RetrogeneDB ID:

retro_mmus_535

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:10:22343438..22345478(+)
Located in intron of:ENSMUSG00000053219
Retrocopy
information
Ensembl ID:ENSMUSG00000097245
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Aco2
Ensembl ID:ENSMUSG00000022477
Aliases:Aco2, Aco-2, Aco3, D10Wsu183e
Description:aconitase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:87880]


Retrocopy-Parental alignment summary:






>retro_mmus_535
ATGGCTCCTTACAGCCTCCTGGTCACCCGGCTGCAGAAGGCCCTGGGTGTGGGGCAGTACCATGTGGCCTCTGTCCTGTG
CCAAAGGGCCAAGGTGGCCATGAGCCATTTTGAGCCCAGTGAGTACATCCGATATGACCTGCTAGAGAAGAACATTAACA
TTGTCTGTAAACGGTTGAACCGGCCTCTTACTCTCTCAGAGAAGATTGTGTATGGACACCTGGATGACCCAGCCAATTGG
GAGATCGAGCAGGGAAAGACATATCTGCGTTTATGGCCTGACCGGGTGGCCATGCAGGATGCCACAGGACAGATGGCTAT
GCTACAGTTCATTAGCAGTGGGCTGCCCAAGGTGGCTGTACCATCAACCATCCACTGTGATCATCTGATTGAGGCCCAGG
TTGGGGGTGAGAAAGACCTGCGCAGGGCCAAGGACATAAACCAGGAAGTGTATAATTTCCTGGCAACTGCAGGTGCCAAG
TATGGCGTGGGCTTCTGGACGCCTGGAACTGGGATCATTTACCAGATCATTCTAGAAAACTATGCATACCCTGGAGTTCT
TCTGATTGGCACTGACTCGCACACCCCCAATGGTGGTGGCCTGGGAGGCATCTGCATTAGAGTAAGGGGTGCTGATGCTG
TGGATGTTATGGCTGGGATCCCCTGGGAGCTGAAGTGTCCCAAGGTGATTGGTGTGAAGCTGACAGGCTCCCTCTCTAGT
TGGACCTCACCCAAAGATGTGATCCTGAAACTGGCAGGTATCCTCACAGTGAAAGGTGGCACAGGTGCTATTGTGGAATA
CCATGGACCCGGTGTCGATTCCATCTCCTGCACTGGCATGGCAACTATCTGCAACATGGGTGCAGAAATTGGGGCCACTA
TATCAGTGTTCCCATACAACCACAGGATGAAAGGTACCTGAGCAAGACAGGCCGAACAGACATTGCCAACCTAGCAGAAG
AATTCAAGGATCACTTAGTGCCTGATCCTGGCTGCCAGTATGACCAAGTGATTGAAATTAACTTCAATGAGCTAAAGCCA
CATATCAATGGGCCCTTTACCCCTGACTTGGCTCATCCAGTGGCAGATGTGGGGACTGTGGCAGAGAAGGAAGGCTGGCC
TCTGGACATCTGAGTAGGTTTGATTGGCAGCTGCACCAATTCAATCTACGAGGACATGGGACGATCAGCAGCTGTGGCTA
AGCAGGCATTGGTCCATGGACTCAAGTGCAAGCCCCAGTTCACCATCACCCCAGGCTCTGAGCAGATCCGTGCTGCTATT
GAGCGGGATGGCTATGCACAGATCCTAAGGGATGTGGGTGGAATCGTTTTGGCCAATGCCTGTGGCTCTTGCATTGGCCA
GTGGGACAGAAAAGACATCAAGAGGGGGGAGAAGAATACAATCGTCACCTTCTACAACAAGAACTTCATAGGCCGTAATG
ATGCAAACCCTGAGACCCATGCCTTTGTCACATCCCCAGAGATTGTCACAGCTCTGGCCATTGCGGGGAAGCCTGAAGTT
CAATCCAGAAACTGACTTCTTGACAGGCAAGGATGGCAAGAAGTTCAAGTTGGAGGCTCCAGATGCAGACGAGCTTCCCC
GATCGGACTTTGATCCAGGGCAGGACACATACCAGCACCCCCCTAAGGACAGCAGTGGGCAGCGGGTGGATGTGAGCCCT
ACCAGCCAGCACCTACAGCTCCTGGAGCCTTTTGACAAGTGGGACGGCAAAGACCTTGAGGACCTGCAAATCCTCATCAA
GGTCAAAGGGAAGTGCACCACAGACCACATTTCTGCTGCCAGCCCCTGGCTCAAGTTCCGTGGTCATCTGGATAACATCT
CTAACAACCTGCTCATCGGTGCCATCAACATCGAAAATGGTAAAGCCAACTCTGTACGAAATGCTGTCACCCAGGAGTTT
GGCCCTGTACCTGACACTGCTCGCTACTACAAGAAACATGGCATCAGGTGGGTGGTGATTGGAGATGAGAACGATGGTGA
GGGCTCAAGCTGGGAGCATGCAGCACTGGAGCCTCGCCAT

ORF - retro_mmus_535 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.16 %
Parental protein coverage: 87.18 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMAPYSLLVTRLQKALGVRQYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIVRKRLNRPLTLSEKIV
MAPYSLLVTRLQKALGV.QYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIV.KRLNRPLTLSEKIV
RetrocopyMAPYSLLVTRLQKALGVGQYHVASVLCQRAKVAMSHFEPSEYIRYDLLEKNINIVCKRLNRPLTLSEKIV
ParentalYGHLDDPANQEIERGKTYLRLRPDRVAMQDATAQMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL
YGHLDDPAN.EIE.GKTYLRL.PDRVAMQDAT.QMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL
RetrocopyYGHLDDPANWEIEQGKTYLRLWPDRVAMQDATGQMAMLQFISSGLPKVAVPSTIHCDHLIEAQVGGEKDL
ParentalRRAKDINQEVYNFLATAGAKYGVGFWRPGSGIIHQIILENYAYPGVLLIGTDSHTPNGGGLGGICIGVGG
RRAKDINQEVYNFLATAGAKYGVGFW.PG.GII.QIILENYAYPGVLLIGTDSHTPNGGGLGGICI.V.G
RetrocopyRRAKDINQEVYNFLATAGAKYGVGFWTPGTGIIYQIILENYAYPGVLLIGTDSHTPNGGGLGGICIRVRG
ParentalADAVDVMAGIPWELKCPKVIGVKLTGSLSGWTSPKDVILKVAGILTVKGGTGAIVEYHGPGVDSISCTGM
ADAVDVMAGIPWELKCPKVIGVKLTGSLS.WTSPKDVILK.AGILTVKGGTGAIVEYHGPGVDSISCTGM
RetrocopyADAVDVMAGIPWELKCPKVIGVKLTGSLSSWTSPKDVILKLAGILTVKGGTGAIVEYHGPGVDSISCTGM
ParentalATICNMGAEIGATTSVFPYNHRMK-KYLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEINLNELKPHI
ATICNMGAEIGAT.SVFPYNHRMK..YLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEIN.NELKPHI
RetrocopyATICNMGAEIGATISVFPYNHRMK<RYLSKTGRTDIANLAEEFKDHLVPDPGCQYDQVIEINFNELKPHI
ParentalNGPFTPDLAHPVADVGTVAEKEGWPLDIRVGLIGSCTNSSYEDMGRSAAVAKQALAHGLKCKSQFTITPG
NGPFTPDLAHPVADVGTVAEKEGWPLDI.VGLIGSCTNS.YEDMGRSAAVAKQAL.HGLKCK.QFTITPG
RetrocopyNGPFTPDLAHPVADVGTVAEKEGWPLDI*VGLIGSCTNSIYEDMGRSAAVAKQALVHGLKCKPQFTITPG
ParentalSEQIRATIERDGYAQILRDVGGIVLANACGPCIGQWDRKDIKKGEKNTIVTSYNRNFTGRNDANPETHAF
SEQIRA.IERDGYAQILRDVGGIVLANACG.CIGQWDRKDIK.GEKNTIVT.YN.NF.GRNDANPETHAF
RetrocopySEQIRAAIERDGYAQILRDVGGIVLANACGSCIGQWDRKDIKRGEKNTIVTFYNKNFIGRNDANPETHAF
ParentalVTSPEIVTALAIA-GTLKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV
VTSPEIVTALAIA.G.LKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV
RetrocopyVTSPEIVTALAIA>GSLKFNPETDFLTGKDGKKFKLEAPDADELPRSDFDPGQDTYQHPPKDSSGQRVDV
ParentalSPTSQRLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAAGPWLKFRGHLDNISNNLLIGAINIENGK
SPTSQ.LQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAA.PWLKFRGHLDNISNNLLIGAINIENGK
RetrocopySPTSQHLQLLEPFDKWDGKDLEDLQILIKVKGKCTTDHISAASPWLKFRGHLDNISNNLLIGAINIENGK
ParentalANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENYGEGSSREHAALEPRH
ANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDEN.GEGSS.EHAALEPRH
RetrocopyANSVRNAVTQEFGPVPDTARYYKKHGIRWVVIGDENDGEGSSWEHAALEPRH

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 .68 RPM 403 .43 RPM
SRP007412_cerebellum 0 .87 RPM 495 .96 RPM
SRP007412_heart 4 .58 RPM 2501 .31 RPM
SRP007412_kidney 2 .71 RPM 1359 .28 RPM
SRP007412_liver 0 .41 RPM 243 .59 RPM
SRP007412_testis 0 .18 RPM 147 .33 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_535 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_535 retrocopy.

TSS - click to see more details



TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_2495468 libraries467 libraries133 libraries4 libraries0 libraries
TSS #2 TSS_2496423 libraries509 libraries136 libraries4 libraries0 libraries
TSS #3 TSS_2497516 libraries400 libraries149 libraries6 libraries1 library

The graphical summary, for retro_mmus_535 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Display detail expression values in each library
... or ...
Directly download all expression values

Lab - click to see more details

retro_mmus_535 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_535 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 8 parental genes, and 11 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001004122 retrocopies
retro_hsap_2583, retro_hsap_324,
Myotis lucifugus ENSMLUG000000024721 retrocopy
retro_mluc_2566,
Macaca mulatta ENSMMUG000000014542 retrocopies
retro_mmul_647, retro_mmul_694,
Mus musculus ENSMUSG00000022477 1 retrocopy
retro_mmus_535 ,
Nomascus leucogenys ENSNLEG000000154822 retrocopies
retro_nleu_1519, retro_nleu_1767,
Pongo abelii ENSPPYG000000118711 retrocopy
retro_pabe_1903,
Pan troglodytes ENSPTRG000000144281 retrocopy
retro_ptro_260,
Drosophila melanogaster FBgn00101001 retrocopy
retro_dmel_56,


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