General information for g5450.t1
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.t1 | TTS | g5450.t1 | 9661308 | 9661308 |
| chr_2 | g5450 | g5450.t1 | isoform | g5450.t1 | 9661398 | 9666587 |
| chr_2 | g5450 | g5450.t1 | exon | g5450.t1.exon1 | 9661398 | 9661744 |
| chr_2 | g5450 | g5450.t1 | cds | g5450.t1.CDS1 | 9661398 | 9661744 |
| chr_2 | g5450 | g5450.t1 | exon | g5450.t1.exon2 | 9661805 | 9666587 |
| chr_2 | g5450 | g5450.t1 | cds | g5450.t1.CDS2 | 9661805 | 9666587 |
| chr_2 | g5450 | g5450.t1 | TSS | g5450.t1 | 9662193 | 9662193 |
Sequences
>g5450.t1 Gene=g5450 Length=5130
ATGAATGTGAACAAAAACTTACATAGTAAAACACTTTTGACTGAATTCGCCAGAAATTTT
GAAGAGGAATCAAATGAAACTGTTATATCAAAATTAGTTAATAAACTTTATGAAGCATGC
AATAATGTTAACAATGACAGTTCTTCTTCATCCAATAGTCAGGAGCAACAGCAACATAAA
AACAATGATGAAATACAAAATGAAAGTTCTTCAACATCTATGCAATCAAGTTCAAGCAGT
AGTAGTGCTACTGCCACTACATCTCAAAATTCCCCTGAAAAAAATAAAGAATCCTCTGTG
CTAGTTTATCAAGTTGATACTTCACAAGGTAGAACATCTTTAAATGTAATTAAAAGAATA
AGTAATCTTATTGCTATGAAAGATAAAGATCTTAATGATTACAAAAATACTGATTTGCAA
AAACTATGGATGCCCGATGACAAATCGCGCGAATGCTATGATTGTAGTCAAAAATTTACT
ACATTTAGGAGAAAGCATCATTGTCGCTTGTGTGGTCAAATCTTTTGTTCAAGATGTTGC
AGAACAATCATCCCTGGAAAAATCATTAATTGCAATGGTGATTTAAGAGTATGTACGTAT
TGCTCTAAAGTAGTGCTATCTTATATCAAATCACCAGACATCAATCGCGAATTGAAATCT
GATCTGCAAGCATTAGAGGAGGATTTATCCAATAAATTTGTTGGTGTGAGTAATAATGCA
AATAGTAACAATACAGCAGAATCAAGCCCTCATAGAAAAATCTCAGTTGGTTATCAAGAA
GAAAGATTAATTACGAATTCCAATGTATTGTCAAATGCCGACAGAAAAACAATTTTACAG
CAATCAAACACACTAAAATCACTTTACGAAGATATGCTTTGTGGTCTTCAATATCATAAC
AAAGGAGTAGATCTCGTAAATTTTCTCATTACTACACAAAAGTCTTCAAATAAAGCACAA
GCTGTAACGGTTTTAAATGCTATGATTGAAGCTGGATTTATAGTTCCAATGATACAGTAT
GAAAATATAGAACCCCATAATACTGTCAATATAGAGTTTAATGAAAATTTGTACTATAAA
GTTTTAAAATTAGATGACATTGAAACAATTAATGAAACAGAAAAAAATGAAAACATTCCA
ACAGAAACCACTGCGGACGATATTATGAGAGACGATCTTTTACTACCAAACATAAATGTA
GACAATTTATATTCCAATGAAAAGGAAAATGAACTTCAAAATTCATTCATATCAACAGTT
GGCTCTAAACCTTTATTAGAAGCATATTGTGAACATGAGGAACTTCTTTTAAATCAAATG
CTACGTAATGAAAATTTAGATACAACATGGGCAAAAGTGTTGATACCACAATGTGCCAGA
ATCGCTCATAACATTCATCCTGAATGTTCGAGTCGATTTTTTGAATCAATGGACGTAAGA
AATTTTGTAAACATTAAGAAAATTTCTGGTGGAACTAGAAATGAATGCATGATAATTGGT
GGTGTAGTTTTTAGTAAAAATGTCGCTCATAAAGATATGAAAACAAAAATCGATAATCCA
AAAGTATTGTTGCTTCAATGTCCAATTGCCTATCAAAGAGTTGAAGGAAAATTTGTTACA
ATTGAATCACTTATACTTCAAGAAAAGGAATATTTACGAAATGTAACATCTCGAATTTTA
TCATTATCACCTGATATTGTTCTCGTTCATAAAAATGTAGCTGGTATTGCACAAGATTTA
TTAAGAGACAATGGTATCACTCTGGTACTTGATGTAAAATTATCCGTATTTGAACGTTTA
GCTAGATGTATGCAATGTGATATTGTAACATCAATTGATTCTAACATTGGAAGACCGAAA
TTGGGAACATGCAAACGTTTTTACACTAAAAATTACATCGATGGTAATGGATTTGTTAAA
AGTCTAATGTTTTTCGATATACTTTATAGTCAACGAGGATGTTCATTGCTTTTAAGAGGT
GGTTCAGAAGATGAATTGGCACGATTGAAAAAAGTTTCAAGTTTTCTACTTTTTGCCAGA
TACAATTGGCGTTTGGAACTTTCTTATTTACTTGATAGCTTTGCTCAACCACCTCTACCA
AAATCAAGCATTTTTGATTCAATTGATCAAAGTCAAATGAGTCCGGTAGATAATAAGACA
AAAGTTGACACGATTGTAACTGCAAATTTTGATCTGTCAAAAACGGAAAACTCGAAAAAA
GAAAAGACAGTGAATATCGAAAATGTTTCAGATTTCTCTGATCCTCTTCGAGCAAGCACC
TTTGAAATGAACACAATTGAAAATGTTGAATTCGAAGTTCAAGATTCTTTTGATAATAAA
TTTAGAACATCATTGGCATCGACAATTCTTTCCATTAGTCCATTTATAAACTTTCCTTTA
CCGTACTTTGAAACAGAAGCAGGAAAACGATGTGAATTAAGAAAGTTCTTTCCTAAAGAA
CTCTTTTTCTCTAAGCAATGGATAGAAAAGAACAATGAAAAAATTGAATTTTCAACTGTA
TTATCAACACAAACTATTGAGAAAAATGAAGATTCACGGCAGACAATAAATCCGACACAT
GATTTCCTTACGATGAAAATTACAGTTCCTGCTGATGATAAAAATTTTCAAACAGCACTT
GCCGATTATCGAAGAAAAGGATCCACATATCAAAAAGTTATGCGAATGAAAACCATCGAG
AAAAAGCAAGAAGGTGCAAAAATTCTTTCTCGGCAAAAGTCTATCAGTGAATCATCAAAA
GATGCATTTAATATATTAAATCATCAAAGACTTCCTGTATTGTTTTGCAGTTTCTATTTG
AATAATAATAGTAAAGAAGTACCAACATCTTTCTGTGCACAACCATTAATTCTTGATATG
CATTTTTATGGACAAGATGATATAATGTTGGGTTTATTCCTAGAGCGCTATTGTTTTAAA
AACTCGTACATATGTCAATCATGCAAACTTCCAATGATGGACCACGTTAGAAGATATGCT
CATTCAATGGGTGTAGTTCAAGTAAAATTAGATAATGATCCTAATAAAAATGAGACAAAT
TCAGCAAACATTTTAATGACTTCTCGTTGCACTATTTGCAATACAATGTCAAAAAGTGTT
ACTATGTCACCTGACACATGGTGCTTATCATTTGCCAAATTTCTTGAACTTAAATTTCAT
GGAAATTTTTACACAAGAAGAAACATTGAACAAGATGATGCTGAATCATCTCAATTTTCT
CAACAATCCGTATGCCGTCATTCACTTTATCACGATCACATACAATATTTTTCAAATAAT
GGTATAATTGTTAGTTTCATGTATACACCAGTTGAAATATGGGAAATTAAACTGCCACTT
TTATCACTTCCTCTCAAATCACCTGAAACAATCAACAAAAAAACTTTTACTGAAAAAATA
AAATCGTTTTCAGTACGTGGTTATGATGTTTATGCAAAAATACATGAAAAACTGGCAAAT
TTATCAACTGAAGATGGAAGTCCTATACTAACAAATTTAAAGAAAGTTTTAAATCGTGAT
CAATTGATATTTAAGCATCGTGTTGAAGTTGTTCATACTTTATTAGCATCCTCTGATATT
AATCAATATGAAATTCATGATGCAATGTATATGGTTTATAAAGAACTTGCTGATAGTATT
GAACTTTGGGGACCAAGATTAAATGAAGTTGCTATCCATTTGAAAAATGCACAAAAACAA
GGAGAAATAACATCTCAAACGTCTGTTGAAGTTTTTGATGAATTAGAAGACAATAATACA
CAAAGCACTGATGACTTGGAACTTGATTTGGATGGTGGGCTAATGATGCGTTCAACAGAT
GAATTACAAAATGAGAAAAAGGATAAAATTGATAAGAAAACAATTCGAAAATTATTAAGT
ACAATTTTACCATCTAGCTCTGATCAAAATCCACTTCCAACTCCTTTTACACCTAATGAA
CATTATTGCATATCAATTGGTCAATTTCCGGTCTTAGTGCATGATCAAGATTTAAGTTCA
ATAATTGCTTACTGTTTAATGTCTTATGAATATAAAAAAATGCTTGAAAATCTTACATTT
TCGACTTCAAATGATAACAGTAATAGTCCAAATTTAAAACGAAAAAATACAAACGATGGA
CTAGTTGAAAATGAAGAAAAAGATAAAGAAAATAAAGATTCAAATGAAAAAAATAACAAA
AAGCATTCAAATAGTCACATTGAATATCACTTTCAAGATTCATATACTCAATTTACATGC
AAATGTTATTTTGCCAAAGAATTTGATGAACTACGTAATAAATGTTTAACAACTAATAAA
AAGCAACAACAATTAAATGAGGAAATGACTCAATCCGCATTATATGATGACATACGTAAA
AATTATGCTCGTTCATTGAGTGAGAGTTTAAGATGGGATGCAAAAGGCGGAAAAAGTGGA
TCAAAATTTAGTAAAACAAAAGATGATCGTTTTATTTTGAAAGAGATGTCAAAGCAAGAT
GTAGGTGAATTTGAAAAATTTGCACCAAACTACTTTGAGTATGTCAATGATTGCGTTTTG
AAAAATCATCCAACATTATTAGCAAAAATATTTGGAATATACAAAGTCATTATAAAGAAG
AAGGAGTCAGTTACTGAAAAAGCCGTTTTAGTAATTGAAAATTTATTTTGCAATAGAAGA
GTTACAAACAAATATGACTTGAAAGGTTCTGAACGAAATAGATTAGTAGATACAGCGGGC
CAAACTGGTGATACTGTTTTGTTGGATGAAAATTTAATTAAAACTTCTTGGTCGAGACCT
CTTTATATTTTAACACATTCAAGGATAGTTTTGCGAAACGCTATTCTCAGAGATTCGTCA
TTTTTGGAGAAGAATCATGTAATGGATTATTCATTATTGGTTGGACTGGATGACGATAAT
TTCCTTATTGTTGGCATTATTGATTACATAAGAAAATACACTATCGATAAAAGAGTTGAA
TCTTTTCTAAAGCAAGTAGTAGATCAAAGTAAATTACCAACTATAGTTTCACCAAACGTC
TATAAAAATCGCTTTATTGATGCTATGGATCGTTATTTCCTTTGCATTCCTGAGCGTTTT
GATTCCAAATTTATGTCAGTTATGAAATAA
>g5450.t1 Gene=g5450 Length=1709
MNVNKNLHSKTLLTEFARNFEEESNETVISKLVNKLYEACNNVNNDSSSSSNSQEQQQHK
NNDEIQNESSSTSMQSSSSSSSATATTSQNSPEKNKESSVLVYQVDTSQGRTSLNVIKRI
SNLIAMKDKDLNDYKNTDLQKLWMPDDKSRECYDCSQKFTTFRRKHHCRLCGQIFCSRCC
RTIIPGKIINCNGDLRVCTYCSKVVLSYIKSPDINRELKSDLQALEEDLSNKFVGVSNNA
NSNNTAESSPHRKISVGYQEERLITNSNVLSNADRKTILQQSNTLKSLYEDMLCGLQYHN
KGVDLVNFLITTQKSSNKAQAVTVLNAMIEAGFIVPMIQYENIEPHNTVNIEFNENLYYK
VLKLDDIETINETEKNENIPTETTADDIMRDDLLLPNINVDNLYSNEKENELQNSFISTV
GSKPLLEAYCEHEELLLNQMLRNENLDTTWAKVLIPQCARIAHNIHPECSSRFFESMDVR
NFVNIKKISGGTRNECMIIGGVVFSKNVAHKDMKTKIDNPKVLLLQCPIAYQRVEGKFVT
IESLILQEKEYLRNVTSRILSLSPDIVLVHKNVAGIAQDLLRDNGITLVLDVKLSVFERL
ARCMQCDIVTSIDSNIGRPKLGTCKRFYTKNYIDGNGFVKSLMFFDILYSQRGCSLLLRG
GSEDELARLKKVSSFLLFARYNWRLELSYLLDSFAQPPLPKSSIFDSIDQSQMSPVDNKT
KVDTIVTANFDLSKTENSKKEKTVNIENVSDFSDPLRASTFEMNTIENVEFEVQDSFDNK
FRTSLASTILSISPFINFPLPYFETEAGKRCELRKFFPKELFFSKQWIEKNNEKIEFSTV
LSTQTIEKNEDSRQTINPTHDFLTMKITVPADDKNFQTALADYRRKGSTYQKVMRMKTIE
KKQEGAKILSRQKSISESSKDAFNILNHQRLPVLFCSFYLNNNSKEVPTSFCAQPLILDM
HFYGQDDIMLGLFLERYCFKNSYICQSCKLPMMDHVRRYAHSMGVVQVKLDNDPNKNETN
SANILMTSRCTICNTMSKSVTMSPDTWCLSFAKFLELKFHGNFYTRRNIEQDDAESSQFS
QQSVCRHSLYHDHIQYFSNNGIIVSFMYTPVEIWEIKLPLLSLPLKSPETINKKTFTEKI
KSFSVRGYDVYAKIHEKLANLSTEDGSPILTNLKKVLNRDQLIFKHRVEVVHTLLASSDI
NQYEIHDAMYMVYKELADSIELWGPRLNEVAIHLKNAQKQGEITSQTSVEVFDELEDNNT
QSTDDLELDLDGGLMMRSTDELQNEKKDKIDKKTIRKLLSTILPSSSDQNPLPTPFTPNE
HYCISIGQFPVLVHDQDLSSIIAYCLMSYEYKKMLENLTFSTSNDNSNSPNLKRKNTNDG
LVENEEKDKENKDSNEKNNKKHSNSHIEYHFQDSYTQFTCKCYFAKEFDELRNKCLTTNK
KQQQLNEEMTQSALYDDIRKNYARSLSESLRWDAKGGKSGSKFSKTKDDRFILKEMSKQD
VGEFEKFAPNYFEYVNDCVLKNHPTLLAKIFGIYKVIIKKKESVTEKAVLVIENLFCNRR
VTNKYDLKGSERNRLVDTAGQTGDTVLLDENLIKTSWSRPLYILTHSRIVLRNAILRDSS
FLEKNHVMDYSLLVGLDDDNFLIVGIIDYIRKYTIDKRVESFLKQVVDQSKLPTIVSPNV
YKNRFIDAMDRYFLCIPERFDSKFMSVMK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 16 | g5450.t1 | CDD | cd15725 | FYVE_PIKfyve_Fab1 | 143 | 203 | 2.23464E-39 |
| 17 | g5450.t1 | CDD | cd03334 | Fab1_TCP | 434 | 694 | 1.38608E-111 |
| 15 | g5450.t1 | CDD | cd17300 | PIPKc_PIKfyve | 1416 | 1693 | 2.85782E-113 |
| 14 | g5450.t1 | Coils | Coil | Coil | 1428 | 1448 | - |
| 12 | g5450.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 130 | 209 | 5.2E-21 |
| 10 | g5450.t1 | Gene3D | G3DSA:3.50.7.10 | GroEL | 494 | 660 | 6.3E-45 |
| 11 | g5450.t1 | Gene3D | G3DSA:3.30.800.10 | Phosphatidylinositol Phosphate Kinase II Beta | 1368 | 1552 | 1.2E-19 |
| 13 | g5450.t1 | Gene3D | G3DSA:1.20.58.1870 | - | 1555 | 1694 | 2.3E-36 |
| 20 | g5450.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 45 | 99 | - |
| 21 | g5450.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1363 | 1405 | - |
| 23 | g5450.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1363 | 1377 | - |
| 22 | g5450.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1378 | 1405 | - |
| 5 | g5450.t1 | PANTHER | PTHR45748:SF7 | 1-PHOSPHATIDYLINOSITOL 3-PHOSPHATE 5-KINASE-RELATED | 140 | 1700 | 0.0 |
| 6 | g5450.t1 | PANTHER | PTHR45748 | 1-PHOSPHATIDYLINOSITOL 3-PHOSPHATE 5-KINASE-RELATED | 140 | 1700 | 0.0 |
| 3 | g5450.t1 | Pfam | PF01363 | FYVE zinc finger | 143 | 205 | 6.8E-16 |
| 4 | g5450.t1 | Pfam | PF00118 | TCP-1/cpn60 chaperonin family | 470 | 670 | 7.3E-27 |
| 1 | g5450.t1 | Pfam | PF01504 | Phosphatidylinositol-4-phosphate 5-Kinase | 1474 | 1638 | 7.0E-34 |
| 2 | g5450.t1 | Pfam | PF01504 | Phosphatidylinositol-4-phosphate 5-Kinase | 1639 | 1691 | 4.2E-8 |
| 24 | g5450.t1 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 146 | 206 | 11.822 |
| 26 | g5450.t1 | ProSiteProfiles | PS50186 | DEP domain profile. | 302 | 363 | 9.63 |
| 25 | g5450.t1 | ProSiteProfiles | PS51455 | Phosphatidylinositol phosphate kinase (PIPK) domain profile. | 1350 | 1693 | 53.321 |
| 19 | g5450.t1 | SMART | SM00064 | fyve_4 | 138 | 207 | 9.8E-14 |
| 18 | g5450.t1 | SMART | SM00330 | PIPK_2 | 1389 | 1694 | 3.7E-102 |
| 8 | g5450.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 142 | 213 | 1.1E-19 |
| 7 | g5450.t1 | SUPERFAMILY | SSF52029 | GroEL apical domain-like | 495 | 660 | 1.36E-34 |
| 9 | g5450.t1 | SUPERFAMILY | SSF56104 | SAICAR synthase-like | 1392 | 1693 | 3.92E-68 |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5450/g5450.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5450.t1.fa.iupred3.txt does not exist
GO terms from InterProScan
| GOID | TERM | ONTOLOGY |
|---|---|---|
| GO:0016307 | phosphatidylinositol phosphate kinase activity | MF |
| GO:0046872 | metal ion binding | MF |
| GO:0046488 | phosphatidylinositol metabolic process | BP |
| GO:0005524 | ATP binding | MF |
| GO:0035556 | intracellular signal transduction | BP |
| GO:0016887 | ATP hydrolysis activity | MF |
KEGG
Orthology
- This transcript has been annotated with K00921 (1-phosphatidylinositol-3-phosphate 5-kinase)
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.
