General information for g2603.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Protein phosphatase 1D.
Parent gene
- The parent gene g2603 is located on chr_3: 19010038..19010961 (- 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_3 | g2603 | g2603.t1 | TTS | g2603.t1 | 19006301 | 19006301 |
| chr_3 | g2603 | g2603.t1 | isoform | g2603.t1 | 19006746 | 19010038 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon1 | 19006746 | 19008393 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS1 | 19006746 | 19008393 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon2 | 19008457 | 19008898 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS2 | 19008457 | 19008898 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon3 | 19009320 | 19009382 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS3 | 19009320 | 19009382 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon4 | 19009488 | 19009579 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS4 | 19009488 | 19009579 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon5 | 19009764 | 19009860 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS5 | 19009764 | 19009860 |
| chr_3 | g2603 | g2603.t1 | exon | g2603.t1.exon6 | 19009972 | 19010038 |
| chr_3 | g2603 | g2603.t1 | cds | g2603.t1.CDS6 | 19009972 | 19010038 |
| chr_3 | g2603 | g2603.t1 | TSS | g2603.t1 | 19010126 | 19010126 |
Sequences
>g2603.t1 Gene=g2603 Length=2409
ATGAGCATAAAAAGTTGTAAAAGTAATGAAAGGATCGGCCTACGTGTGACGGCTTACAGT
GATATGGGATGTCGGAGATATATGGAAGATTGTTTTAGTGTGGCTTATCAGAAGAGTAAC
GATGGCAAGGATCTTGAATTTGCGTATTTTGGCATGTTCGATGGACATGGTGGCGATTGT
GCTGCAAAATTTGCTAAAGATCATTTAATGAACTTTATTGTTGATCAACCGGGATTTTGG
TCAGAGAATGATGAAGATATTCTGCAAGCAATTAAGGAAGGTTTTAATGAATGTCACATG
GCCATGTGGAGGGACTTAGACAACTGGCCACCAACAAGTAGTGGACTCCCAAGTACGGCT
GGTACAACAGCTAGCATAGCATTTATTCGTAAAGGTAAATTGTATATTGGGCATTGTGGA
GATTCTGGAATAGTGCTTGCAAAAGAACAACATGACTCATCGTGGAAAGCAGTGCCGCTA
ACGCTTGATCATAAACCCGATAGCATTTTAGAAAAGCAGCGTATTGAAGCTTGTGGAGGA
AAAGTTGTTGAAAAACAAGGAATTCATAGAGTAGTATGGTATCGTCCAAAATATCCACAT
CAAGGACCAATAAGAAGAAATACAAGGATCGAAGAGATTCCTTTTTTAGCTGTTGCTCGT
TCGTTAGGAGACTTGTGGTCCTACAATTTGAAAACTCAAAAATTTATGGTTTCACCAGAA
CCCGATGTTTCAGTTTATGAGATAAATACGCTCACTGACAAATGTCTAATTTTTGCGAGT
GATGGGCTTTGGAATATAATGGAAGCACAAATGGCTGCAAATCTTGTACATGAAGCAGAA
TCAGCGAATGAACAAAATGCAAAAATTGGAATGAAAAGTTGGAGAAATCCTTCACGTTAT
CTTGTAGATATAGCGCTTCAACGATGGCGAGATAATCGTTTACGATCTGATAACACATCA
GTTGTTTGTGTGATGCTGGATATTCCAAATAAGAAAAATAATAGTAACATTTTTGGCTGT
ATGCAACAACAAGAACAAAATAATTGTAGAACAATATATGATTATAGCACAAATGAGGCA
TATAATTTGGATTATATGGATATAAATTCATATACAAATGAAGATATTGAACGTCAAAAT
TATAATTTATTAACACCTGCATCTTATCAAGACTTTTTCTCTTCTCATTCACATCTATCA
AATCAATTACCATCATTTTCGAGTGAAAGAGGCTATCAAAATTTATCACAATCAACTTCT
TCATCATCAACCTCGCTGTCAAATTATGAGAATTCAATTTCAGCTGAATTAACGTATCAT
ACAAGTAGCAATGAAAGTGCCTTTGTAAAAGGTTGCTGTCCTAATGAGCGTTTCATGTTA
GCAAAAGCTAATGAGCACATAAATTATCATATGAGCTACGAACATCATAAAGAAATGTAT
CGAAGTATGGCTCAACAGCCTCTTCCGCCGTTGCATTACGCATATCGACCAGTTGTTTCA
CAATCCTATTTAGGACTCCCATCTATAAATGATAACAGTTTCAATCATTTTACTCCACGT
CCAATGGAACGGTATAATTATTTACGTCCAACTGAGGCTGAATTTCAAGAATTACATAAA
GCAACTGAAGAAGAGGAAGATGAAGGTGGAGAAAGTACTTCATTAGAAAAGGAACCGAAT
GTTGAGAGCGATATAGATACAGATGATGGAGAAATGGAATGGTCAGATGATGAAGAAGAA
GAGAAAAATAATGAAGAAGTCAATGTAAATACAAAAACAACTGTATCTACCAATAATGAA
GCGGAAACAAATGAGAACGATGATATCATGGAAATGAAAAATTCAGATGATTCAATACAA
ATTTTTGAAATTTCTTCATCAAATATTGGCATTAGTGGGAAATCTAAAAACAAAGATAAA
ACTAATGAAAAGAACAAAGAAAATTCAGAAACACCCGTTCTTAAGCGTAAACCAAACAAA
TCTCAAGTTAAAGGAAGGTATTATGAGACACGTCAAAAAAATCGGAAAATGAGATCGGGA
AATATATGCAGTGGCGTTCAAAAGACAATTACAAAAGATAAACAGAGAAAAATTTCTCGG
TGTGTAAAGAAAACTGTTAAAGTACTCAATGATCTTAAATCAAGTACATCGATTGCATTA
AAAAAATTGGAATCACTTTCAATAATTAAAACAGCAGCAGCATCAAAATCGAACAAACCA
TGTAAAACCAATAATATTCCTACTGTTTCATCCAACGACAATAACAGCAAGTCCTCCACG
ACAAAAATCTTACGCAGCTCACAGATTTCAGTAAAAAAAGCAAAGAATAGTTTAATTCGC
AATTTAAGAAGCAATGCAGTTTTAACTGAAAAATCAATTCAACGTAAAAGAAATTCAAAA
ATAAAATAG
>g2603.t1 Gene=g2603 Length=802
MSIKSCKSNERIGLRVTAYSDMGCRRYMEDCFSVAYQKSNDGKDLEFAYFGMFDGHGGDC
AAKFAKDHLMNFIVDQPGFWSENDEDILQAIKEGFNECHMAMWRDLDNWPPTSSGLPSTA
GTTASIAFIRKGKLYIGHCGDSGIVLAKEQHDSSWKAVPLTLDHKPDSILEKQRIEACGG
KVVEKQGIHRVVWYRPKYPHQGPIRRNTRIEEIPFLAVARSLGDLWSYNLKTQKFMVSPE
PDVSVYEINTLTDKCLIFASDGLWNIMEAQMAANLVHEAESANEQNAKIGMKSWRNPSRY
LVDIALQRWRDNRLRSDNTSVVCVMLDIPNKKNNSNIFGCMQQQEQNNCRTIYDYSTNEA
YNLDYMDINSYTNEDIERQNYNLLTPASYQDFFSSHSHLSNQLPSFSSERGYQNLSQSTS
SSSTSLSNYENSISAELTYHTSSNESAFVKGCCPNERFMLAKANEHINYHMSYEHHKEMY
RSMAQQPLPPLHYAYRPVVSQSYLGLPSINDNSFNHFTPRPMERYNYLRPTEAEFQELHK
ATEEEEDEGGESTSLEKEPNVESDIDTDDGEMEWSDDEEEEKNNEEVNVNTKTTVSTNNE
AETNENDDIMEMKNSDDSIQIFEISSSNIGISGKSKNKDKTNEKNKENSETPVLKRKPNK
SQVKGRYYETRQKNRKMRSGNICSGVQKTITKDKQRKISRCVKKTVKVLNDLKSSTSIAL
KKLESLSIIKTAAASKSNKPCKTNNIPTVSSNDNNSKSSTTKILRSSQISVKKAKNSLIR
NLRSNAVLTEKSIQRKRNSKIK
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 6 | g2603.t1 | CDD | cd00143 | PP2Cc | 15 | 324 | 7.38743E-59 |
| 5 | g2603.t1 | Gene3D | G3DSA:3.60.40.10 | Phosphatase 2c; Domain 1 | 2 | 328 | 2.5E-75 |
| 13 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 541 | 611 | - |
| 11 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 562 | 584 | - |
| 10 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 588 | 603 | - |
| 9 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 630 | 664 | - |
| 14 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 636 | 654 | - |
| 12 | g2603.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 734 | 765 | - |
| 2 | g2603.t1 | PANTHER | PTHR47992 | ALPHABET, ISOFORM E-RELATED | 7 | 564 | 1.0E-145 |
| 3 | g2603.t1 | PANTHER | PTHR47992:SF79 | PROTEIN PHOSPHATASE 1D | 7 | 564 | 1.0E-145 |
| 1 | g2603.t1 | Pfam | PF00481 | Protein phosphatase 2C | 23 | 287 | 1.1E-56 |
| 7 | g2603.t1 | ProSitePatterns | PS01032 | PPM-type phosphatase domain signature. | 49 | 57 | - |
| 15 | g2603.t1 | ProSiteProfiles | PS51746 | PPM-type phosphatase domain profile. | 15 | 326 | 37.796 |
| 8 | g2603.t1 | SMART | SM00332 | PP2C_4 | 6 | 324 | 7.4E-59 |
| 4 | g2603.t1 | SUPERFAMILY | SSF81606 | PP2C-like | 12 | 327 | 7.72E-58 |
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:0043169 | cation binding | MF |
| GO:0016791 | phosphatase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K10147 (protein phosphatase 1D)
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.
