RetrogeneDB ID:

retro_mmus_1021

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:13:62813081..62814787(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Me1
Ensembl ID:ENSMUSG00000032418
Aliases:Me1, D9Ertd267e, Mdh-1, Mod-1, Mod1
Description:malic enzyme 1, NADP(+)-dependent, cytosolic [Source:MGI Symbol;Acc:MGI:97043]


Retrocopy-Parental alignment summary:






>retro_mmus_1021
CCGAGCCCCCCCCGCCGCCGACACACCCACCAGCGCGGCTACCTGCTGACGCGGGACCGCATCTCAACAAGGACTTGGCT
TTTACTCTGGAAGAGAGACAGCAGTTGAACATTCATGGATTGTTGCCGCCCTGCATCATCAGCCAGGAACTCCAGGTCCT
TAGAATAATTAAGAATTTCGAGCGACTGAACTCTGACTTCGACAGGTATCTCCTGTTAATGGACCTGCAAGACAGAAATG
AGAAGCTCTTCTACAGCGTGCTCATGTCTGATGTTGAAAAGTTCATGCCTATTGTTTACACCCCCACCGTGGGCCTCGCA
TGCCAGCAGTACAGTTTGGCATTCCGGAAGCCAAGAGGCCTCTTTATTAGTATCCATGACAAAGGGCACATTGCTTCAGT
TCTTAATGCATGGCCAGAGGATGTCCTCAAGGCTATTGTGGTAACTGATGGAGAGCGCATCCTTGGCTTGGGAGACCTTG
GCTGTAATGGAATGGGCATCCCTATGGGTAAACTGGCCTTGTACACGGCATGTGGAGGGGTGAACCCACAACAGTGTCTA
CCCATCACTTTGGACGTGGGAACAGAAAATGAGTTACTTAAGGATCCACTGTACATCGGGCTGCGGCACCGGCGAGTCAG
AGGCCCTGAGTACGACGCCTTCCTGGATGAGTTCATGGAGGCAGCGTCTTCCAAATACTGCATGAATTGCCTTATTCAGT
TTGAAGATTTTGCCAATCGGAATGCATTTCGTCTCCTGAACAAGTATTGAAACAAGTGTTGCACATTTAACGATGATATT
CAAGGAACAGCGTCTGTTGCGGTTGCGGGTCTCCTTGCAGCTCTTCGAATTACCAAGAACAAGCTCTCTGATCAGACAGT
GCTGTTCCAGGGAGCTGGAGAGGCTGCCTTGGGGATTGCTCACTTGGTTGTTATGGCCATGGAGAAAGAAGGTTTATCAA
AGGAGAATGCTAGAAAGAAGACATGGTTGGTTGACTCAAAAGGACTAATAGTTAAGGGTCGTGCTTCTCTCACAGAAGAG
AAAGAGGTGTTTGCCCATGAACATGAAGAAATGAAGAATCTGGAAGCCATTGTTCAAAAGATAAAACCAACTGCTCTCAT
AGGAGTTGCTGCAATTGGTGGTGCTTTCACTGAACAAATTCTCAAGGATATGGCTGCCTTCAACGAGCGGCCCATCATCT
TTGCTTTGAGCAATCCGACCAGCAAAGCGGAGTGCTCTGCAGAGCAGTGCTACAAGGTGACCAAGGGACGTGCAATCTTT
GCCAGCGGCAGTCCTTTTGATCCAGTCACTCTCCCAGATGGACGGACTCTGTTTCCTGGCCAAGGCAACAATTCCTACGT
GTTCCCTGGAGTTGCTCTTGGGGTGGTGGCCTGCGGACTGAGACACATCGATGATAAGGTCTTCCTCACCACTGCTGAGG
TCATATCTCAGCAAGTGTCAGATAAACACCTGCAAGAAGGCCGGCTCTATCCTCCTTTGAATACCATTCGAGACGATTCG
TTGAAAATTGCAGTAAAGATTGTGCAAGATGCATACAAAGAAAAGATGGCCACTGTTTATCCTGAACCCCAAAACAAAGA
AGAAGTTGTCTCCTCCCAGATGTACAGCACTAATTATGACCAGATCCTACCTGATTGTTATCCGTGGCCTGCAGAAGTCC
AGAAATTACAGACCAAAGTCAACCAG

ORF - retro_mmus_1021 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.55 %
Parental protein coverage: 99.65 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPRAPRRRHTHQRGYLLTRD-PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR
P..PRRRHTHQRGYLLTRD.PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR
RetrocopyPSPPRRRHTHQRGYLLTRD<PHLNKDLAFTLEERQQLNIHGLLPPCIISQELQVLRIIKNFERLNSDFDR
ParentalYLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP
YLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP
RetrocopyYLLLMDLQDRNEKLFYSVLMSDVEKFMPIVYTPTVGLACQQYSLAFRKPRGLFISIHDKGHIASVLNAWP
ParentalEDVVKAIVVTDGERILGLGDLGCNGMGIPVGKLALYTACGGVNPQQCLPITLDVGTENEELLKDPLYIGL
EDV.KAIVVTDGERILGLGDLGCNGMGIP.GKLALYTACGGVNPQQCLPITLDVGTENE.LLKDPLYIGL
RetrocopyEDVLKAIVVTDGERILGLGDLGCNGMGIPMGKLALYTACGGVNPQQCLPITLDVGTENE-LLKDPLYIGL
ParentalRHRRVRGPEYDAFLDEFMEAASSKYGMNCLIQFEDFANRNAFRLLNKYRNKYCTFNDDIQGTASVAVAGL
RHRRVRGPEYDAFLDEFMEAASSKY.MNCLIQFEDFANRNAFRLLNKY.NK.CTFNDDIQGTASVAVAGL
RetrocopyRHRRVRGPEYDAFLDEFMEAASSKYCMNCLIQFEDFANRNAFRLLNKY*NKCCTFNDDIQGTASVAVAGL
ParentalLAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKKIWLVDSKGLIVKGRASLTEEK
LAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKK.WLVDSKGLIVKGRASLTEEK
RetrocopyLAALRITKNKLSDQTVLFQGAGEAALGIAHLVVMAMEKEGLSKENARKKTWLVDSKGLIVKGRASLTEEK
ParentalEVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY
EVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY
RetrocopyEVFAHEHEEMKNLEAIVQKIKPTALIGVAAIGGAFTEQILKDMAAFNERPIIFALSNPTSKAECSAEQCY
ParentalKVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD
KVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD
RetrocopyKVTKGRAIFASGSPFDPVTLPDGRTLFPGQGNNSYVFPGVALGVVACGLRHIDDKVFLTTAEVISQQVSD
ParentalKHLQEGRLYPPLNTIRGVSLKIAVKIVQDAYKEKMATVYPEPQNKEEFVSSQMYSTNYDQILPDCYPWPA
KHLQEGRLYPPLNTIR..SLKIAVKIVQDAYKEKMATVYPEPQNKEE.VSSQMYSTNYDQILPDCYPWPA
RetrocopyKHLQEGRLYPPLNTIRDDSLKIAVKIVQDAYKEKMATVYPEPQNKEEVVSSQMYSTNYDQILPDCYPWPA
ParentalEVQKIQTKVNQ
EVQK.QTKVNQ
RetrocopyEVQKLQTKVNQ

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 .44 RPM 27 .61 RPM
SRP007412_cerebellum 0 .69 RPM 24 .79 RPM
SRP007412_heart 0 .28 RPM 64 .60 RPM
SRP007412_kidney 3 .58 RPM 163 .10 RPM
SRP007412_liver 2 .10 RPM 84 .63 RPM
SRP007412_testis 4 .39 RPM 135 .71 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1021 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1021 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1021 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1021 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1021 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000090641 retrocopy
retro_cjac_2740,
Mus musculus ENSMUSG00000032418 1 retrocopy
retro_mmus_1021 ,


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