILSLSAVCMSGATQVGFNRVSGNFIATAHDGD
LRIWDIRKGSRPVQYITAHLNRIHGINWSHTEESNLITASQDGSVKFFDINNPRRAERII
TTPTPSPVWRARYTPPAFK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g16268.t3 | Gene3D | G3DSA:2.130.10.10 | - | 16 | 255 | 3.8E-34 |
| 4 | g16268.t3 | PANTHER | PTHR46170 | GATOR COMPLEX PROTEIN WDR59 | 23 | 255 | 9.3E-93 |
| 2 | g16268.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 106 | 141 | 0.0063 |
| 1 | g16268.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 168 | 185 | 0.033 |
| 3 | g16268.t3 | Pfam | PF00400 | WD domain, G-beta repeat | 193 | 229 | 0.044 |
| 9 | g16268.t3 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 128 | 142 | - |
| 11 | g16268.t3 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 108 | 238 | 19.248 |
| 13 | g16268.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 108 | 150 | 9.539 |
| 12 | g16268.t3 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 196 | 238 | 9.874 |
| 8 | g16268.t3 | SMART | SM00320 | WD40_4 | 101 | 141 | 1.9E-6 |
| 7 | g16268.t3 | SMART | SM00320 | WD40_4 | 145 | 185 | 3.1 |
| 6 | g16268.t3 | SMART | SM00320 | WD40_4 | 189 | 229 | 7.2E-5 |
| 5 | g16268.t3 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 25 | 255 | 7.75E-33 |
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 gene did not have any KEGG ortholog annotations (KAAS, GHOSTZ).
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.
