General information for g16268.t2
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.t2 | TSS | g16268.t2 | 8926139 | 8926139 |
| chr_4 | g16268 | g16268.t2 | isoform | g16268.t2 | 8926269 | 8930024 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon1 | 8926269 | 8927045 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS1 | 8926269 | 8927045 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon2 | 8927190 | 8927553 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS2 | 8927190 | 8927553 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon3 | 8927670 | 8928519 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS3 | 8927670 | 8928519 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon4 | 8928603 | 8928726 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS4 | 8928603 | 8928726 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon5 | 8929350 | 8929808 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS5 | 8929350 | 8929808 |
| chr_4 | g16268 | g16268.t2 | exon | g16268.t2.exon6 | 8929935 | 8930024 |
| chr_4 | g16268 | g16268.t2 | cds | g16268.t2.CDS6 | 8929935 | 8930024 |
| chr_4 | g16268 | g16268.t2 | TTS | g16268.t2 | 8930101 | 8930101 |
Sequences
>g16268.t2 Gene=g16268 Length=2664
ATGGAAATTGAAATAGAAGAGAAAAGTCCGGTAATAAGAACAGCAGAATATTGTATGAAC
CTCGAAGATTTACAAGCAACAGCTTTGTCAATAAATTACACTGGACAATATTTGTTACTT
GCTGGTCGTCGTCATCTTGCCTTAAAAAATCTTTATGATTACACAGAGCCATTAAAGCTT
TTTAATAGAAATAGCAAATTTGAAGTTTCATGTGCAGAATTTGCAATTTGTAACAATTCA
TCAGCATTTTGTGCCATTGCAACTTCACAACTCATTGAAGTTCTAAAATGGACAGAATCA
AGTCCAGTGCTGGAATATTCATTACGTGCTCATACTCGAGTTGTTACTGATATTGATTGG
CACAGTAAACATCCTTATATGCTCGCTACATGCAGCATAGACACTTATACACATCTTTGG
GACTTGCGAGATCCAAAAAGACCAATTTTATCACTTTCTGCTGTTTGTATGTCTGGTGCC
ACTCAAGTTGGCTTTAATAGAGTTAGTGGAAATTTCATAGCAACAGCACATGATGGAGAT
TTAAGAATTTGGGATATTCGAAAAGGTTCAAGACCTGTGCAGTACATTACAGCACATTTG
AATCGAATTCATGGAATTAATTGGAGTCATACAGAAGAAAGTAATTTAATAACAGCAAGT
CAAGATGGAAGTGTGAAATTTTTTGATATCAATAATCCAAGGAGAGCTGAAAGAATTATT
ACGACCCCAACGCCATCACCTGTATGGAGGGCTAGATATACTCCACCTGCTTTTAAGGAA
GGTCTAGTAACAATAATTGTTCCTTTAGTTGGCTCAGAAAGTGGTGAAAATTCTCTCCTT
TTATGGAGTAACTCAAAAAATAGCCAAAGTCCAATATGCTCCTTTACTGGTCATAATGAT
GTTATTTTAGACTTTGCTTATAGAAATGATCCTTATAGACAATCAAATGATATTGAAATT
TTTACTTGGAGTCGAGATCAAACTTTTAGAGTTTGGAAATTGGATAAAGAATTGCAAAAA
CTTTGTATTCAAAATACAATTGAAACTGAAAATGGAGAAAGTGCACTTGAATATCATCAG
AGAAATTCAACACAACCAAGTTGCTCACTACAGCATGAATTTTCGATTATTTTCTTTCCT
AGCATTCCTGGAATCCAAAAATATGAACTTGACACTGACAAACGCAATGCAATGATTCGA
ATAGTAGCAAATGGTTTCATAATCATTCTTCAAGTGATTTTTCCATCAGGCTATCCATTC
TCAAGTCCACCAATTTTTGAATTCTGTCCAGGCACAACACTTGATGACAATTTGTCACTT
AAACTAATGAAATCACTCAAAGATTCTTCAGCAAGTCGAGTAAAAAAAGGCAAAGCTTGT
TTGGAACATTGCTTGAGAGCTCTTGTGAGTGATTTGAAAAAAGAAACTGGTGGTGATAAA
GCACATTATTTGAGACTTCAATCACCAAGACTTGAAGGTGCGCTGTCCAAAGCACTTTCA
GATTCTTTAATTCCTTTTCCTAAAACTTCTGGTGTGAGATTCAATGCAACTGGAATTTTA
GTAACTTTTGCACGACCTTTTACCGCCAAAAGATTCAGTTTAAGAAATCAAACAACAACA
CCAAGAGCTTTATCAGCACTTTCTGGTGGATATCTTGGAAATGTCAATGGTTCAAAACCA
GTTTTTTATCCATCAAAAGATATCGATCGAAAGTCATCAACTGGTGTCAGCATTTGCATT
TATGATGCTTCAAAATTGCTAATGGTTTCAAGAGAATTGGCAGAAAATTATGTCATAATT
CCAACAAATCTGCCAAGAATGTGTCGAAAAAATAGAGAAGTTGCAGAAGAATTTGGAAGA
GCTGATTTAGTACAAACTTGGAGCATTGCTGAAACTATTGCTTTAGCACTTGCTAGTAGT
GATTTTGAATTGTCTGATGATGAAATGTTTTCAAGTCCTAATCCTTTTGCAAAAACATTT
TTGGAAGCTTTAATTAATCACTATGCAAAACTTGGAGATGTCCAAACTGCAGCAATGCTT
TGTGTAACTTTTGGTCGTTATTATCAAGAAATCTCATCTAGAACTTCATCATTTTCAACA
AAATCAAACACAAGTCAAAGTGTTTCACCTTATCACACAGTGACAGCAATGGACGTCAAC
TCACAATCAGTCATAAAATACAATGCTTGGGTTCTCGCACAACATCTTAAAGGTCAAACT
CGTAGTAATTCTTGGTCAGACTCACTCGATGATTTTCGTATTAATGAAGTCAATCGAAGT
GTTTTAGGAGAAAGCAATCGAAATTTTTATGACAATTTAAAGAAATTTTATGCTGACATT
CTTTATTGTTACAATTTATTGCCTGCAAGAGCGCTGATTTTAAAATTTGTTTCATCACCT
GCTGCATTTTCAAGCACCGTTGAATTTGTGACTGAATGTCAAATTTGCAAGAAAACATCA
AAAAGTCCATCATGTCTTCATTGCAAGAAATTTTTACTTTATTGCTCTTACTGTCAACTT
CCAATAAAAGGATCTGCAAATAGTTGCTTATCATGCAGTCATTCTTTTCATACTGCACAT
TTGTTAGAATGGTTTGAAAATCATGATGTCTGTCCTGTTGCTGGCTGTCGATGTCCATGT
GCTGACAATTTCGGAATGACCTGA
>g16268.t2 Gene=g16268 Length=887
MEIEIEEKSPVIRTAEYCMNLEDLQATALSINYTGQYLLLAGRRHLALKNLYDYTEPLKL
FNRNSKFEVSCAEFAICNNSSAFCAIATSQLIEVLKWTESSPVLEYSLRAHTRVVTDIDW
HSKHPYMLATCSIDTYTHLWDLRDPKRPILSLSAVCMSGATQVGFNRVSGNFIATAHDGD
LRIWDIRKGSRPVQYITAHLNRIHGINWSHTEESNLITASQDGSVKFFDINNPRRAERII
TTPTPSPVWRARYTPPAFKEGLVTIIVPLVGSESGENSLLLWSNSKNSQSPICSFTGHND
VILDFAYRNDPYRQSNDIEIFTWSRDQTFRVWKLDKELQKLCIQNTIETENGESALEYHQ
RNSTQPSCSLQHEFSIIFFPSIPGIQKYELDTDKRNAMIRIVANGFIIILQVIFPSGYPF
SSPPIFEFCPGTTLDDNLSLKLMKSLKDSSASRVKKGKACLEHCLRALVSDLKKETGGDK
AHYLRLQSPRLEGALSKALSDSLIPFPKTSGVRFNATGILVTFARPFTAKRFSLRNQTTT
PRALSALSGGYLGNVNGSKPVFYPSKDIDRKSSTGVSICIYDASKLLMVSRELAENYVII
PTNLPRMCRKNREVAEEFGRADLVQTWSIAETIALALASSDFELSDDEMFSSPNPFAKTF
LEALINHYAKLGDVQTAAMLCVTFGRYYQEISSRTSSFSTKSNTSQSVSPYHTVTAMDVN
SQSVIKYNAWVLAQHLKGQTRSNSWSDSLDDFRINEVNRSVLGESNRNFYDNLKKFYADI
LYCYNLLPARALILKFVSSPAAFSSTVEFVTECQICKKTSKSPSCLHCKKFLLYCSYCQL
PIKGSANSCLSCSHSFHTAHLLEWFENHDVCPVAGCRCPCADNFGMT
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g16268.t2 | PANTHER | PTHR46170 | GATOR COMPLEX PROTEIN WDR59 | 23 | 345 | 1.0E-208 |
| 6 | g16268.t2 | PANTHER | PTHR46170 | GATOR COMPLEX PROTEIN WDR59 | 347 | 883 | 1.0E-208 |
| 3 | g16268.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 106 | 141 | 0.032 |
| 2 | g16268.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 168 | 185 | 0.16 |
| 4 | g16268.t2 | Pfam | PF00400 | WD domain, G-beta repeat | 193 | 229 | 0.22 |
| 1 | g16268.t2 | Pfam | PF17120 | Zinc-ribbon, C4HC2 type | 833 | 883 | 5.4E-10 |
| 16 | g16268.t2 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 1 | 396 | - |
| 18 | g16268.t2 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 397 | 418 | - |
| 17 | g16268.t2 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 419 | 887 | - |
| 12 | g16268.t2 | ProSitePatterns | PS00678 | Trp-Asp (WD) repeats signature. | 128 | 142 | - |
| 13 | g16268.t2 | ProSiteProfiles | PS50294 | Trp-Asp (WD) repeats circular profile. | 108 | 342 | 19.354 |
| 15 | g16268.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 108 | 150 | 9.539 |
| 14 | g16268.t2 | ProSiteProfiles | PS50082 | Trp-Asp (WD) repeats profile. | 196 | 238 | 9.874 |
| 11 | g16268.t2 | SMART | SM00320 | WD40_4 | 101 | 141 | 1.9E-6 |
| 9 | g16268.t2 | SMART | SM00320 | WD40_4 | 145 | 185 | 3.1 |
| 8 | g16268.t2 | SMART | SM00320 | WD40_4 | 189 | 229 | 7.2E-5 |
| 10 | g16268.t2 | SMART | SM00320 | WD40_4 | 288 | 333 | 0.16 |
| 7 | g16268.t2 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 25 | 336 | 3.97E-38 |
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 K20409 (SEA/GATOR complex protein SEA3/WDR59)
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.
