RetrogeneDB ID:

retro_mmus_1242

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:14:3876442..3877636(-)
Located in intron of:ENSMUSG00000096793
Retrocopy
information
Ensembl ID:ENSMUSG00000097594
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl3
Ensembl ID:ENSMUSG00000060036
Aliases:Rpl3, F2, J1
Description:ribosomal protein L3 [Source:MGI Symbol;Acc:MGI:1351605]


Retrocopy-Parental alignment summary:






>retro_mmus_1242
ATGCCTCACAGGAAATTCTCAGCTCCCAGGCATGGGTCATTGGGCTTCTTGCCTCACAGGCACAACAGCCGGCATCATGG
GAAAATTAAGAGCCTCCCCAAGGATGACCCTTCCAAGCCTGTTCACCTCACAGCTTTTCTAGGCTACAAGGGTGCCATGA
CCCACATCGTCTGGGAAGTTGACAGGCCAGGATCTAAGGTGAACAAAAAAGAAGTTCTGGAGGCTGTGACCATTGTGGAA
ACCCCACCAATGGTGGTTGTGGGCATTGTAAGATATGTTGAAACCCCACGAGGCCTCTGGACCTTCATGACTATATTTGT
TGAGCATATCAGTGATGAGTGTAAAAGGCAGTTCTATAAGAAGTGGCACAAATCTAAGAAGACGACTTTTACCAAGTACT
GTGAGAAATGGCAGGATGACACAGGCAAGAAGCAGTTGGAAAATGACTTCAACAGCATGAAGAACTATTGCCAGGCCATT
CGCATAATTGTTCACACTCAGATGAGTCTGCTTCCTCTGTGCCAGAAGGCACACTTGTTGGAGATCCAGGTGAATGGAGG
CACTGTGGCTGAGAATCAAGACTGGGCCCAAGAGAAGTTGGAGCAGCAGGTTCCTGTAAACCAGGTGTTGGGGCAGGATG
GGATGATTGATGTCATCAGCGTGACAAAAGGCAAAGGATACAAAGGGGTGACCAGTTGTTGGCAGACAAAGAAACTACCC
CAAAAGACCCATTGAGGTTTGCACAAAGTTGCCTGGATTAGAGCCTGGAACCCTGCCTGTGCAGCCTTCTCTATGGCTCC
AGCTGGACAGAAAGGCTACCATCACTGAACAGAGATTATCAAGAAGATTTACAAGATTGGTCAAGGATACCTCATCAAGG
ATGGTAAACTGATCAAGAACAATGCATCTACTGACTATGTCCTGTCTGATAAGAGCATCAACCCACTGGGTGGCTTTGTC
CATTATGGTGAGGTAACCAATGACTTCATCATGATCAAAGGCTGTGTGGTGGGGACCAAGAAGCGAGTGCTTACCCTTTG
TAAGTCCTTACAGGTCCAGATCAAAAGTCAGGCCCTTGAGAAGATTGACCTGAAGTTCATTGACACCGCCTCCAAGTTTT
GTCATGGTCATTTCCAGACCATGGAGGGGAATAAAGCATTCATGGGACCACTCAAGAAAGATCTCATTGCCAAG

ORF - retro_mmus_1242 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.71 %
Parental protein coverage: 99.01 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
M.HRKFSAPRHGSLGFLP....SRH.GK.KS.PKDD.SKPVHLTAFLGYK..MTHIV.EVDRPGSKVNKK
RetrocopyMPHRKFSAPRHGSLGFLPHRHNSRHHGKIKSLPKDDPSKPVHLTAFLGYKGAMTHIVWEVDRPGSKVNKK
ParentalEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDD
EV.EAVTIVETPPMVVVGIV.YVETPRGL.TF.T.F.EHISDECKR.FYK.WHKSKK..FTKYC.KWQDD
RetrocopyEVLEAVTIVETPPMVVVGIVRYVETPRGLWTFMTIFVEHISDECKRQFYKKWHKSKKTTFTKYCEKWQDD
ParentalTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQV
TGKKQLE.DFNSMK.YCQ.IRII.HTQM.LLPL.QK.AHL.EIQVNGGTVAE..DWA.E.LEQQVPVNQV
RetrocopyTGKKQLENDFNSMKNYCQAIRIIVHTQMSLLPLCQK-AHLLEIQVNGGTVAENQDWAQEKLEQQVPVNQV
ParentalFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
.GQD.MIDVI.VTKGKGYKGVTS.W.TKKLP.KTH.GL.KVA.I.AW.PA..AFS.A.AGQKGYHH.TEI
RetrocopyLGQDGMIDVISVTKGKGYKGVTSCWQTKKLPQKTH*GLHKVAWIRAWNPACAAFSMAPAGQKGYHH*TEI
ParentalNKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKS
.KKIYKIGQGYLIKDGKLIKNNASTDY.LSDKSINPLGGFVHYGEVTNDFIM.KGCVVGTKKRVLTL.KS
RetrocopyIKKIYKIGQGYLIKDGKLIKNNASTDYVLSDKSINPLGGFVHYGEVTNDFIMIKGCVVGTKKRVLTLCKS
ParentalLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAK
L.VQ.K..ALEKIDLKFIDT.SKF.HG.FQTME..KAFMGPLKKD.IAK
RetrocopyLQVQIKSQALEKIDLKFIDTASKFCHGHFQTMEGNKAFMGPLKKDLIAK

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 .00 RPM 182 .07 RPM
SRP007412_cerebellum 0 .00 RPM 112 .33 RPM
SRP007412_heart 0 .00 RPM 83 .24 RPM
SRP007412_kidney 0 .02 RPM 150 .53 RPM
SRP007412_liver 0 .03 RPM 142 .14 RPM
SRP007412_testis 0 .00 RPM 55 .30 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_1242 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_1242 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_1242 retrocopy 5' end.

Lab - click to see more details

retro_mmus_1242 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_1242 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 131 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000108531 retrocopy
retro_amel_1115,
Bos taurus ENSBTAG000000032283 retrocopies
retro_btau_1644, retro_btau_281, retro_btau_341,
Canis familiaris ENSCAFG000000013461 retrocopy
retro_cfam_97,
Callithrix jacchus ENSCJAG000000162766 retrocopies
retro_cjac_1198, retro_cjac_1972, retro_cjac_2157, retro_cjac_2264, retro_cjac_3079, retro_cjac_823,
Dasypus novemcinctus ENSDNOG000000011214 retrocopies
retro_dnov_1359, retro_dnov_1641, retro_dnov_652, retro_dnov_788,
Erinaceus europaeus ENSEEUG000000146612 retrocopies
retro_eeur_488, retro_eeur_557,
Echinops telfairi ENSETEG000000113805 retrocopies
retro_etel_1646, retro_etel_2199, retro_etel_2212, retro_etel_657, retro_etel_972,
Felis catus ENSFCAG000000058201 retrocopy
retro_fcat_1809,
Gorilla gorilla ENSGGOG0000000232610 retrocopies
retro_ggor_1043, retro_ggor_1295, retro_ggor_1582, retro_ggor_1822, retro_ggor_2329, retro_ggor_2616, retro_ggor_2713, retro_ggor_2736, retro_ggor_2955, retro_ggor_36,
Macropus eugenii ENSMEUG0000000978926 retrocopies
retro_meug_1045, retro_meug_118, retro_meug_1210, retro_meug_1403, retro_meug_1452, retro_meug_1492, retro_meug_1516, retro_meug_1554, retro_meug_1589, retro_meug_1604, retro_meug_1698, retro_meug_1856, retro_meug_2150, retro_meug_2151, retro_meug_221, retro_meug_367, retro_meug_412, retro_meug_461, retro_meug_592, retro_meug_677, retro_meug_683, retro_meug_831, retro_meug_851, retro_meug_886, retro_meug_889, retro_meug_898,
Myotis lucifugus ENSMLUG000000237111 retrocopy
retro_mluc_810,
Macaca mulatta ENSMMUG000000100294 retrocopies
retro_mmul_1170, retro_mmul_149, retro_mmul_2334, retro_mmul_973,
Monodelphis domestica ENSMODG000000095392 retrocopies
retro_mdom_380, retro_mdom_408,
Mustela putorius furoENSMPUG000000132713 retrocopies
retro_mputfur_1284, retro_mputfur_199, retro_mputfur_774,
Mus musculus ENSMUSG00000060036 30 retrocopies
retro_mmus_1148, retro_mmus_1158, retro_mmus_1164, retro_mmus_1165, retro_mmus_1167, retro_mmus_1183, retro_mmus_1238, retro_mmus_1239, retro_mmus_1240, retro_mmus_1241, retro_mmus_1242 , retro_mmus_1243, retro_mmus_1244, retro_mmus_1245, retro_mmus_1246, retro_mmus_1465, retro_mmus_1548, retro_mmus_2231, retro_mmus_2275, retro_mmus_2276, retro_mmus_2474, retro_mmus_2501, retro_mmus_2547, retro_mmus_2849, retro_mmus_3125, retro_mmus_3215, retro_mmus_3422, retro_mmus_3467, retro_mmus_361, retro_mmus_897,
Oryctolagus cuniculus ENSOCUG000000277124 retrocopies
retro_ocun_105, retro_ocun_179, retro_ocun_1893, retro_ocun_558,
Otolemur garnettii ENSOGAG000000000327 retrocopies
retro_ogar_1264, retro_ogar_1679, retro_ogar_2096, retro_ogar_2122, retro_ogar_2448, retro_ogar_3431, retro_ogar_960,
Ochotona princeps ENSOPRG000000130883 retrocopies
retro_opri_1004, retro_opri_1014, retro_opri_432,
Procavia capensis ENSPCAG000000106421 retrocopy
retro_pcap_115,
Pongo abelii ENSPPYG0000001183710 retrocopies
retro_pabe_1113, retro_pabe_1861, retro_pabe_2167, retro_pabe_2743, retro_pabe_2985, retro_pabe_3170, retro_pabe_3318, retro_pabe_3349, retro_pabe_3696, retro_pabe_3761,
Pteropus vampyrus ENSPVAG000000032042 retrocopies
retro_pvam_1220, retro_pvam_1390,
Rattus norvegicus ENSRNOG000000168962 retrocopies
retro_rnor_1333, retro_rnor_731,
Sarcophilus harrisii ENSSHAG000000032122 retrocopies
retro_shar_154, retro_shar_662,
Tupaia belangeri ENSTBEG000000059891 retrocopy
retro_tbel_939,


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