General information for g5543.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Tyrosine-protein phosphatase Lar.
Parent gene
- The parent gene g5543 is located on chr_2: 10189830..10192754 (- strand)
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.t1 | TTS | g5543.t1 | 10189449 | 10189449 |
| chr_2 | g5543 | g5543.t1 | isoform | g5543.t1 | 10189830 | 10192754 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon1 | 10189830 | 10189898 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS1 | 10189830 | 10189898 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon2 | 10189969 | 10190099 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS2 | 10189969 | 10190099 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon3 | 10190157 | 10190266 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS3 | 10190157 | 10190266 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon4 | 10190332 | 10190563 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS4 | 10190332 | 10190563 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon5 | 10190622 | 10191036 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS5 | 10190622 | 10191036 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon6 | 10191112 | 10191565 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS6 | 10191112 | 10191565 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon7 | 10191623 | 10191841 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS7 | 10191623 | 10191841 |
| chr_2 | g5543 | g5543.t1 | exon | g5543.t1.exon8 | 10191907 | 10192754 |
| chr_2 | g5543 | g5543.t1 | cds | g5543.t1.CDS8 | 10191907 | 10192754 |
| chr_2 | g5543 | g5543.t1 | TSS | g5543.t1 | NA | NA |
Sequences
>g5543.t1 Gene=g5543 Length=2478
ATGGCCGCACCTCAACCTATGGTTGAACCAGACTTTTATGGTGTTGTCAATCATGAAGAG
ATTCAAGTGATTCTCCCACAAGCCTCTGAGGAATATGGTCCAATTTCGCATTATTATCTA
ATTGTGGTACCTGAAGATAAATCAAATTTACACAAACAACCTGATCAATTCCTTACTGAT
GAAATGCTGCCATCTCGCACAAATCGTCATGATATGTCAAATGCGCCTTATATTGCTGCC
ATGTTCTTGCAACGTAACATTCCTTACACATTCCATCTTGGCTCAGGCGACACATATCAC
AACTTTACTAACAAAAAATTGGAACGTGGTAAACGATACAGAATTTTCGTACGAGCTGTT
GTCGACACACCACAGAAACATCTGTACACTTCAAGCCCATTCTCAGAGTTTCTTGCACTC
GACATGCGAGAAGCGCCTGTTGGAGAACCACCACAACGTCCCGATCCAAATACAGCGTCA
CATGATGAGGGCATTCATGTTAAAGTTAATACAGCTGAGCAGGGACTAATTTGGGTTGTA
GTACCTATTATTGCAGCATTTGTATTATGCTTTTTCCTCATTATCGTATATATTGTAAAA
AGAAAAAATCAACCATGCAAGAATCCCGACACTGCTGTGACTCGTCCACTCATGGCAGCC
GATCTCGGTGGTCCAGCACCGACTGATCCCGTTGACATGCGTCGATTGAATTTCCAAACA
CCTGGAATGATTCATCACCCGCCAATTCCCATCTCAGAGCTTGCTAATCACATTGAGCGA
TTGAAAGCTAACGGAAACTTGAAGTTTTCTCAAGAGTATGAATCGATTGAGCCGGGACAA
CAATTCAGTTGGGAAAACTCGAATATGGAAATCAATAAACCGAAAAACAGATATGCAAAC
GTATGCGCATACGATCATAGTCGTGTTATTTTGTCAACAATTGAAGGTCAACCTGGAAGT
GATTACATTAATGCAAATTATTGTGATGGATATCGTAAGCACAATGCATATATTGCAACT
CAAGGACCGTTAACACACACTTTCGCTGATTTTTGGAGAATGATTTGGGAAGTGGAATCA
ACGACAATAGTAATGATGACAAGATTGGAAGAGAGAATGAGGAAAAAGTGTGATCAATAT
TGGCCCACAAGAGGATCAGAAACATATGGACAAATGACAGTTACAATAACGGCAACACAA
GAGCTGGCAACTTATAGCATAAGAACTTTCCATCTCAGTCGCGCTGGGCGCAACGAGTCA
AGAGAAATTAAACTTGTTCAATTTGTTGGTTGGCCAGACCATGGAGTGCCAGACAATCCT
GCACCATTTTTGCAATTCTTGCGTCGAACAAGATCTTTGACACCGAGTGAGTCAGGTCCT
ATTGTAGTTCACTGTTCGGCAGGTGTCGGTAGAACTGGCTGCTATATTGTCGTTGATTCG
ATGCTTGAAAGAATTGAAAAAGAGAAAATGGTTGACATTTATGGACATGTGACATGTCTG
AGAGCTCAACGTAATTATATGGTTCAAACTGAGGAACAATACATTTTCATACATGATGCT
TTACTTGAAGCTGTCGTCTGTGGCAACACAGAAATTCCCGCGACTGAACTGCATACACAC
ATTCAGAAATTAATGCAAATCATTCCGAGTGAAAATATATCGGCCATGGAGATGGAATTT
AAAAAGTTGGCCAACGTTAAAATAGACAGCTCAAAATTCGTATCAGCTAATAATCCCGTT
AATAAAGACAAGAATCGATTAGTTCATATTTTACCGTTTGAATCGACACGAGTTTGTTTA
TCAGTTGATCGTGGAATTGAGGGATCAGATTATATTAATGCCAGTTTCATCGATGGATAT
CGTTTTAGAATGGCCTATATTGCGACACAAGCGCCACTTCAAAATACTGCTGAAGATTTT
TGGCGTATGCTTTGGGAACATAATTCAACAATAATTGTTATGTTAACGAAATTAAAAGAA
ATGGGCAAAGAAAAATGCACACAATATTGGCCAGATACGAGATCTGTTCGTTATCAGTAT
TATGTGGTAGATCCAGTGGCAGAATATAATATGCCACAATATAAATTAAGAGAATTCAAA
GTTACTGATGCACGTGATGGAAGCAGCAGGACTGTGAGACAATTTCAATTCACAGAATGG
CCCGAGCAGGGTGTGCCTAAATCAGGTGAAGCATTTATTGATTTTATTGGTCAAGTGCAC
AAGACAAAAGAACAATTTGGATTAGAAAATTCTCCTATTACGATACATTGTTCAGCAGGT
GTTGGTCGAACTGGTGTTTTTATAACGCTAAGTATAGTCCTTGAACGAATGCAATATGAA
GGAGTCCTTGATGTATTTCAAACAGTTAGGATTTTACGATCTCAGCGAATTCACATGGTC
CAAACGGAGGATCAATATCAATTTTGTTATAGAGCAGCTTTGGAATATTTGGGTTCTTTC
GATCACTATACAAACTAA
>g5543.t1 Gene=g5543 Length=825
MAAPQPMVEPDFYGVVNHEEIQVILPQASEEYGPISHYYLIVVPEDKSNLHKQPDQFLTD
EMLPSRTNRHDMSNAPYIAAMFLQRNIPYTFHLGSGDTYHNFTNKKLERGKRYRIFVRAV
VDTPQKHLYTSSPFSEFLALDMREAPVGEPPQRPDPNTASHDEGIHVKVNTAEQGLIWVV
VPIIAAFVLCFFLIIVYIVKRKNQPCKNPDTAVTRPLMAADLGGPAPTDPVDMRRLNFQT
PGMIHHPPIPISELANHIERLKANGNLKFSQEYESIEPGQQFSWENSNMEINKPKNRYAN
VCAYDHSRVILSTIEGQPGSDYINANYCDGYRKHNAYIATQGPLTHTFADFWRMIWEVES
TTIVMMTRLEERMRKKCDQYWPTRGSETYGQMTVTITATQELATYSIRTFHLSRAGRNES
REIKLVQFVGWPDHGVPDNPAPFLQFLRRTRSLTPSESGPIVVHCSAGVGRTGCYIVVDS
MLERIEKEKMVDIYGHVTCLRAQRNYMVQTEEQYIFIHDALLEAVVCGNTEIPATELHTH
IQKLMQIIPSENISAMEMEFKKLANVKIDSSKFVSANNPVNKDKNRLVHILPFESTRVCL
SVDRGIEGSDYINASFIDGYRFRMAYIATQAPLQNTAEDFWRMLWEHNSTIIVMLTKLKE
MGKEKCTQYWPDTRSVRYQYYVVDPVAEYNMPQYKLREFKVTDARDGSSRTVRQFQFTEW
PEQGVPKSGEAFIDFIGQVHKTKEQFGLENSPITIHCSAGVGRTGVFITLSIVLERMQYE
GVLDVFQTVRILRSQRIHMVQTEDQYQFCYRAALEYLGSFDHYTN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 18 | g5543.t1 | CDD | cd14553 | R-PTPc-LAR-1 | 290 | 527 | 6.34621E-173 |
| 13 | g5543.t1 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 242 | 533 | 7.4E-120 |
| 14 | g5543.t1 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 534 | 825 | 5.1E-114 |
| 3 | g5543.t1 | PANTHER | PTHR19134 | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE | 67 | 811 | 0.0 |
| 4 | g5543.t1 | PANTHER | PTHR19134:SF203 | RECEPTOR-TYPE TYROSINE-PROTEIN PHOSPHATASE F | 67 | 811 | 0.0 |
| 5 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 321 | 328 | 3.2E-39 |
| 8 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 337 | 357 | 3.2E-39 |
| 10 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 421 | 438 | 3.2E-39 |
| 7 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 460 | 478 | 3.2E-39 |
| 6 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 491 | 506 | 3.2E-39 |
| 9 | g5543.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 507 | 517 | 3.2E-39 |
| 1 | g5543.t1 | Pfam | PF00102 | Protein-tyrosine phosphatase | 292 | 523 | 4.5E-83 |
| 2 | g5543.t1 | Pfam | PF00102 | Protein-tyrosine phosphatase | 581 | 815 | 5.0E-78 |
| 16 | g5543.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 1 | 175 | - |
| 17 | g5543.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 199 | - |
| 15 | g5543.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 200 | 825 | - |
| 25 | g5543.t1 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 463 | 473 | - |
| 24 | g5543.t1 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 755 | 765 | - |
| 28 | g5543.t1 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 269 | 524 | 58.487 |
| 26 | g5543.t1 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 441 | 515 | 20.929 |
| 29 | g5543.t1 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 556 | 816 | 58.403 |
| 27 | g5543.t1 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 733 | 807 | 21.493 |
| 23 | g5543.t1 | SMART | SM00194 | PTPc_3 | 268 | 526 | 1.1E-124 |
| 21 | g5543.t1 | SMART | SM00404 | ptp_7 | 422 | 523 | 2.3E-41 |
| 22 | g5543.t1 | SMART | SM00194 | PTPc_3 | 555 | 818 | 4.9E-129 |
| 20 | g5543.t1 | SMART | SM00404 | ptp_7 | 711 | 815 | 1.0E-43 |
| 11 | g5543.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 254 | 563 | 4.49E-105 |
| 12 | g5543.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 520 | 823 | 4.59E-103 |
| 19 | g5543.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 176 | 198 | - |
Transmembrane regions from TMHMM
Disordered region
IUPRED3 score over 0.5 is predictive of a disordered region.
Data is missing for g5543/g5543.t1; file /home/yuki.yoshida/nias/analysis/reanalysis/18_revice/midgebase/iupred3/g5543.t1.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
- This transcript has been annotated with K06777 (receptor-type tyrosine-protein phosphatase delta)
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.
