RetrogeneDB ID: | retro_mmus_3006 | ||
Retrocopy location | Organism: | Mouse (Mus musculus) | |
| Coordinates: | 7:18509975..18511478(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | None | |
| Aliases: | None | ||
| Status: | NOVEL | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | Mtmr2 | ||
| Ensembl ID: | ENSMUSG00000031918 | ||
| Aliases: | Mtmr2, 6030445P13Rik | ||
| Description: | myotubularin related protein 2 [Source:MGI Symbol;Acc:MGI:1924366] |
Retrocopy-Parental alignment summary:
>retro_mmus_3006
GCTTCCACTTCTCATTCAGAGAACTCGGTGCATAGCAAATCAGCTTCTGCTATATCATCAGATTCCATTTCAACTTCTGT
AGACAACTTTTCTCGTGATTTGAGGGTCCTGAGGGAGTCAAAGAAGTTAGCAGAAATGGAGGAACCAGCCCTGCTTCCAG
GAAAGAGCATTAAAGATATGGCCAAAGATGTGACTTACATATGTCCATTCACTGGTGCTGTACGAGGAACGCTGACTGTC
ACAAATTACAGATTATATTTCACGAGCATGGAGAAGGACCCCCTATTTGTTCTAGATGCTTCTCTTGGAGTGATAAGTAG
AGTAGAAAAGATTGGTGGTGCATCTAGCAGAGGTGAAAACTCTTATGGCCTTGAAACTGTGTGCAAGGATATCAGGAACT
TACGATTTGCTCATAAACCGGAGGGGCGAACAAGAAGATCCATATTTGAGAATCTAATGAAATATGCATTTCCTGTGTCT
AATGGCTTGCCTCTTTTTGCTTTTGAGTATAAAGAAGTATTCCCCGAAAATAGGTGGAAACTGTATGACCCTCTTCTAGA
GTACAGAAGTCAGGGAATTCCAAAAGAATGCTGGAGAATAACAAAGATAAATGAACTCTATGAACTCTGTGACACATATT
CTGCCCTCTTGGTTGTGCCAGCAAACATTCCTGATGAGAAGCTAAAGAGAGTGGCATCCTTTAGATCACGGGGCTGGATC
TCAGTTGCATCCTGGATTCATCCTGAAAGTCAAGCCACAGTCACTCGCTGCAGCCAGCCCATGGTTGGAGTGAGTGGGAA
GCAAAGCAAAGAGGATGAAAAGTACCTTCAGGCTATCATGGACTCCAATGCCCAGTCTCACAAAATATTTACATTTGATG
CTCAGCCAAGTCTCAGTGCTGTTGCCAATAAGGCAAAGGGGAGAGGTTATGAAAGTAAAGATGCCTATCAAAATGCAGAA
CTCATTTTTCTGGATATTCATAATATCGATGTTATGAGAGAATCATTACGGAAGCTTAAGGAGACTGTGTACCCCAACAT
TGAAGAAACTCACTGGTTGTCTAACTTAGAATCTACACACTGGCTGGAACACATTAAGCTCATTCTTACAGGGGCTCTTA
GGATTGCTGGCAAGGTCGAGTCTGGGAAGACGTCTGTGGTGGTAAACTGCATTGATGGATGGGATCGCACAGCTCAGCTC
ACTTCCCTGGCCATGGTCATGTTGAATGGATACTACCGAACCATACGAGGATTTGAAGTCCTTGTGGAGGAAGAATGGCT
GAGCTTTGGACATAGATTCCAACTAAGAGTTGGCCATGGAGATAAGAACCATGCTGATGCAGACAGATCACCTGTTTTCC
TTTAGTTTATTGACTGTGTCTGGCAAATGACAAGACAGTTCCCTACTGCATTTGAATTCAATGAGTATTTCCTCATTACC
ATCCTGGACCACTTGTACAGCTCTTTATTTGGAACATTCCTTTGTACTTGCCAAAAGAGCAGA
ORF - retro_mmus_3006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 90.82 % |
| Parental protein coverage: | 77.92 % |
| Number of stop codons detected: | 1 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | ASTSHSENSVHTKSASAISSDSISTSADNFSPDLRVLREANKLAEMEEPALLPGENIKDMAKDVTYICPF |
| ASTSHSENSVH.KSASAISSDSISTS.DNFS.DLRVLRE..KLAEMEEPALLPG..IKDMAKDVTYICPF | |
| Retrocopy | ASTSHSENSVHSKSASAISSDSISTSVDNFSRDLRVLRESKKLAEMEEPALLPGKSIKDMAKDVTYICPF |
| Parental | TGAVRGTLTVTSYRLYFKSMERDPPFVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP |
| TGAVRGTLTVT.YRLYF.SME.DP.FVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP | |
| Retrocopy | TGAVRGTLTVTNYRLYFTSMEKDPLFVLDASLGVISRVEKIGGASSRGENSYGLETVCKDIRNLRFAHKP |
| Parental | EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPENGWKLYDPLLEYRRQGIPNESWRITKINERYELC |
| EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPEN.WKLYDPLLEYR.QGIP.E.WRITKINE.YELC | |
| Retrocopy | EGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPENRWKLYDPLLEYRSQGIPKECWRITKINELYELC |
| Parental | DTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATVTRCSQPMVGVSGKRSKEDEKYLQAIM |
| DTY.ALLVVPANIPDE.LKRVASFRSRG.I.V.SWIHPESQATVTRCSQPMVGVSGK.SKEDEKYLQAIM | |
| Retrocopy | DTYSALLVVPANIPDEKLKRVASFRSRGWISVASWIHPESQATVTRCSQPMVGVSGKQSKEDEKYLQAIM |
| Parental | DSNAQSHKIFIFDARPSVNAVANKAKGGGYESEDAYQNAELVFLDIHNIHVMRESLRKLKEIVYPTIEET |
| DSNAQSHKIF.FDA.PS..AVANKAKG.GYES.DAYQNAEL.FLDIHNI.VMRESLRKLKE.VYP.IEET | |
| Retrocopy | DSNAQSHKIFTFDAQPSLSAVANKAKGRGYESKDAYQNAELIFLDIHNIDVMRESLRKLKETVYPNIEET |
| Parental | HWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHCSDGWDRTAQLTSLAMLMLDGYYRTIRGFEV |
| HWLSNLESTHWLEHIKLIL.GALRIA.KVESGKTSVVV.C.DGWDRTAQLTSLAM.ML.GYYRTIRGFEV | |
| Retrocopy | HWLSNLESTHWLEHIKLILTGALRIAGKVESGKTSVVVNCIDGWDRTAQLTSLAMVMLNGYYRTIRGFEV |
| Parental | LVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAFEFNEYFLITILDHLYSCLF |
| LVE.EWLSFGHRFQLRVGHGDKNHADADRSPVFL.FIDCVWQMTRQFPTAFEFNEYFLITILDHLYS.LF | |
| Retrocopy | LVEEEWLSFGHRFQLRVGHGDKNHADADRSPVFL*FIDCVWQMTRQFPTAFEFNEYFLITILDHLYSSLF |
| Parental | GTFLCNSEQQR |
| GTFLC.....R | |
| Retrocopy | GTFLCTCQKSR |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
Expression validation based on RNA-Seq data:
| Library | Retrocopy expression | Parental gene expression |
|---|---|---|
| SRP007412_brain | 0 .07 RPM | 42 .15 RPM |
| SRP007412_cerebellum | 0 .00 RPM | 46 .98 RPM |
| SRP007412_heart | 0 .06 RPM | 15 .63 RPM |
| SRP007412_kidney | 0 .10 RPM | 39 .89 RPM |
| SRP007412_liver | 0 .00 RPM | 23 .81 RPM |
| SRP007412_testis | 0 .05 RPM | 59 .55 RPM |
RNA Polymerase II activity near the 5' end of retro_mmus_3006 was not detected
No EST(s) were mapped for retro_mmus_3006 retrocopy.
No TSS is located nearby retro_mmus_3006 retrocopy 5' end.
retro_mmus_3006 was not experimentally validated.
Retrocopy orthology:
Retrocopy retro_mmus_3006 has 0 orthologous retrocopies within eutheria group .Parental genes homology:
Parental genes homology involve 2 parental genes, and 4 retrocopies.| Species | Parental gene accession | Retrocopies number | |
|---|---|---|---|
| Mus musculus | ENSMUSG00000031918 | 3 retrocopies |
retro_mmus_3004, retro_mmus_3005, retro_mmus_3006 ,
|
| Nomascus leucogenys | ENSNLEG00000007138 | 1 retrocopy |