General information for g3834.t1
Yuki Yoshida
22/1/2022
Gene loci information
Transcript annotation
- This transcript has been annotated as Myotubularin-related protein 3.
Parent gene
- The parent gene g3834 is located on chr_3: 28293759..28295674 (+ 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 | g3834 | g3834.t1 | TSS | g3834.t1 | 28291517 | 28291517 |
| chr_3 | g3834 | g3834.t1 | isoform | g3834.t1 | 28291665 | 28295674 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon1 | 28291665 | 28291676 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS1 | 28291665 | 28291676 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon2 | 28292107 | 28292263 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS2 | 28292107 | 28292263 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon3 | 28292332 | 28293429 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS3 | 28292332 | 28293429 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon4 | 28293535 | 28293632 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS4 | 28293535 | 28293632 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon5 | 28293690 | 28294664 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS5 | 28293690 | 28294664 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon6 | 28294718 | 28294818 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS6 | 28294718 | 28294818 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon7 | 28294898 | 28295048 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS7 | 28294898 | 28295048 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon8 | 28295109 | 28295237 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS8 | 28295109 | 28295237 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon9 | 28295309 | 28295453 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS9 | 28295309 | 28295453 |
| chr_3 | g3834 | g3834.t1 | exon | g3834.t1.exon10 | 28295514 | 28295674 |
| chr_3 | g3834 | g3834.t1 | cds | g3834.t1.CDS10 | 28295514 | 28295674 |
| chr_3 | g3834 | g3834.t1 | TTS | g3834.t1 | 28295766 | 28295766 |
Sequences
>g3834.t1 Gene=g3834 Length=3027
ATGGTTAAAGAAGTATTCGGAGAAGAACTTATAGAAGAAGAACATCAACAGCAACAAGCT
GAAGATATGCCTTCTTCTTCATATATGATAAAAATTAAGGCAACAGAGCTATTTCCCAAA
GAAAAAGTAGAAAAAGAAGATGACAGCTTGCAAATTCCGTTTGCTGAGCTGTCTGGTGAA
TTCGTAAAATATATTGGAAGATATGACAGTGGGATCTTGGCAATATCAAATTATCGTTTA
TATTTATCAAACTCAACAAAGTCTTTTGAGACCTCAATACCATTGCGTCTTATCGAAAAT
GTTTCAATTAAGGAGATGTTTCAGTTAGTGATTAGTTGCAAAGATGCATGTACACATGTC
TGCTCATTTTCAACAAACGAATTATGCAACGACTGGCACTCAAGAATTAGTGCTGCCACT
AGTGTTCCCGATCAACTCGAGAATCTTTTTGCTTTTGCATTTTACGCTTGGGAATCTGAA
AAGGAGTCATCACATGATCACGAATCAAATCGTTTGAAACATGCAATTAGTTATGATGTT
CACTTTAAAGAAGAACTTGACCGATTAAAATTTGATTTAAAAGGGGCATGGCGAGTTTCC
AATATCAATTCAGATTTCAAGCTTTGTTCATCTTATCCGAAACAACTTATTGTACCTGCA
TGTATTTCTGATGAAACACTCGCAGCTGTTGCAAATTTTCGTAGTTCAAAACGCATTCCC
ATTGTTACTTATCGACATCCATCTGGAGCTGTTATTGCAAGGTCTTCGCAACCTGAGGTC
GGCTGGCTTGGCTGGCGCAACAATAAAGATGAACAGCTTCTGAAAGCTCTTGCTGATGCT
TGCTCATTTGATAATGGGAAAATAAATTCGTCATCATTGCCAACTAAAGTCGAAAGTGAT
AGTGACCATTCTCTCGATACTTCAAATCCTGAAAAAGTAGATCTTGAGACACCTAAGAAA
ATTTTAATTATTGATGCACGAAGTTATGCATCAGCAGTAACAAATAGAGCTCGAGGAGGC
GGCGTTGAATGTGCAGAATACTATCCCAATGCTGAAATTGAGTTCATGAATTTGGGAAAT
ATTCATGTTATTCGAAAGTCATTTCAAAGTTTACGACAACTCTGTATTGATGCTGATATT
CCAAATTGGTTTAGTTTACTTGAGAAAACTAACTGGTTGCAGCATATTTCGGGTCTATTA
TCCGCTGCCAATATTGTTGTTCATGCAATAGAGAAAAATAATCGGCCCGTTCTTGTACAT
TGTTCAGATGGGTGGGATCGTACTTCGCAAATTTCTAGTATATCGCAATTGCTGCTTGAT
CCGTATTATAGAACTATGGAAGGATTTATGGTTTTAGTTGAAAAGGAATGGTTGGCATTT
GGCCACAAATTCGGTGATAGAGTTGGACACGGAGTTGGTAGTGATGATACAAATGAACGT
TGTCCAGTTTTTCTTCAATGGATTGACTGCGTATATCAGATTCATAATCAATTTCCTTGT
AGTTTTGAGTTTACAACATCATACCTCATTAAACTAGCTCAGCACGTGCACTCTTGCTTA
TTTGGCACATTTTTGTGCAACACTCTTAAAGAAAGAATTGAAAATTTCATTAACGAACGT
ACATTTTCCGTGTGGCCTTTCTTATCTACGCCCATTTACAAAAATCCTCTATATCAAACT
ACTCTTGACAAAGTCTTGTGGCCGTCGCATAGAATAAGTTCGCTGGTATTTTGGAGAGAA
TTATATGGTGGAAGTTTTCATACACCACATTCAAATGGAAATGATAATTTAAAGATATCG
AGTGATACGATCTATACTGAGACTGGTCTCATTAAAACGAGAAGTTTTGACGATTTAGTT
TCAGAAATTAAAAGCAGTAAAGATTCAGTGAGAAGACTTAGTGATCCCTCAGTATTTGCA
GATAGCAACACTATCTCAATGAGAGTTAGCATTTTGTCATGTGACAGTGGAACAAGCAAT
GGTCATAATGATGACATTAATAATCAGGAAAAAGGAATTAAAACCAATATTAATAATCAT
ATATTGCCGTTATGCACTAATAATAATAATCATATTATCAATAATCACAATAATGGTGAC
ATAAACATTGATGAACTCGCTAATAACGAGCAATCAACTACAGCAAAAGAAGAGATGATG
ATACAAACAAATCTCGATGTGAAAATTCCTGAGTGTACTATTGTTGAGCACCAAAAAAAT
AATGAAGAAAAAAAAGAAATAAAACGAGGAGTTGAAAAAGAAGACGAAAACAATCATGAA
GGTCAAGAACAAATTGCCGATGATGATTTAAATAACAAAGATGAGATTGATGGGCATAAA
CTTTCGATACAGATGATTGAAACAGTCGAGAATTTAGAGCAGCACTTCAAGAAGCTCAAG
TCAAATTTTCAAAATGGGCATTCAAAAAGTAAAAAAGAAAGCACATCATCAAATGATTCA
CAATTTTCAACGCCAGTTTTACGCTCAATAACACCAGCAACGCTCGAAAAAACCATTTCT
TCTGTGGATGGTCTTTCATTTGCTCTAAGTCAGGAAAATTTGCGATTGCAACAGTTAGTT
CATGAATATAAACTTAAAGAAGAGAAACTTTATTATGAACTGCTTGTAACAAGAAGAGCA
TTAGTGAATGCAACCTCATGTCAGTGTGGAAAAAACCAAAATAACCAAAGGGCTCATAGT
GCAGCCACATCTGAGGACCCACATCAAGAATATAATTCTGAAAATTCTGTTTGCTCATGG
GAGGCAGTCGATGAAAAACCTAATGATGGCCACAACAATCATGTTCCATGGATTCCTGAT
TTTGCAAGGAGCAAATGTAAAAATTGTCAAATTGAATTTTGGCTAGGAAGAAGACGGCAT
CATTGTCGACTTTGTATGGAAATATTCTGTGCAGATTGCAGTGATCATTTTGCTCAGTTG
CCAAATAATGAAAACATTCAATGTCAATATCCTGTGCGATTGTGTGAGCCTTGCTTCAAA
TCTATCGTCGAGAAAGAAACTAATTAA
>g3834.t1 Gene=g3834 Length=1008
MVKEVFGEELIEEEHQQQQAEDMPSSSYMIKIKATELFPKEKVEKEDDSLQIPFAELSGE
FVKYIGRYDSGILAISNYRLYLSNSTKSFETSIPLRLIENVSIKEMFQLVISCKDACTHV
CSFSTNELCNDWHSRISAATSVPDQLENLFAFAFYAWESEKESSHDHESNRLKHAISYDV
HFKEELDRLKFDLKGAWRVSNINSDFKLCSSYPKQLIVPACISDETLAAVANFRSSKRIP
IVTYRHPSGAVIARSSQPEVGWLGWRNNKDEQLLKALADACSFDNGKINSSSLPTKVESD
SDHSLDTSNPEKVDLETPKKILIIDARSYASAVTNRARGGGVECAEYYPNAEIEFMNLGN
IHVIRKSFQSLRQLCIDADIPNWFSLLEKTNWLQHISGLLSAANIVVHAIEKNNRPVLVH
CSDGWDRTSQISSISQLLLDPYYRTMEGFMVLVEKEWLAFGHKFGDRVGHGVGSDDTNER
CPVFLQWIDCVYQIHNQFPCSFEFTTSYLIKLAQHVHSCLFGTFLCNTLKERIENFINER
TFSVWPFLSTPIYKNPLYQTTLDKVLWPSHRISSLVFWRELYGGSFHTPHSNGNDNLKIS
SDTIYTETGLIKTRSFDDLVSEIKSSKDSVRRLSDPSVFADSNTISMRVSILSCDSGTSN
GHNDDINNQEKGIKTNINNHILPLCTNNNNHIINNHNNGDINIDELANNEQSTTAKEEMM
IQTNLDVKIPECTIVEHQKNNEEKKEIKRGVEKEDENNHEGQEQIADDDLNNKDEIDGHK
LSIQMIETVENLEQHFKKLKSNFQNGHSKSKKESTSSNDSQFSTPVLRSITPATLEKTIS
SVDGLSFALSQENLRLQQLVHEYKLKEEKLYYELLVTRRALVNATSCQCGKNQNNQRAHS
AATSEDPHQEYNSENSVCSWEAVDEKPNDGHNNHVPWIPDFARSKCKNCQIEFWLGRRRH
HCRLCMEIFCADCSDHFAQLPNNENIQCQYPVRLCEPCFKSIVEKETN
Protein features from InterProScan
| Transcript | Database | ID | Name | Start | End | E.value | |
|---|---|---|---|---|---|---|---|
| 10 | g3834.t1 | Coils | Coil | Coil | 734 | 754 | - |
| 9 | g3834.t1 | Coils | Coil | Coil | 849 | 869 | - |
| 8 | g3834.t1 | Gene3D | G3DSA:3.30.40.10 | Zinc/RING finger domain | 924 | 1007 | 3.1E-18 |
| 14 | g3834.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 741 | 765 | - |
| 15 | g3834.t1 | MobiDBLite | mobidb-lite | consensus disorder prediction | 804 | 823 | - |
| 3 | g3834.t1 | PANTHER | PTHR10807:SF75 | LD11744P | 16 | 787 | 5.6E-265 |
| 4 | g3834.t1 | PANTHER | PTHR10807 | MYOTUBULARIN-RELATED | 16 | 787 | 5.6E-265 |
| 2 | g3834.t1 | Pfam | PF06602 | Myotubularin-like phosphatase domain | 171 | 532 | 2.8E-135 |
| 1 | g3834.t1 | Pfam | PF01363 | FYVE zinc finger | 936 | 1002 | 4.8E-16 |
| 11 | g3834.t1 | ProSitePatterns | PS00383 | Tyrosine specific protein phosphatases active site. | 419 | 429 | - |
| 16 | g3834.t1 | ProSiteProfiles | PS51339 | Myotubularin phosphatase domain. | 176 | 582 | 117.635 |
| 17 | g3834.t1 | ProSiteProfiles | PS50178 | Zinc finger FYVE/FYVE-related type profile. | 940 | 1003 | 11.673 |
| 12 | g3834.t1 | SMART | SM00404 | ptp_7 | 385 | 517 | 0.0072 |
| 13 | g3834.t1 | SMART | SM00064 | fyve_4 | 932 | 1004 | 6.0E-16 |
| 5 | g3834.t1 | SUPERFAMILY | SSF50729 | PH domain-like | 62 | 153 | 4.73E-9 |
| 6 | g3834.t1 | SUPERFAMILY | SSF52799 | (Phosphotyrosine protein) phosphatases II | 179 | 583 | 1.5E-138 |
| 7 | g3834.t1 | SUPERFAMILY | SSF57903 | FYVE/PHD zinc finger | 936 | 1003 | 4.93E-15 |
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:0046872 | metal ion binding | MF |
| GO:0016311 | dephosphorylation | BP |
| GO:0004725 | protein tyrosine phosphatase activity | MF |
KEGG
Orthology
- This transcript has been annotated with K18082 (myotubularin-related protein 3/4)
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.
