General information for g9530.t4
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as WD repeat domain phosphoinositide-interacting protein 2.
Parent gene
- The parent gene g9530 is located on chr_1: 3913658..3914687 (- 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_1 | g9530 | g9530.t4 | TTS | g9530.t4 | 3912653 | 3912653 |
| chr_1 | g9530 | g9530.t4 | isoform | g9530.t4 | 3912800 | 3914687 |
| chr_1 | g9530 | g9530.t4 | exon | g9530.t4.exon1 | 3912800 | 3912900 |
| chr_1 | g9530 | g9530.t4 | cds | g9530.t4.CDS1 | 3912800 | 3912900 |
| chr_1 | g9530 | g9530.t4 | exon | g9530.t4.exon2 | 3912964 | 3913049 |
| chr_1 | g9530 | g9530.t4 | cds | g9530.t4.CDS2 | 3912964 | 3913049 |
| chr_1 | g9530 | g9530.t4 | exon | g9530.t4.exon3 | 3913109 | 3913658 |
| chr_1 | g9530 | g9530.t4 | cds | g9530.t4.CDS3 | 3913109 | 3913658 |
| chr_1 | g9530 | g9530.t4 | exon | g9530.t4.exon4 | 3913719 | 3914125 |
| chr_1 | g9530 | g9530.t4 | cds | g9530.t4.CDS4 | 3913719 | 3913977 |
| chr_1 | g9530 | g9530.t4 | exon | g9530.t4.exon5 | 3914242 | 3914687 |
| chr_1 | g9530 | g9530.t4 | TSS | g9530.t4 | 3915105 | 3915105 |
Sequences
>g9530.t4 Gene=g9530 Length=1590
ATGGCAGTGAATATCGATGAAGGGGGAAATTGTTATGTTAATTTTAACCAGGATTTTACG
TAAGTAGAGTGAATAAACAATTGTTGATATCGATACTTTATTGTCTTCTTTGAGACAGTA
ATAATTATCGATTTTTTATACTTTTGCAAATCTTCACTTTGCTTTCATCCCTCCTTTAGA
AAATTTGTTACATTTCACGTTTAAACGAGTTTCTAAAAATAGTTCTTCTAATGCATTTTA
ATCACACAATTTCATAATTGAAGTAATAACTTATTCAAATGATGTTTATCCTTTCAATTT
GATAAGAATTTCTCGTTTTGCGTCTTTAACAAGCTGTGTCTAATATATACACACAAGTCT
CCATGTATTTTTGTTTTTCAAATATATTTTATTTGGCCTTGAAATGTTATGAATAAAAAT
TCGTTCATGCTGTCGATGTAAAACAAGTCACTTTCAGTTGGCTATAAGAATGCATATACA
TTATATTCATTGAATTCAGTTGACCAACAACTTGAAGAAATATATTCAAACTTTGGCGAT
GATATATGTCTTGTTGAGCGTCTCTTTAGTAGCTCTCTACTTGCCATTGTGTCAATGAAT
GCACCAAGGAAATTAAAAGTATGTCACTTTAAGAAAGGAACAGAAATTTGCAATTACTCA
TATTCAAACACCATCAAAACGGTCAAATTGAATCGCGCTCGTTTGGTCGTTTGCTTAGAA
GAGAGTCTTTATATTCACAATATACGCGATATGAAGGTTGTACATACAATAAGAGATACT
CCAATAAATTCAAATGGCTTATGTGCATTGGCTGCCGATTCTGATAATTGTTATTTGGCT
TATCCAGGTTCAGCTGTATCTGGAGAGTTACAAATATTTGATGCTGTTAATTTAAATGCA
AAAACAATGATACCCGCTCATGATTCGCCACTTGCGGCAATGGCTTTTAGTTTAAATGGT
TCAGAGATTGCGACAGCAAGTGAAAAAGGTACAGTTATCAGAGTATTCTCTGTTAACGAT
GGAGTAAAACTATACGAATTTCGTCGCGGTGTTAAACGCTGTGTATCGATATCTTCCTTA
TCATTTTCCACTTGCAAGCAATATCTTTGTTGCAGTAGTAATACCGAAACAGTCCACATC
TTTAAATTGGAAAAGACTACAGGAACTACAGCAGCAACAAGTGAACGTGCAGGAACTGTA
AATCAATATGCAATCGGACAGAAATCATCAGACGAAAATTGGATGGGATATTTGAAAAGT
ACTGTTGCTAGCTATCTTCCTTATGCATTGCCAACACAGGTTACTGACGTTTTCACACAA
GGACGCGCTTTTGCATCAGCGATGCTCCCAATATCGGGAATAAAGCATGCATGTGCAATA
ACAACTATTCAAAAATCATTAAGATTATTGGTTGCATCACAAAATGGTTATATGTACATC
TACTCAATTCCACTCGATGGCGGTGAATGTCAGTTAATTAAAAAACATGATTTGAAGAAC
ATAGATCAGAATTCATCGAAAGAACAACAACAATCTTCAAGACAACCGCCAAACGAGCCA
TCAGCGCCGATAAACATTACTGAAAATTAA
>g9530.t4 Gene=g9530 Length=331
MNAPRKLKVCHFKKGTEICNYSYSNTIKTVKLNRARLVVCLEESLYIHNIRDMKVVHTIR
DTPINSNGLCALAADSDNCYLAYPGSAVSGELQIFDAVNLNAKTMIPAHDSPLAAMAFSL
NGSEIATASEKGTVIRVFSVNDGVKLYEFRRGVKRCVSISSLSFSTCKQYLCCSSNTETV
HIFKLEKTTGTTAATSERAGTVNQYAIGQKSSDENWMGYLKSTVASYLPYALPTQVTDVF
TQGRAFASAMLPISGIKHACAITTIQKSLRLLVASQNGYMYIYSIPLDGGECQLIKKHDL
KNIDQNSSKEQQQSSRQPPNEPSAPINITEN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 8 | g9530.t4 | Gene3D | G3DSA:2.130.10.10 | - | 2 | 205 | 8.2E-19 |
| 6 | g9530.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 304 | 331 | - |
| 7 | g9530.t4 | MobiDBLite | mobidb-lite | consensus disorder prediction | 306 | 331 | - |
| 1 | g9530.t4 | PANTHER | PTHR11227:SF27 | WD REPEAT DOMAIN PHOSPHOINOSITIDE-INTERACTING PROTEIN 2 | 2 | 312 | 1.3E-127 |
| 2 | g9530.t4 | PANTHER | PTHR11227 | WD-REPEAT PROTEIN INTERACTING WITH PHOSPHOINOSIDES WIPI -RELATED | 2 | 312 | 1.3E-127 |
| 4 | g9530.t4 | SMART | SM00320 | WD40_4 | 99 | 139 | 0.21 |
| 5 | g9530.t4 | SMART | SM00320 | WD40_4 | 142 | 184 | 4.2 |
| 3 | g9530.t4 | SUPERFAMILY | SSF50978 | WD40 repeat-like | 6 | 289 | 2.9E-26 |
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:0080025 | phosphatidylinositol-3,5-bisphosphate binding | MF |
| GO:0005515 | protein binding | MF |
| GO:0006914 | autophagy | BP |
| GO:0000407 | phagophore assembly site | CC |
| GO:0032266 | phosphatidylinositol-3-phosphate binding | MF |
| GO:0000045 | autophagosome assembly | 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.
