Gene loci information

Transcript annotation

  • This transcript has been annotated as Tyrosine-protein phosphatase Lar.

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 g5543 g5543.t2 isoform g5543.t2 10189423 10191036
chr_2 g5543 g5543.t2 exon g5543.t2.exon1 10189423 10189898
chr_2 g5543 g5543.t2 TTS g5543.t2 10189449 10189449
chr_2 g5543 g5543.t2 cds g5543.t2.CDS1 10189830 10189898
chr_2 g5543 g5543.t2 exon g5543.t2.exon2 10189969 10190099
chr_2 g5543 g5543.t2 cds g5543.t2.CDS2 10189969 10190099
chr_2 g5543 g5543.t2 exon g5543.t2.exon3 10190157 10190266
chr_2 g5543 g5543.t2 cds g5543.t2.CDS3 10190157 10190266
chr_2 g5543 g5543.t2 exon g5543.t2.exon4 10190332 10190563
chr_2 g5543 g5543.t2 cds g5543.t2.CDS4 10190332 10190563
chr_2 g5543 g5543.t2 exon g5543.t2.exon5 10190622 10191036
chr_2 g5543 g5543.t2 cds g5543.t2.CDS5 10190622 10190925
chr_2 g5543 g5543.t2 TSS g5543.t2 NA NA

Sequences

>g5543.t2 Gene=g5543 Length=1364
GTTCAAACTGAGGAACAATACATTTTCATACATGATGCTTTACTTGAAGCTGTCGTCTGT
GGCAACACAGAAATTCCCGCGACTGAACTGCATACACACATTCAGAAATTAATGCAAATC
ATTCCGAGTGAAAATATATCGGCCATGGAGATGGAATTTAAAAAGTTGGCCAACGTTAAA
ATAGACAGCTCAAAATTCGTATCAGCTAATAATCCCGTTAATAAAGACAAGAATCGATTA
GTTCATATTTTACCGTTTGAATCGACACGAGTTTGTTTATCAGTTGATCGTGGAATTGAG
GGATCAGATTATATTAATGCCAGTTTCATCGATGGATATCGTTTTAGAATGGCCTATATT
GCGACACAAGCGCCACTTCAAAATACTGCTGAAGATTTTTGGCGTATGCTTTGGGAACAT
AATTCAACAATAATTGTTATGTTAACGAAATTAAAAGAAATGGGCAAAGAAAAATGCACA
CAATATTGGCCAGATACGAGATCTGTTCGTTATCAGTATTATGTGGTAGATCCAGTGGCA
GAATATAATATGCCACAATATAAATTAAGAGAATTCAAAGTTACTGATGCACGTGATGGA
AGCAGCAGGACTGTGAGACAATTTCAATTCACAGAATGGCCCGAGCAGGGTGTGCCTAAA
TCAGGTGAAGCATTTATTGATTTTATTGGTCAAGTGCACAAGACAAAAGAACAATTTGGA
TTAGAAAATTCTCCTATTACGATACATTGTTCAGCAGGTGTTGGTCGAACTGGTGTTTTT
ATAACGCTAAGTATAGTCCTTGAACGAATGCAATATGAAGGAGTCCTTGATGTATTTCAA
ACAGTTAGGATTTTACGATCTCAGCGAATTCACATGGTCCAAACGGAGGATCAATATCAA
TTTTGTTATAGAGCAGCTTTGGAATATTTGGGTTCTTTCGATCACTATACAAACTAAATT
ATCGTAGATTGTAGCGTATTTAAAGGCATTTACTCATTTTTCGGCATAAATATTTTACGT
TACTTAATAATTCTTCGAATAATTGTTTAAAAAAATTTAAGTTTCTCATTTATTCTTTAA
AATAAAGACTGAGATGTATATTTTTTTCCTCTTTTTATCGCGATAGACATAAGTCTTTAT
ATTTTTTTGTATGAGTTTTTTTTATATAGCCAAGTCAATAATTATAAAAATAAAAAGAAA
AATTAAATTCTCATATCAGGCAAATATCAGATAATTAATTAATTAATGTTTAATTAGCGC
ATTATAAAACAATTATCTTCCAAGACAAGAAAGCTATTATAAATTAGTGTACATTATTAC
TCTTAAATAAAAAAAAATGAAAAATTTCATTCAAGCTTAATAAT

>g5543.t2 Gene=g5543 Length=281
MQIIPSENISAMEMEFKKLANVKIDSSKFVSANNPVNKDKNRLVHILPFESTRVCLSVDR
GIEGSDYINASFIDGYRFRMAYIATQAPLQNTAEDFWRMLWEHNSTIIVMLTKLKEMGKE
KCTQYWPDTRSVRYQYYVVDPVAEYNMPQYKLREFKVTDARDGSSRTVRQFQFTEWPEQG
VPKSGEAFIDFIGQVHKTKEQFGLENSPITIHCSAGVGRTGVFITLSIVLERMQYEGVLD
VFQTVRILRSQRIHMVQTEDQYQFCYRAALEYLGSFDHYTN

Protein features from InterProScan

Transcript Database ID Name Start End E.value
12 g5543.t2 CDD cd14554 R-PTP-LAR-2 32 270 7.38963E-174
11 g5543.t2 Gene3D G3DSA:3.90.190.10 Protein tyrosine phosphatase superfamily 2 281 2.6E-112
2 g5543.t2 PANTHER PTHR19134 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE 2 267 1.7E-160
3 g5543.t2 PANTHER PTHR19134:SF203 RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F 2 267 1.7E-160
9 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 66 73 2.2E-39
7 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 82 102 2.2E-39
6 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 166 183 2.2E-39
8 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 208 226 2.2E-39
4 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 239 254 2.2E-39
5 g5543.t2 PRINTS PR00700 Protein tyrosine phosphatase signature 255 265 2.2E-39
1 g5543.t2 Pfam PF00102 Protein-tyrosine phosphatase 37 271 3.2E-79
13 g5543.t2 ProSitePatterns PS00383 Tyrosine specific protein phosphatases active site. 211 221 -
17 g5543.t2 ProSiteProfiles PS50055 PTP type protein phosphatase family profile. 12 272 58.403
16 g5543.t2 ProSiteProfiles PS50056 Tyrosine specific protein phosphatases family profile. 189 263 21.493
15 g5543.t2 SMART SM00194 PTPc_3 11 274 4.9E-129
14 g5543.t2 SMART SM00404 ptp_7 167 271 1.0E-43
10 g5543.t2 SUPERFAMILY SSF52799 (Phosphotyrosine protein) phosphatases II 8 279 8.25E-102

Transmembrane regions from TMHMM

Disordered region

IUPRED3 score over 0.5 is predictive of a disordered region.

Data is missing for g5543/g5543.t2; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5543.t2.fa.iupred3.txt does not exist

GO terms from InterProScan

GOID TERM ONTOLOGY
GO:0006470 protein dephosphorylation BP
GO:0016311 dephosphorylation BP
GO:0004725 protein tyrosine phosphatase activity MF
GO:0016791 phosphatase activity MF

KEGG

Orthology

Pathway

This gene does not belong to any 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