RetrogeneDB ID:

retro_mmus_1339

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:15:38990233..38992007(+)
Located in intron of:ENSMUSG00000097875
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Atad3a
Ensembl ID:ENSMUSG00000029036
Aliases:Atad3a, 2400004H09Rik, Atad3, Tob3, mKIAA1273
Description:ATPase family, AAA domain containing 3A [Source:MGI Symbol;Acc:MGI:1919214]


Retrocopy-Parental alignment summary:






>retro_mmus_1339
ATGTCGTGGCTCTTCGGCATCAAGGGTCCTAAGGGCGAAGGCACAGGGCCTCCGCTGCCCTTGCCGCCCGCTCAACCTGG
GGCGGAGGGCGGCGGTGACCGCGGTGCGGGAGACCGGCCATCGCCCAAGGACAAATGGAGCAACTTCGACCCGACGGGCC
TGGAACGTGCGGCCAAAGTGGCGCGCGAGTTGGAGCACTCGCGCCATGCCAAGGAGGCACGGAGTCTTGCACAGATGCAG
GAGCAGACACTGCAGCTGGAACAACAGTCCAAGCTCAAGGAGTACGAAGCTGCCGTAGAGCAGCTGAAGAGTGAACAGAT
CCGTGTGCAAGCCGAGGAAAGAAGGAAAACCCTGACTGAAGAGACACGACAGCACCAGGCTAGGGCCCAGTACCAGGATA
AGCTAGCTCGACAACGCTATGAGGACCAGCTGAAACAACAGCAACTTCTGAATGGAGAGAATTTAAGGAAACAAGAGGAG
TCTGTGCAGAAACAGGAGGCCATACGGCGAGCCACTGTGGAGCGCGAGATGGAGCTGCGGCATAAAAAACGAGATGTTGC
GGGTGGAAGCTGAAGCCGGAGCACGGGTCAAGGCTGATCAAGAGAATGCAGATATCATCCGGGAACAGATTTGACTCAAG
GCTGCTGAGCACCTCCAGACAATCTTGGAGTCTATCAGGACAGCTGGAACCTTGTTTGGTGAAGGATTCCGTGCCTTTGT
GACAGACTGGGACAAAGTGACAGCTACGGTGGCTGGGTTGACACTATTAGCTGTTGGAGTCTATTCTGCCAAGAATGCTA
CCTCTGTTGCTGGTCGGTATATTGAGGCCCGATTGGGAAAGCCGTCCTTGGTGAGAGAGACCTCCCGAATCTCAGTGCTA
GAGGCATTGAGGCATCCCATCCAGGTCAGCAGGCGACTGGTCAGCAGACCCCAGGATGCATTGGAGGGCGTCATCCTCAG
TCCTAGCCTGGAGGCACGGGTACGAAATATTGCCATCGCAACAAGAAATACCAAGAAGAACAAAAGCCTGTATAGAAACG
TCCTGATGTATGGGCCCCCGGGGACTGGCAAGACACTATTTTCCAAGAAACTTGCACTGCATTCAGGCATGGACTACGCC
ATCATGACAGGCGGGGACGTGGCCCCAATGGGGAGGGAGGGTGTGACTGCCGTGCACGAGGTCTTTGAATGGGCAAGCAC
CAACCGACGAGGCCTCCTGCTCTTTGTGGATGAAGCAGATGCCTTCCTCAGGAAACGAGCGACTGAAAAGATAAGTGAAG
AGCTCAGGGCTACTCTGAATGAATTCCTACATAGGACAGGACAACACAGTAGTAAGTTCATGCTGGTTGTGGCCAGTAAC
CAGCCTGAGCAGTTTGATTGGGCTATCAATGACCGCGTTGACGAGATGGTCTGCTTTGCCCTGCCATAGCGGGAGGAGCG
AGAGCACCTGGTGAGAATGTATTTTGACAAGTATGTCCTTAAGCCGGCCACAGAAGGAAAGCAATGCTTGAAGGTGGCCC
AGTTTGACCACGGAAAGAAATGCTAGGAGGTCGCCCAGCTGAAGGAGGGGATGTCAGGCCGGGAGATTGCTCAGCTTGCT
GTGGTGTGGCAGGCCATAGCATATTCATCTGAGGACGGAGTCCTCACGGAGGCTATGATGGATGCCCGTGTGCAGGATGC
TGTGCAGCAGCACCAGCAGAAGATGCAGTGGCTTAAAGTAGTGAGACCCGATTCCCAGACCAACAAGCCGCCACATCCTT
CACTCCTCAGCTGT

ORF - retro_mmus_1339 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAKAARELEHSRHA
MSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAK.ARELEHSRHA
RetrocopyMSWLFGIKGPKGEGTGPPLPLPPAQPGAEGGGDRGAGDRPSPKDKWSNFDPTGLERAAKVARELEHSRHA
ParentalKEALSLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY
KEA.SLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY
RetrocopyKEARSLAQMQEQTLQLEQQSKLKEYEAAVEQLKSEQIRVQAEERRKTLTEETRQHQARAQYQDKLARQRY
ParentalEDQLKQQQLLNEENLRKQEESVQKQEAIRRATVEREMELRHK-NEMLRVEAEARARAKADRENADIIREQ
EDQLKQQQLLN.ENLRKQEESVQKQEAIRRATVEREMELRHK.NEMLRVEAEA.AR.KAD.ENADIIREQ
RetrocopyEDQLKQQQLLNGENLRKQEESVQKQEAIRRATVEREMELRHK>NEMLRVEAEAGARVKADQENADIIREQ
ParentalIRLKAAEHRQTILESIRTAGTLLGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG
I.LKAAEH.QTILESIRTAGTL.GEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG
RetrocopyI*LKAAEHLQTILESIRTAGTLFGEGFRAFVTDWDKVTATVAGLTLLAVGVYSAKNATSVAGRYIEARLG
ParentalKPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVRDIAIATRNTKKNKSLYRNVLM
KPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVR.IAIATRNTKKNKSLYRNVLM
RetrocopyKPSLVRETSRISVLEALRHPIQVSRRLVSRPQDALEGVILSPSLEARVRNIAIATRNTKKNKSLYRNVLM
ParentalYGPPGTGKTLFAKKLALHSGMDYAIMTGGDVAPMGREGVTAMHKVFDWASTSRRGLLLFVDEADAFLRKR
YGPPGTGKTLF.KKLALHSGMDYAIMTGGDVAPMGREGVTA.H.VF.WAST.RRGLLLFVDEADAFLRKR
RetrocopyYGPPGTGKTLFSKKLALHSGMDYAIMTGGDVAPMGREGVTAVHEVFEWASTNRRGLLLFVDEADAFLRKR
ParentalATEKISEDLRATLNAFLHRTGQHSSKFMLVLASNQPEQFDWAINDRIDEMVCFALPQREERERLVRMYFD
ATEKISE.LRATLN.FLHRTGQHSSKFMLV.ASNQPEQFDWAINDR.DEMVCFALP.REERE.LVRMYFD
RetrocopyATEKISEELRATLNEFLHRTGQHSSKFMLVVASNQPEQFDWAINDRVDEMVCFALP*REEREHLVRMYFD
ParentalKYVLKPATEGKQRLKVAQFDYGKKCSEVAQLTEGMSGREIAQLAVAWQAMAYSSEDGVLTEAMMDARVQD
KYVLKPATEGKQ.LKVAQFD.GKKC.EVAQL.EGMSGREIAQLAV.WQA.AYSSEDGVLTEAMMDARVQD
RetrocopyKYVLKPATEGKQCLKVAQFDHGKKC*EVAQLKEGMSGREIAQLAVVWQAIAYSSEDGVLTEAMMDARVQD
ParentalAVQQHQQKMQWLKVERPDSQTNKPPHPSLLSC
AVQQHQQKMQWLKV.RPDSQTNKPPHPSLLSC
RetrocopyAVQQHQQKMQWLKVVRPDSQTNKPPHPSLLSC

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 30 .68 RPM
SRP007412_cerebellum 0 .04 RPM 47 .16 RPM
SRP007412_heart 0 .12 RPM 53 .33 RPM
SRP007412_kidney 0 .17 RPM 69 .49 RPM
SRP007412_liver 0 .03 RPM 65 .68 RPM
SRP007412_testis 0 .23 RPM 14 .18 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1339 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1339 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1339 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1339 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1339 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000029036 1 retrocopy
retro_mmus_1339 ,




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