Gene loci information

Transcript annotation

  • This transcript has been annotated as Protein phosphatase 1B.

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_3 g2337 g2337.t15 isoform g2337.t15 16899819 16903773
chr_3 g2337 g2337.t15 exon g2337.t15.exon1 16899819 16900382
chr_3 g2337 g2337.t15 cds g2337.t15.CDS1 16899820 16900382
chr_3 g2337 g2337.t15 exon g2337.t15.exon2 16900447 16900776
chr_3 g2337 g2337.t15 cds g2337.t15.CDS2 16900447 16900537
chr_3 g2337 g2337.t15 exon g2337.t15.exon3 16903710 16903773
chr_3 g2337 g2337.t15 TSS g2337.t15 16903772 16903772
chr_3 g2337 g2337.t15 TTS g2337.t15 NA NA

Sequences

>g2337.t15 Gene=g2337 Length=958
TGAGTGAGTTGCTAGAAAATGTCAGTGTTAAACTGAAAAAAGTTTTCAAATCAAATTAAA
TTAGACATCATTTACGGAACGTCAACGCAAAAATATTAATTTTATTACACAAACATTCGT
AACAACACATGACATTTTGTGCAACAATTATTTGAAAGAGAAAGGATATTAGTATATTGA
CGGTCAACAAGCGAGTGATTATAAGGAACAACCCTTTTTGACTTTCACATTGAAGGTTTT
AAGGGATATGCTAAATGCAAAAATTGTAAAAAAAAACCAATTAAAGTTTGATTAGATCAC
AAGATGGGAGCATTTTTGGAAAAGCCCAATACAAACAAACACAATGAGAATGGTGAGGGC
AATGGATTGCGATTTGGAGTGAGTTCAATGCAAGGATGGCGTTGCGAAATGGAAGATGCT
CATTTTGCAAGAACAAATTTAGGAGAAGATTTGGCAGATTGGAGTTATTTTGCGGTGTTT
GACGGACATGCAGGTTTTAAAGTGTCTGAACATTGTGCGCAGCATTTATTAGAAGCGATC
ATACACACAGAAGAGTTTAAAGGCAATGATGTTGTGAAGGGAATACACTCTGGCTTCTTA
AAATTGGATAACATAATGCGAGATATACCTGAATTAGCAAGCGGTGCTGATAAATCTGGA
ACTACTGCCGTTTGTGCATTCATATCAAGTGATAGTATTTATATTGCAAATTGCGGTGAT
TCACGTGCTGTATTGTGTCGAAATGGCAATCCAGTATTCTCAACGCAAGATCACAAACCG
ATTCTGCCATCTGAAAAGGAACGAATTGTAAATGCAGGAGGATCGGTTATGGTACAACGT
GTCAACGGTAGCCTCGCAGTATCGAGAGCACTTGGAGATTATGATTACAAAAATGTCTCG
GAATTGGGTCAATGTGAACAGTTGGTATCACCTGAACCCGAGATTTTCTGCAAAGAAC

>g2337.t15 Gene=g2337 Length=218
MGAFLEKPNTNKHNENGEGNGLRFGVSSMQGWRCEMEDAHFARTNLGEDLADWSYFAVFD
GHAGFKVSEHCAQHLLEAIIHTEEFKGNDVVKGIHSGFLKLDNIMRDIPELASGADKSGT
TAVCAFISSDSIYIANCGDSRAVLCRNGNPVFSTQDHKPILPSEKERIVNAGGSVMVQRV
NGSLAVSRALGDYDYKNVSELGQCEQLVSPEPEIFCKE

Protein features from InterProScan

Transcript Database ID Name Start End E.value
7 g2337.t15 CDD cd00143 PP2Cc 23 218 3.71399E-69
6 g2337.t15 Coils Coil Coil 218 218 -
5 g2337.t15 Gene3D G3DSA:3.60.40.10 Phosphatase 2c; Domain 1 1 218 4.0E-85
10 g2337.t15 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
2 g2337.t15 PANTHER PTHR47992:SF121 PROTEIN PHOSPHATASE 1A 2 215 3.2E-81
3 g2337.t15 PANTHER PTHR47992 ALPHABET, ISOFORM E-RELATED 2 215 3.2E-81
1 g2337.t15 Pfam PF00481 Protein phosphatase 2C 23 214 1.2E-60
9 g2337.t15 ProSitePatterns PS01032 PPM-type phosphatase domain signature. 55 63 -
11 g2337.t15 ProSiteProfiles PS51746 PPM-type phosphatase domain profile. 23 218 37.769
8 g2337.t15 SMART SM00332 PP2C_4 13 218 4.2E-50
4 g2337.t15 SUPERFAMILY SSF81606 PP2C-like 3 216 9.42E-63

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:0043169 cation binding MF
GO:0016791 phosphatase activity MF

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