General information for g5450.t11
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Putative 1-phosphatidylinositol 3-phosphate 5-kinase.
Parent gene
- The parent gene g5450 is located on chr_2: 9665280..9666587 (- 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 | g5450 | g5450.t11 | isoform | g5450.t11 | 9665280 | 9666587 |
| chr_2 | g5450 | g5450.t11 | exon | g5450.t11.exon1 | 9665280 | 9666587 |
| chr_2 | g5450 | g5450.t11 | cds | g5450.t11.CDS1 | 9665280 | 9666587 |
| chr_2 | g5450 | g5450.t11 | TSS | g5450.t11 | 9667233 | 9667233 |
| chr_2 | g5450 | g5450.t11 | TTS | g5450.t11 | NA | NA |
Sequences
>g5450.t11 Gene=g5450 Length=1308
ATGAATGTGAACAAAAACTTACATAGTAAAACACTTTTGACTGAATTCGCCAGAAATTTT
GAAGAGGAATCAAATGAAACTGTTATATCAAAATTAGTTAATAAACTTTATGAAGCATGC
AATAATGTTAACAATGACAGTTCTTCTTCATCCAATAGTCAGGAGCAACAGCAACATAAA
AACAATGATGAAATACAAAATGAAAGTTCTTCAACATCTATGCAATCAAGTTCAAGCAGT
AGTAGTGCTACTGCCACTACATCTCAAAATTCCCCTGAAAAAAATAAAGAATCCTCTGTG
CTAGTTTATCAAGTTGATACTTCACAAGGTAGAACATCTTTAAATGTAATTAAAAGAATA
AGTAATCTTATTGCTATGAAAGATAAAGATCTTAATGATTACAAAAATACTGATTTGCAA
AAACTATGGATGCCCGATGACAAATCGCGCGAATGCTATGATTGTAGTCAAAAATTTACT
ACATTTAGGAGAAAGCATCATTGTCGCTTGTGTGGTCAAATCTTTTGTTCAAGATGTTGC
AGAACAATCATCCCTGGAAAAATCATTAATTGCAATGGTGATTTAAGAGTATGTACGTAT
TGCTCTAAAGTAGTGCTATCTTATATCAAATCACCAGACATCAATCGCGAATTGAAATCT
GATCTGCAAGCATTAGAGGAGGATTTATCCAATAAATTTGTTGGTGTGAGTAATAATGCA
AATAGTAACAATACAGCAGAATCAAGCCCTCATAGAAAAATCTCAGTTGGTTATCAAGAA
GAAAGATTAATTACGAATTCCAATGTATTGTCAAATGCCGACAGAAAAACAATTTTACAG
CAATCAAACACACTAAAATCACTTTACGAAGATATGCTTTGTGGTCTTCAATATCATAAC
AAAGGAGTAGATCTCGTAAATTTTCTCATTACTACACAAAAGTCTTCAAATAAAGCACAA
GCTGTAACGGTTTTAAATGCTATGATTGAAGCTGGATTTATAGTTCCAATGATACAGTAT
GAAAATATAGAACCCCATAATACTGTCAATATAGAGTTTAATGAAAATTTGTACTATAAA
GTTTTAAAATTAGATGACATTGAAACAATTAATGAAACAGAAAAAAATGAAAACATTCCA
ACAGAAACCACTGCGGACGATATTATGAGAGACGATCTTTTACTACCAAACATAAATGTA
GACAATTTATATTCCAATGAAAAGGAAAATGAACTTCAAAATTCATTCATATCAACAGTT
GGCTCTAAACCTTTATTAGAAGCATATTGTGAACATGAGGAACTTCTT
>g5450.t11 Gene=g5450 Length=436
MNVNKNLHSKTLLTEFARNFEEESNETVISKLVNKLYEACNNVNNDSSSSSNSQEQQQHK
NNDEIQNESSSTSMQSSSSSSSATATTSQNSPEKNKESSVLVYQVDTSQGRTSLNVIKRI
SNLIAMKDKDLNDYKNTDLQKLWMPDDKSRECYDCSQKFTTFRRKHHCRLCGQIFCSRCC
RTIIPGKIINCNGDLRVCTYCSKVVLSYIKSPDINRELKSDLQALEEDLSNKFVGVSNNA
NSNNTAESSPHRKISVGYQEERLITNSNVLSNADRKTILQQSNTLKSLYEDMLCGLQYHN
KGVDLVNFLITTQKSSNKAQAVTVLNAMIEAGFIVPMIQYENIEPHNTVNIEFNENLYYK
VLKLDDIETINETEKNENIPTETTADDIMRDDLLLPNINVDNLYSNEKENELQNSFISTV
GSKPLLEAYCEHEELL
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 5 | g5450.t11 | CDD | cd15725 | FYVE_PIKfyve_Fab1 | 143 | 203 | 4.02504E-40 |
| 4 | g5450.t11 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 130 | 209 | 8.5E-22 |
| 7 | g5450.t11 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 99 | - |
| 2 | g5450.t11 | PANTHER | PTHR46715 | 1-PHOSPHATIDYLINOSITOL 3-PHOSPHATE 5-KINASE | 14 | 342 | 3.0E-47 |
| 1 | g5450.t11 | Pfam | PF01363 | FYVE zinc finger | 143 | 205 | 1.2E-16 |
| 8 | g5450.t11 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 146 | 206 | 11.822 |
| 9 | g5450.t11 | ProSiteProfiles | PS50186 | DEP domain profile. | 302 | 363 | 9.63 |
| 6 | g5450.t11 | SMART | SM00064 | fyve_4 | 138 | 207 | 9.8E-14 |
| 3 | g5450.t11 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 142 | 213 | 1.82E-20 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5450/g5450.t11; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5450.t11.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0046872 | metal ion binding | MF |
| GO:0000285 | 1-phosphatidylinositol-3-phosphate 5-kinase activity | MF |
| GO:0035556 | intracellular signal transduction | BP |
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.
