Gene loci information

Transcript annotation

  • This transcript has been annotated as Putative Type 1 phosphatidylinositol 4,5-bisphosphate 4-phosphatase.

Parent gene

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 g8538 g8538.t12 TSS g8538.t12 31155464 31155464
chr_2 g8538 g8538.t12 isoform g8538.t12 31156226 31157131
chr_2 g8538 g8538.t12 exon g8538.t12.exon1 31156226 31156408
chr_2 g8538 g8538.t12 cds g8538.t12.CDS1 31156374 31156408
chr_2 g8538 g8538.t12 exon g8538.t12.exon2 31156588 31156954
chr_2 g8538 g8538.t12 cds g8538.t12.CDS2 31156588 31156954
chr_2 g8538 g8538.t12 exon g8538.t12.exon3 31157015 31157131
chr_2 g8538 g8538.t12 cds g8538.t12.CDS3 31157015 31157131
chr_2 g8538 g8538.t12 TTS g8538.t12 31158033 31158033

Sequences

>g8538.t12 Gene=g8538 Length=667
AGTGCAGTTCAACAGCAAACATCTGGATTTAGTGTCCCGCAAGATGAACTTCCTCCTCCA
TATACGTCGAATGAGGAGCGAGGATTGCCAATGGTCACTTGTCGCGTTTGTTCTGCAATG
ATTGACATCTCTTGGAAGCGAGAACAACATGTTGTCAAATGTAACCAATGCAATGAAGCA
ACGAAATGCTCCACCAGGAAAAAAATACGTCAGATGTCCATGCAATTGTTTGTTAATTTG
CAAGAGCTCTTCTCAACGTGTTGCATGTCCACGACCAAATTGCAAACGAATCATCAATTT
AGCACCAAGTCCTGTTACGCCACCTGTTCCGACAATGCCGGGAATGTGCCGAGTAACTTG
TGGCCATTGTCATGATACTTTCTTATTCAATACGCTCACAAATGCGCTAGCTAGATGCCC
ACATTGTCGTAAAGTCTCTTCAGTTGGTGTGGAATTTGCAAAAAATCGAAGCAATGTCTA
TCTTGCTCTTGGAATAGTTTTTCTTGCCATCGGTTTTGCAATTTTGTGGGCTACATATTC
ATATGCATCTACACACACCGGTATATGGCTTGCATATGTTGGCATGTTCTTAGTTTCAGC
ATTGCTCTTTGCACGTACATTCTACTATCGACGAATGAAAGTAAGCGTTATAGAAGGACC
AATATAA

>g8538.t12 Gene=g8538 Length=172
MLSNVTNAMKQRNAPPGKKYVRCPCNCLLICKSSSQRVACPRPNCKRIINLAPSPVTPPV
PTMPGMCRVTCGHCHDTFLFNTLTNALARCPHCRKVSSVGVEFAKNRSNVYLALGIVFLA
IGFAILWATYSYASTHTGIWLAYVGMFLVSALLFARTFYYRRMKVSVIEGPI

Protein features from InterProScan

Transcript Database ID Name Start End E.value
2 g8538.t12 PANTHER PTHR21014:SF6 PHOSPHATIDYLINOSITOL-4,5-BISPHOSPHATE 4-PHOSPHATASE 7 171 3.9E-74
3 g8538.t12 PANTHER PTHR21014 UNCHARACTERIZED 7 171 3.9E-74
1 g8538.t12 Pfam PF09788 Transmembrane protein 55A 7 166 1.9E-70
6 g8538.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 1 109 -
10 g8538.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 110 133 -
8 g8538.t12 Phobius NON_CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. 134 138 -
9 g8538.t12 Phobius TRANSMEMBRANE Region of a membrane-bound protein predicted to be embedded in the membrane. 139 159 -
7 g8538.t12 Phobius CYTOPLASMIC_DOMAIN Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. 160 172 -
4 g8538.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 111 133 -
5 g8538.t12 TMHMM TMhelix Region of a membrane-bound protein predicted to be embedded in the membrane. 138 160 -

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:0034597 phosphatidylinositol-4,5-bisphosphate 4-phosphatase activity MF
GO:0046856 phosphatidylinositol dephosphorylation 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.

Raw TPM values