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.t12 TTS g2337.t12 16896666 16896666
chr_3 g2337 g2337.t12 isoform g2337.t12 16897223 16903773
chr_3 g2337 g2337.t12 exon g2337.t12.exon1 16897223 16897292
chr_3 g2337 g2337.t12 cds g2337.t12.CDS1 16897223 16897292
chr_3 g2337 g2337.t12 exon g2337.t12.exon2 16897364 16897466
chr_3 g2337 g2337.t12 cds g2337.t12.CDS2 16897364 16897466
chr_3 g2337 g2337.t12 exon g2337.t12.exon3 16899432 16899549
chr_3 g2337 g2337.t12 cds g2337.t12.CDS3 16899432 16899549
chr_3 g2337 g2337.t12 exon g2337.t12.exon4 16899606 16899731
chr_3 g2337 g2337.t12 cds g2337.t12.CDS4 16899606 16899731
chr_3 g2337 g2337.t12 exon g2337.t12.exon5 16899796 16900382
chr_3 g2337 g2337.t12 cds g2337.t12.CDS5 16899796 16900382
chr_3 g2337 g2337.t12 exon g2337.t12.exon6 16900447 16900776
chr_3 g2337 g2337.t12 cds g2337.t12.CDS6 16900447 16900537
chr_3 g2337 g2337.t12 exon g2337.t12.exon7 16903710 16903773
chr_3 g2337 g2337.t12 TSS g2337.t12 16903772 16903772

Sequences

>g2337.t12 Gene=g2337 Length=1398
TGAGTGAGTTGCTAGAAAATGTCAGTGTTAAACTGAAAAAAGTTTTCAAATCAAATTAAA
TTAGACATCATTTACGGAACGTCAACGCAAAAATATTAATTTTATTACACAAACATTCGT
AACAACACATGACATTTTGTGCAACAATTATTTGAAAGAGAAAGGATATTAGTATATTGA
CGGTCAACAAGCGAGTGATTATAAGGAACAACCCTTTTTGACTTTCACATTGAAGGTTTT
AAGGGATATGCTAAATGCAAAAATTGTAAAAAAAAACCAATTAAAGTTTGATTAGATCAC
AAGATGGGAGCATTTTTGGAAAAGCCCAATACAAACAAACACAATGAGAATGGTGAGGGC
AATGGATTGCGATTTGGAGTGAGTTCAATGCAAGGATGGCGTTGCGAAATGGAAGATGCT
CATTTTGCAAGAACAAATTTAGGAGAAGATTTGGCAGATTGGAGTTATTTTGCGGTGTTT
GACGGACATGCAGGTTTTAAAGTGTCTGAACATTGTGCGCAGCATTTATTAGAAGCGATC
ATACACACAGAAGAGTTTAAAGGCAATGATGTTGTGAAGGGAATACACTCTGGCTTCTTA
AAATTGGATAACATAATGCGAGATATACCTGAATTAGCAAGCGGTGCTGATAAATCTGGA
ACTACTGCCGTTTGTGCATTCATATCAAGTGATAGTATTTATATTGCAAATTGCGGTGAT
TCACGTGCTGTATTGTGTCGAAATGGCAATCCAGTATTCTCAACGCAAGATCACAAACCG
ATTCTGCCATCTGAAAAGGAACGAATTGTAAATGCAGGAGGATCGGTTATGGTACAACGT
GTCAACGGTAGCCTCGCAGTATCGAGAGCACTTGGAGATTATGATTACAAAAATGTCTCG
GAATTGGGTCAATGTGAACAGTTGGTATCACCTGAACCCGAGATTTTCTGCAAAGAACGT
GATCCTCAGGACTTTTTTCTAGCTTGCGACGGTGTATGGGATGTGATGAGTAACGAGGCC
GTCTGTAATTTTGTTCATAATCGCCTTCGAATTTCTGATGACTTGGTGTGGATTTGTAAT
CAAGTTATTGACACATGCTTGCACAAGGGTTCTCGCGATAATATGAGCATCATTCTAATA
GTATTCCCCGGAGCGCCGAAACCTTCCAGTGAAGCTATTGAAGCAGAAGAGGAGCTTGAG
AGGAATATACGTAAAACTATAAAAGAATTCACAGAAAATACGGAGGCTGCATACGATGTG
AGTTCATTAATGCGCTTATTAGCCAGCAGTAACATTCAGTGGCCGGAAGGTGGTGGTATA
GAATCTAAATATAAACTTATTACGGAAGTATTTAAGGAAATCTGTCCTGATCTCACTGAT
GCAGAATTCGAGTTTTAA

>g2337.t12 Gene=g2337 Length=364
MGAFLEKPNTNKHNENGEGNGLRFGVSSMQGWRCEMEDAHFARTNLGEDLADWSYFAVFD
GHAGFKVSEHCAQHLLEAIIHTEEFKGNDVVKGIHSGFLKLDNIMRDIPELASGADKSGT
TAVCAFISSDSIYIANCGDSRAVLCRNGNPVFSTQDHKPILPSEKERIVNAGGSVMVQRV
NGSLAVSRALGDYDYKNVSELGQCEQLVSPEPEIFCKERDPQDFFLACDGVWDVMSNEAV
CNFVHNRLRISDDLVWICNQVIDTCLHKGSRDNMSIILIVFPGAPKPSSEAIEAEEELER
NIRKTIKEFTENTEAAYDVSSLMRLLASSNIQWPEGGGIESKYKLITEVFKEICPDLTDA
EFEF

Protein features from InterProScan

Transcript Database ID Name Start End E.value
10 g2337.t12 CDD cd00143 PP2Cc 23 281 6.73547E-94
9 g2337.t12 Coils Coil Coil 288 312 -
8 g2337.t12 Gene3D G3DSA:3.60.40.10 Phosphatase 2c; Domain 1 1 286 1.4E-111
7 g2337.t12 Gene3D G3DSA:1.10.10.430 Phosphatase 2C; domain 2 287 356 2.6E-13
13 g2337.t12 MobiDBLite mobidb-lite consensus disorder prediction 1 20 -
3 g2337.t12 PANTHER PTHR47992:SF121 PROTEIN PHOSPHATASE 1A 2 323 4.8E-115
4 g2337.t12 PANTHER PTHR47992 ALPHABET, ISOFORM E-RELATED 2 323 4.8E-115
2 g2337.t12 Pfam PF00481 Protein phosphatase 2C 23 274 1.1E-76
1 g2337.t12 Pfam PF07830 Protein serine/threonine phosphatase 2C, C-terminal domain 275 351 4.4E-23
12 g2337.t12 ProSitePatterns PS01032 PPM-type phosphatase domain signature. 55 63 -
14 g2337.t12 ProSiteProfiles PS51746 PPM-type phosphatase domain profile. 23 281 48.097
11 g2337.t12 SMART SM00332 PP2C_4 13 279 1.4E-87
5 g2337.t12 SUPERFAMILY SSF81606 PP2C-like 3 283 1.27E-84
6 g2337.t12 SUPERFAMILY SSF81601 Protein serine/threonine phosphatase 2C, C-terminal domain 288 355 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