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.t4 isoform g2337.t4 16896421 16903773
chr_3 g2337 g2337.t4 exon g2337.t4.exon1 16896421 16897292
chr_3 g2337 g2337.t4 cds g2337.t4.CDS1 16897223 16897292
chr_3 g2337 g2337.t4 exon g2337.t4.exon2 16897364 16897466
chr_3 g2337 g2337.t4 cds g2337.t4.CDS2 16897364 16897466
chr_3 g2337 g2337.t4 exon g2337.t4.exon3 16899432 16899549
chr_3 g2337 g2337.t4 cds g2337.t4.CDS3 16899432 16899549
chr_3 g2337 g2337.t4 exon g2337.t4.exon4 16899606 16899731
chr_3 g2337 g2337.t4 cds g2337.t4.CDS4 16899606 16899731
chr_3 g2337 g2337.t4 exon g2337.t4.exon5 16899790 16900382
chr_3 g2337 g2337.t4 cds g2337.t4.CDS5 16899790 16900382
chr_3 g2337 g2337.t4 exon g2337.t4.exon6 16900447 16900776
chr_3 g2337 g2337.t4 cds g2337.t4.CDS6 16900447 16900537
chr_3 g2337 g2337.t4 exon g2337.t4.exon7 16903710 16903773
chr_3 g2337 g2337.t4 TSS g2337.t4 16903772 16903772
chr_3 g2337 g2337.t4 TTS g2337.t4 NA NA

Sequences

>g2337.t4 Gene=g2337 Length=2206
TGAGTGAGTTGCTAGAAAATGTCAGTGTTAAACTGAAAAAAGTTTTCAAATCAAATTAAA
TTAGACATCATTTACGGAACGTCAACGCAAAAATATTAATTTTATTACACAAACATTCGT
AACAACACATGACATTTTGTGCAACAATTATTTGAAAGAGAAAGGATATTAGTATATTGA
CGGTCAACAAGCGAGTGATTATAAGGAACAACCCTTTTTGACTTTCACATTGAAGGTTTT
AAGGGATATGCTAAATGCAAAAATTGTAAAAAAAAACCAATTAAAGTTTGATTAGATCAC
AAGATGGGAGCATTTTTGGAAAAGCCCAATACAAACAAACACAATGAGAATGGTGAGGGC
AATGGATTGCGATTTGGAGTGAGTTCAATGCAAGGATGGCGTTGCGAAATGGAAGATGCT
CATTTTGCAAGAACAAATTTAGGAGAAGATTTGGCAGATTGGAGTTATTTTGCGGTGTTT
GACGGACATGCAGGTTTTAAAGTGTCTGAACATTGTGCGCAGCATTTATTAGAAGCGATC
ATACACACAGAAGAGTTTAAAGGCAATGATGTTGTGAAGGGAATACACTCTGGCTTCTTA
AAATTGGATAACATAATGCGAGATATACCTGAATTAGCAAGCGGTGCTGATAAATCTGGA
ACTACTGCCGTTTGTGCATTCATATCAAGTGATAGTATTTATATTGCAAATTGCGGTGAT
TCACGTGCTGTATTGTGTCGAAATGGCAATCCAGTATTCTCAACGCAAGATCACAAACCG
ATTCTGCCATCTGAAAAGGAACGAATTGTAAATGCAGGAGGATCGGTTATGGTACAACGT
GTCAACGGTAGCCTCGCAGTATCGAGAGCACTTGGAGATTATGATTACAAAAATGTCTCG
GAATTGGGTCAATGTGAACAGTTGGTATCACCTGAACCCGAGATTTTCTGCAAAGAACGT
GATCCTCAGGACTTTTTTCTAGTGCTTGCTTGCGACGGTGTATGGGATGTGATGAGTAAC
GAGGCCGTCTGTAATTTTGTTCATAATCGCCTTCGAATTTCTGATGACTTGGTGTGGATT
TGTAATCAAGTTATTGACACATGCTTGCACAAGGGTTCTCGCGATAATATGAGCATCATT
CTAATAGTATTCCCCGGAGCGCCGAAACCTTCCAGTGAAGCTATTGAAGCAGAAGAGGAG
CTTGAGAGGAATATACGTAAAACTATAAAAGAATTCACAGAAAATACGGAGGCTGCATAC
GATGTGAGTTCATTAATGCGCTTATTAGCCAGCAGTAACATTCAGTGGCCGGAAGGTGGT
GGTATAGAATCTAAATATAAACTTATTACGGAAGTATTTAAGGAAATCTGTCCTGATCTC
ACTGATGCAGAATTCGAGTTTTAAAGAAAACCCTTTTTTACAATAGAATATTGATTATGA
TTTTCTTTGATAAAAAAAAACAACCTTTGATACAATTATTCAGCCAAATAACTATTGGAA
CAATATTTCAAACTACTATTTCAAATGAAGAAGAAAATAAGAAATGAGTAAAAATGATAT
CCGTGATTACAAATGAAGTAGAAATAAGCTGTTCTAATTTCCATCTTAAAATATTGTACA
TAAATTTTACTTAAATTTCCTCTTAAATATTCTAATTTTGACGATTTTTTTTACAATGAA
ATTCTTTTCCATCAACTTTTTTTTTCTTAAAATAAAATCAAATTTACACTTTTACAAACA
TACGCCAGTTTCTATTTTATGCGTGTGTAATTAAATATTTAATGATGAGAAAGATATCTA
AATCATGAGAAAAAGGACATGAAAACGAATTGGAATAAAAAAGAATCACAACACGCTGTT
TAAGGAGAGTACAAAATAGTGACAAAACTTTTACTTAATTTTTTTATTATTTCGATTGCA
CAGTTCTTACTTCCTAAATAAAAAATTAATTTCCACTCGTTAAAAATTTTTATTTGTTAA
TTTTTGTTTATTACAGAATTATGATTTCTTATGTTTAAAAAAAAGTCTGATGATTGAGGA
AGCATTTTTTAATGAAATAGAAAAATTTCATTTACATGAAAACAGAAGAAAGTAAAAAAA
ATATGTGTATGTGTATTTAAAAAAAATTGCAGCATTTAAGCTCCCCAAAAAGAAGAAAAA
AAAATATTTAATGATGAAAAATAAAAAAATAATTTTAGTGAATAAA

>g2337.t4 Gene=g2337 Length=366
MGAFLEKPNTNKHNENGEGNGLRFGVSSMQGWRCEMEDAHFARTNLGEDLADWSYFAVFD
GHAGFKVSEHCAQHLLEAIIHTEEFKGNDVVKGIHSGFLKLDNIMRDIPELASGADKSGT
TAVCAFISSDSIYIANCGDSRAVLCRNGNPVFSTQDHKPILPSEKERIVNAGGSVMVQRV
NGSLAVSRALGDYDYKNVSELGQCEQLVSPEPEIFCKERDPQDFFLVLACDGVWDVMSNE
AVCNFVHNRLRISDDLVWICNQVIDTCLHKGSRDNMSIILIVFPGAPKPSSEAIEAEEEL
ERNIRKTIKEFTENTEAAYDVSSLMRLLASSNIQWPEGGGIESKYKLITEVFKEICPDLT
DAEFEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2337.t4 CDD cd00143 PP2Cc 23 283 3.54658E-97
9 g2337.t4 Coils Coil Coil 290 314 -
8 g2337.t4 Gene3D G3DSA:3.60.40.10 Phosphatase 2c; Domain 1 1 288 8.8E-116
7 g2337.t4 Gene3D G3DSA:1.10.10.430 Phosphatase 2C; domain 2 289 358 2.6E-13
13 g2337.t4 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
3 g2337.t4 PANTHER PTHR47992:SF121 PROTEIN PHOSPHATASE 1A 2 325 1.6E-117
4 g2337.t4 PANTHER PTHR47992 ALPHABET, ISOFORM E-RELATED 2 325 1.6E-117
2 g2337.t4 Pfam PF00481 Protein phosphatase 2C 23 276 7.8E-81
1 g2337.t4 Pfam PF07830 Protein serine/threonine phosphatase 2C, C-terminal domain 277 353 4.5E-23
12 g2337.t4 ProSitePatterns PS01032 PPM-type phosphatase domain signature. 55 63 -
14 g2337.t4 ProSiteProfiles PS51746 PPM-type phosphatase domain profile. 23 283 50.875
11 g2337.t4 SMART SM00332 PP2C_4 13 281 4.1E-92
5 g2337.t4 SUPERFAMILY SSF81606 PP2C-like 3 285 2.35E-88
6 g2337.t4 SUPERFAMILY SSF81601 Protein serine/threonine phosphatase 2C, C-terminal domain 290 357 4.97E-11

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:0000287 magnesium ion binding MF
GO:0043169 cation binding MF
GO:0004721 phosphoprotein phosphatase activity MF
GO:0016791 phosphatase activity MF
GO:0030145 manganese ion binding MF

KEGG

Orthology

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.

Raw TPM values