RetrogeneDB ID:

retro_mmus_3005

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:7:18454914..18456414(-)
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_3005
AAGAGCATTAAAGATATGGCCAAAGATGTGACTTACATATGTCCATTCACTGGTGCTGTACGAGGAACGCTGACTGTCAC
AAATTACAGATTATGTTTTAAGAGCATGGAGCAGGACCCCCCATTTGTTCTAGATGCTTCTCTTGGAGTGATAAGTACAG
TAGAAAAAATAGTAGTGCATCTAGCCAAGGTGAAAACTCTTATGGCCTTGAAACTGTGTGCAAGGATATCAGGAACTTAG
AATTTGCTCTTAAACCGGAGGGGCGAACAAGAAGATCCATATTTAAGAATCTAATGAAATATGCATTTCCTGTGTCTAAT
AGCCTGCCTCTTTTTGCTTTTGAGTATAAAGAAGTATTCCCTGAAAATGGGTGGAAACTGTATGACCCTCTTCTAGAGTA
CAGAAGTCAGGGAATTCCAAAAGAAAGCTGGAGAATAACAAAGATAAATGCACGTTATGAACTCTGTGACACATATCCTG
CCCTCTTAGTTGTGCCAGCAAACATTCCTGATGAGAAGCTAAAGAGAGTGGCATCCTTTAGGTCACTGGGCCAGATCCCA
GATGCATCTTGGATTCATCCTGAAAGTCAAGCCACAGTCACTCGCTGCAGCCAGCCCATGGTTGGAGTGAGCAGGAAGTG
CATTAAAGAGGATGAGAAGTACCTTCAGGCTATCATGGACTCCAATGCCCAGTCTCACAAAATATTTATATTTGATGCTC
GGCCAAGTGTCAGTGCTGTTGCCAATAAGGCAAAGGGGGGGTTATGAAAGTGAAGATGCCTATCAAAATGCAGAACTCAT
TTTTCTGGATATTCATAATATCCATGTTATGAGAAAATCATTATGGAAGCTTAAGGAGATTGTGTACTCCAACATTGAAG
AAACTCACTGGTTGTCTAACTTAGAATCTAAACACTGGCTGGAACACATTAAGCTCATTCTTGCAGGGGCTCTTAGGATT
GCTGGCAAGGTCGAGTCTGGGAAGATGTCTGTGGTGGTGCACTGCAGTGATGGATGTCATTGCACAACTCAGCTCACGTC
CCTGGCCATGCTCACGTTGAATGGATACTACCGAAACATAAGAGGACTTGAAGTCCTTGTGGAGAAAGAATGGCTGAGCT
TTGGACATAGATTCCAACTAAGAGTTGGCCGTGGAGATAAGAACCATGCTGATGCAGACAGATCACCTGTTTTCCTTTAG
TTTATTGACTGTGTCTGGCAAATGACAAGACAGTTCCCTACTATATTTGAATTCAATGAGTATTTTCTCATTACCATCCT
GGACCACTTGTACAGCTTTTTATTTGGAACACTCCTTTGTAACATCGAACAGCAGAGGGGAAAAGCGAATCTTCCTAAGA
AGACAGTGTTACTGTGGTCCTATATAAATAGCCAGCTGGAAGAATTTACTAATCCTCTTTATGGAAGCTACTTCAATCAT
ATCCTTTACCCAGTAGCCAGCATGCCCCACCTAGAACTCTGGGTGGGACATTATGTAAGG

ORF - retro_mmus_3005 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.49 %
Parental protein coverage: 87.74 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalENIKDMAKDVTYICPFTGAVRGTLTVTSYRLYFKSMERDPPFVLDASLGVISRVEKI-GGASSRGENSYG
..IKDMAKDVTYICPFTGAVRGTLTVT.YRL.FKSME.DPPFVLDASLGVIS.VEKI...ASS.GENSYG
RetrocopyKSIKDMAKDVTYICPFTGAVRGTLTVTNYRLCFKSMEQDPPFVLDASLGVISTVEKI<SSASSQGENSYG
ParentalLETVCKDIRNLRFAHKPEGRTRRSIFENLMKYAFPVSNGLPLFAFEYKEVFPENGWKLYDPLLEYRRQGI
LETVCKDIRNL.FA.KPEGRTRRSIF.NLMKYAFPVSN.LPLFAFEYKEVFPENGWKLYDPLLEYR.QGI
RetrocopyLETVCKDIRNLEFALKPEGRTRRSIFKNLMKYAFPVSNSLPLFAFEYKEVFPENGWKLYDPLLEYRSQGI
ParentalPNESWRITKINERYELCDTYPALLVVPANIPDEELKRVASFRSRGRIPVLSWIHPESQATVTRCSQPMVG
P.ESWRITKIN.RYELCDTYPALLVVPANIPDE.LKRVASFRS.G.IP..SWIHPESQATVTRCSQPMVG
RetrocopyPKESWRITKINARYELCDTYPALLVVPANIPDEKLKRVASFRSLGQIPDASWIHPESQATVTRCSQPMVG
ParentalVSGKRSKEDEKYLQAIMDSNAQSHKIFIFDARPSVNAVANKA-KGG-GYESEDAYQNAELVFLDIHNIHV
VS.K..KEDEKYLQAIMDSNAQSHKIFIFDARPSV.AVANKA.KGG.GYESEDAYQNAEL.FLDIHNIHV
RetrocopyVSRKCIKEDEKYLQAIMDSNAQSHKIFIFDARPSVSAVANKA<KGG<GYESEDAYQNAELIFLDIHNIHV
ParentalMRESLRKLKEIVYPTIEETHWLSNLESTHWLEHIKLILAGALRIADKVESGKTSVVVHCSDGWDRTAQLT
MR.SL.KLKEIVY..IEETHWLSNLES.HWLEHIKLILAGALRIA.KVESGK.SVVVHCSDG...T.QLT
RetrocopyMRKSLWKLKEIVYSNIEETHWLSNLESKHWLEHIKLILAGALRIAGKVESGKMSVVVHCSDGCHCTTQLT
ParentalSLAMLMLDGYYRTIRGFEVLVEKEWLSFGHRFQLRVGHGDKNHADADRSPVFLQFIDCVWQMTRQFPTAF
SLAML.L.GYYR.IRG.EVLVEKEWLSFGHRFQLRVG.GDKNHADADRSPVFL.FIDCVWQMTRQFPT.F
RetrocopySLAMLTLNGYYRNIRGLEVLVEKEWLSFGHRFQLRVGRGDKNHADADRSPVFL*FIDCVWQMTRQFPTIF
ParentalEFNEYFLITILDHLYSCLFGTFLCNSEQQRGKENLPKKTVSLWSYINSQLEDFTNPLYGSYSNHVLYPVA
EFNEYFLITILDHLYS.LFGT.LCN.EQQRGK.NLPKKTV.LWSYINSQLE.FTNPLYGSY.NH.LYPVA
RetrocopyEFNEYFLITILDHLYSFLFGTLLCNIEQQRGKANLPKKTVLLWSYINSQLEEFTNPLYGSYFNHILYPVA
ParentalSMRHLELWVGYYIR
SM.HLELWVG.Y.R
RetrocopySMPHLELWVGHYVR

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .02 RPM 42 .15 RPM
SRP007412_cerebellum 0 .00 RPM 46 .98 RPM
SRP007412_heart 0 .00 RPM 15 .63 RPM
SRP007412_kidney 0 .00 RPM 39 .89 RPM
SRP007412_liver 0 .00 RPM 23 .81 RPM
SRP007412_testis 0 .00 RPM 59 .55 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3005 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3005 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3005 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3005 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3005 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 ENSNLEG000000071381 retrocopy
retro_nleu_2239,


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