General information for g13260.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Receptor-type tyrosine-protein phosphatase N2.
Parent gene
- The parent gene g13260 is located on chr_1: 28844910..28845862 (+ 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_1 | g13260 | g13260.t1 | isoform | g13260.t1 | 28837536 | 28845300 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon1 | 28837536 | 28837647 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS1 | 28837536 | 28837647 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon2 | 28840991 | 28841044 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS2 | 28840991 | 28841044 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon3 | 28841929 | 28841986 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS3 | 28841929 | 28841986 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon4 | 28842055 | 28842345 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS4 | 28842055 | 28842345 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon5 | 28842415 | 28844353 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS5 | 28842415 | 28844353 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon6 | 28844420 | 28844838 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS6 | 28844420 | 28844838 |
| chr_1 | g13260 | g13260.t1 | exon | g13260.t1.exon7 | 28844910 | 28845300 |
| chr_1 | g13260 | g13260.t1 | cds | g13260.t1.CDS7 | 28844910 | 28845300 |
| chr_1 | g13260 | g13260.t1 | TTS | g13260.t1 | 28845573 | 28845573 |
| chr_1 | g13260 | g13260.t1 | TSS | g13260.t1 | NA | NA |
Sequences
>g13260.t1 Gene=g13260 Length=3264
ATGTCAAATATTGACAAATGGATGAAATTATGGAAGGCACTGTTCTGTGGTAGTTTCCTA
ATAACCATCATATGCGATCATCTTGGCACTGTTACGGGTCAAGAGAATATCGGTTGCCTG
TTTGCGGAGCAACTGTGTGTTCCACATCTAGAATGGTGCTTTGATGATTTTGCATTTGGG
AAATGTCTTCCATATTATGAATCAGATCCACAGCAATTTGAACGTGAGCCGCTGACGCAA
GAGCAAGTCTCTATATTAAAACAAATGCTGCAGGAGCTTCATGCTGCTGGTCTTGACTGG
GATCATCCGTTCACTCAATGTCGCATGCAGAATGCCATGTTTGCAATGCGAAATCGAATC
GATATGGAACGCGACGCTTGCGTGTCTTTGGCACCTCCACCAATCATTCCGAAGTTTCTT
GATCCAACCAATCCGCTCGCCTTCATACGATTCACACAGCCCATCATTGATCTTAACGAT
GAGTACATTTACCCGCCTTTGAAGAAATCTTACGAGTATGAAAATATCCCCAAAACTCCA
CACCATCGACAACAACAACAACAGCCATCAATGGAGCAAATTCTATCATCACCTGACCAG
TATGAATTTCTTCAACGCGAGTATAATGTACCACCATCAAATGAGATTATCGATCCAGCA
GTAGAGAACGAAATGCTGAATGTACTTGAGCGAACGAATGATTTACAGAATCGTATTAGC
GACATCAAAAATCGTATGGAATTGCATCGAATGTTGGCAGAATATGAACAACAAAGTCGC
AAGATGCAAGAAGAAGAGCAACAACTTCCGTCACCAGTCGATGCTCTTTTCGATAGCGGA
GATGAAGAAGTAATTCCAGAATATGAAGAACAGCAACAACCACCATTATTCTTTGAGCGT
GATAATCGTCGAAGTGGATCGCATTTCAAAGAGCGAGAAGAAGAATTAATAAATGCTGAA
CGACTCAAAGATATTCTCGATGATTTACGAGAAGGAGCTTACGAGACCGAACTAGCTCAA
CAAGAACTCGAGCCAGAAGATTATCGTTCAACATCATTTAGAGAAGTGGCAAAGATTGAA
CATATTCCTGAGAAAAATGTTCAACATTATCAAATGGATGACGATGCAATACCAAAGTTC
TTTGACAATCGCAATCCACATAAACTTCGTCTGCCAGATGAAGAATATGAAGATGCAGAG
GCTAATGAATTACCAACTGTCTATCTTACACATCGCGATATGCTATCAAATTTCCGTGAT
GAAGTGCCTGAAGATGGTGGTGTTTATACGGAAGGTGGCCTGGTTTATGTTCCAAATCCC
TCAAGGAATGATGCAACAACAAATCTCTTACAAAGCATCATGGGTTTTCAACGTCATGAA
CGACTAGACGTGAAAAAACCAGGGCCACAACCACCACAAATACCTCCTTCATCTCAATCA
CCGCATGAAGCTCCTAAACTTGACGATCGCAATCTTGAACACCTGCCGGCACACATGAAA
ATGGATGAATTACCAAAAATGAAAAAGCAAATGCATAATGACTTGGATCATTCAAATTAT
TCTGTCGATACCGAATATGCTCATGTCATTTTGAAAAATTCCATTGACAACTGGAAAGAT
GGAGCACGAATTGTTCAAGCACTAGGTGAAATGCTCAATCTGCAAAACTTTTTCACTCAC
ACGCGTGTCGATAGGCATGAGGTGTCATTTAGAGTTGAACCAAATCCCGAGAAAAAGACA
GCTCTTGATGTGGCAAAATCTATCAATGACAGTCGTTTCAAAAACAATCTGTCGCGACGT
CTTGGTGTTTTAGTGCTACGTGCTGGTGTTGGCGATAAAGTGAAAGACTATGAAAACGAT
ATTAATGCGACAAAACTGGAGAATGCTGATGACACAGACATGACGAAGGTCATTTATTTC
ATGATTCTCATTGCTTTCCTTCTCGCTGTCGCACTGTGTGGTATGCTGTTGCTTCTTTAT
CGTCGCTTTTCATATAAAAAAGATAAATTGAGCAATCTACAAGCGGGACTATCAGGAGCA
GAAACGACAAGTAAAGACTATCAAGACCTTTGTCGAGCTCGAATGGCAGGTAAAAATGAC
ACTCAAACATCACGCGTTGCTTCACTATCAAAAGAAAATGAAAGACCGCCATCATCACGC
TCAAGTACATCATCATGGAGTGAAGAACCTGCACTCTCGAATATGGATATTTCTACTGGA
CATATGGTTCTCTCTTATATGGAAGATCATTTACGTAATAAAGGTCGATTGCAACGTGAG
TGGGAAGCATTATGTAGATATGAAGCTGAGCCTGGTGCACGTGAAGCAGCACTTCAAGAA
GAGTGTTCTTCATTTAATCGTATTGGTGCGCCTTTACCATTTGACCATTCTCGTGTTGTA
CTTAATCATCTAGCAAATGCAGAAGGAATGGATTATATAAATGCATCGACTATTACTGAC
CATGATCCAAGGGCACCAGCATATATTGCTGCACAGGCGCCACTGCAATCAACTCTCGCG
CATTTCTGGCAAATGGTTTGGGAGCAAGGATGCGTTGTCCTTGTAGCTCTCTGTCGATTG
CAAGAGAATGGCGAAAGTGCGTGCGCTCGCTATTGGCCTGAAGAAGGCGCCGAAGTGTAT
CATATTTATGAAGTTCATCTCGTCAGCGAACATGTCTGGTGCGATGAATATTTAGTTAGA
TCATTCTATTTGAAAAATCTACGAACTGGTGAGACTCGAACAGTCACACAGTTCCACTTC
CTTTCGTGGCCACAAGGAGGTATTCCATTGTCCGCGAAGGCGCTATTAGAATTTAGACGA
AAAGTCAATAAATCATATCGCGGCAGATCATGTCCGATAGTTGTGCATAGCAGTAATGGT
GCTGGTAGGACGGGTGCATACATACTTCTAGATCTTGTTCTCGGCAGAATGAATAAAGGT
GCTCGCGAAATAGATATTGCAGCAACGCTTGAACATTTAAGAGATCAGCGTGCTGGTCTT
GTTGAGACACGACAACAATTTGAATTTGTGCTCACGGCAGTGGCCGAAGAAGTTCATGCA
ATTCTCAAAGCTCTACCTCAAACACAGAGTACAGAGAAACGTGATGTAGAAAAAGAATCA
CCGGAGAAACAGTCGCCAGAGCAGCAGAAAAAAGCGACAGTGGCAGCAGTAACAACAACA
ACTGCTACATCTACAAAAGAGCAAGAGAATCAAAAAACTGAGAAAACTGATGACGACAAA
CCGGCTAACGAATCTAAAGGATAA
>g13260.t1 Gene=g13260 Length=1087
MSNIDKWMKLWKALFCGSFLITIICDHLGTVTGQENIGCLFAEQLCVPHLEWCFDDFAFG
KCLPYYESDPQQFEREPLTQEQVSILKQMLQELHAAGLDWDHPFTQCRMQNAMFAMRNRI
DMERDACVSLAPPPIIPKFLDPTNPLAFIRFTQPIIDLNDEYIYPPLKKSYEYENIPKTP
HHRQQQQQPSMEQILSSPDQYEFLQREYNVPPSNEIIDPAVENEMLNVLERTNDLQNRIS
DIKNRMELHRMLAEYEQQSRKMQEEEQQLPSPVDALFDSGDEEVIPEYEEQQQPPLFFER
DNRRSGSHFKEREEELINAERLKDILDDLREGAYETELAQQELEPEDYRSTSFREVAKIE
HIPEKNVQHYQMDDDAIPKFFDNRNPHKLRLPDEEYEDAEANELPTVYLTHRDMLSNFRD
EVPEDGGVYTEGGLVYVPNPSRNDATTNLLQSIMGFQRHERLDVKKPGPQPPQIPPSSQS
PHEAPKLDDRNLEHLPAHMKMDELPKMKKQMHNDLDHSNYSVDTEYAHVILKNSIDNWKD
GARIVQALGEMLNLQNFFTHTRVDRHEVSFRVEPNPEKKTALDVAKSINDSRFKNNLSRR
LGVLVLRAGVGDKVKDYENDINATKLENADDTDMTKVIYFMILIAFLLAVALCGMLLLLY
RRFSYKKDKLSNLQAGLSGAETTSKDYQDLCRARMAGKNDTQTSRVASLSKENERPPSSR
SSTSSWSEEPALSNMDISTGHMVLSYMEDHLRNKGRLQREWEALCRYEAEPGAREAALQE
ECSSFNRIGAPLPFDHSRVVLNHLANAEGMDYINASTITDHDPRAPAYIAAQAPLQSTLA
HFWQMVWEQGCVVLVALCRLQENGESACARYWPEEGAEVYHIYEVHLVSEHVWCDEYLVR
SFYLKNLRTGETRTVTQFHFLSWPQGGIPLSAKALLEFRRKVNKSYRGRSCPIVVHSSNG
AGRTGAYILLDLVLGRMNKGAREIDIAATLEHLRDQRAGLVETRQQFEFVLTAVAEEVHA
ILKALPQTQSTEKRDVEKESPEKQSPEQQKKATVAAVTTTTATSTKEQENQKTEKTDDDK
PANESKG
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 15 | g13260.t1 | Coils | Coil | Coil | 245 | 268 | - |
| 14 | g13260.t1 | Gene3D | G3DSA:3.30.70.2470 | - | 518 | 615 | 1.0E-12 |
| 13 | g13260.t1 | Gene3D | G3DSA:3.90.190.10 | Protein tyrosine phosphatase superfamily | 726 | 1026 | 8.3E-98 |
| 28 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 466 | 486 | - |
| 27 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 697 | 731 | - |
| 29 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1029 | 1087 | - |
| 26 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1030 | 1046 | - |
| 31 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1047 | 1067 | - |
| 30 | g13260.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 1068 | 1087 | - |
| 3 | g13260.t1 | PANTHER | PTHR46106 | IA-2 PROTEIN TYROSINE PHOSPHATASE, ISOFORM C | 45 | 1026 | 0.0 |
| 4 | g13260.t1 | PANTHER | PTHR46106:SF4 | IA-2 PROTEIN TYROSINE PHOSPHATASE, ISOFORM C | 45 | 1026 | 0.0 |
| 5 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 811 | 818 | 4.5E-28 |
| 6 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 828 | 848 | 4.5E-28 |
| 10 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 913 | 930 | 4.5E-28 |
| 7 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 952 | 970 | 4.5E-28 |
| 8 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 984 | 999 | 4.5E-28 |
| 9 | g13260.t1 | PRINTS | PR00700 | Protein tyrosine phosphatase signature | 1000 | 1010 | 4.5E-28 |
| 1 | g13260.t1 | Pfam | PF11548 | Protein-tyrosine phosphatase receptor IA-2 | 524 | 613 | 1.7E-26 |
| 2 | g13260.t1 | Pfam | PF00102 | Protein-tyrosine phosphatase | 785 | 1015 | 3.4E-65 |
| 18 | g13260.t1 | Phobius | SIGNAL_PEPTIDE | Signal peptide region | 1 | 33 | - |
| 19 | g13260.t1 | Phobius | SIGNAL_PEPTIDE_N_REGION | N-terminal region of a signal peptide. | 1 | 12 | - |
| 20 | g13260.t1 | Phobius | SIGNAL_PEPTIDE_H_REGION | Hydrophobic region of a signal peptide. | 13 | 25 | - |
| 22 | g13260.t1 | Phobius | SIGNAL_PEPTIDE_C_REGION | C-terminal region of a signal peptide. | 26 | 33 | - |
| 17 | g13260.t1 | Phobius | NON_CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the extracellular region. | 34 | 636 | - |
| 21 | g13260.t1 | Phobius | TRANSMEMBRANE | Region of a membrane-bound protein predicted to be embedded in the membrane. | 637 | 660 | - |
| 16 | g13260.t1 | Phobius | CYTOPLASMIC_DOMAIN | Region of a membrane-bound protein predicted to be outside the membrane, in the cytoplasm. | 661 | 1087 | - |
| 33 | g13260.t1 | ProSiteProfiles | PS50055 | PTP type protein phosphatase family profile. | 757 | 1017 | 46.314 |
| 32 | g13260.t1 | ProSiteProfiles | PS50056 | Tyrosine specific protein phosphatases family profile. | 936 | 1008 | 16.886 |
| 25 | g13260.t1 | SMART | SM00194 | PTPc_3 | 756 | 1019 | 7.6E-95 |
| 24 | g13260.t1 | SMART | SM00404 | ptp_7 | 914 | 1016 | 7.4E-32 |
| 11 | g13260.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 735 | 1022 | 1.03E-80 |
| 12 | g13260.t1 | SignalP_EUK | SignalP-noTM | SignalP-noTM | 1 | 33 | - |
| 23 | g13260.t1 | TMHMM | TMhelix | Region of a membrane-bound protein predicted to be embedded in the membrane. | 638 | 660 | - |
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:0030141 | secretory granule | CC |
| 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 K07817 (receptor-type tyrosine-protein phosphatase N)
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.
