RetrogeneDB ID:

retro_mmus_3422

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:13202571..13203780(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000084349
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_3422
ATGTCTCACAGGAAATTCTCAGCTCCCAGGCATGGGTCCTTGGGCTTCCTGCCTCGAAAGCGCAGCAGCCGGCATCGTGG
GAAAGTGAAGAGCTTCCCTAAGGATGACGCTTCCAAGCCCGTTCACCTCACAGCCTTTCTGGGTTACAAGGCTGGCATGA
CCCACATCGTCCGGGAAGTTGACAGGCCAGGATCTAAGGTGAACAAGAAAGAAGTCGTGGAGGCTGTGACCATTGTGGAA
ACTCCCCCAATGGTGGTTGTGGGCATTGTGGGATATGTTGAGACCCCACGAGGCCTCCGGACCTTCAAGACTGTATTTGC
TGAGCACATCAGCGATGAGTGTAAAAGGCGCTTCTATAAGAACTGGCACAAGTCTAAGAAGAAGGCTTTCACCAAGTACT
GTAAGAAATGGCAGGATGACACAGGCAAGAAGCAGCTGGAGAAGGACTTCAACAGCATGAAGAAGTACTGCCAGGTCATC
CGCATCATTGCCCACACTCAGATGCGTCTGCTTCCTCTACGCCAGAAGAAGGCACACTTGATGGAGATCCAGGTGAATGG
AGGCACTGTGGCTGAGAAGCTCGACTGGGCCCGAGAGCGGCTGGAGCAGCAGGTTCCTGTGAACCAGGTGTTTGGGCAGG
ATGAGATGATTGATGTCATTGGCGTGACAAAAGGCAAAGGGTACAAAGGGGTAACCAGTCGTTGGCATACAAAGAAACTG
CCCCGAAAGACCCATCGAGGTTTGCGCAAAGTTGCCTGTATTGGAGCCTGGCACCCTGCCCGTGTCGCCTTCTCTGTGGC
TCGAGCTGGGCAGAAAGGCTACCATCACCGAACAGAGATTAACAAGAAGATTTACAAGATTGGTCAAGGCTACCTCATCA
AGGATGGCAAACTGATCAAGAACAATGCATCTACTGACTATGACTTGTCTGACAAGAGCATCAACCCACTGGGTGGCTTT
GTGCATTATGGTGAGGTGACCAATGACTTCATCATGCTCAAAGGCTGTGTGGTGGGGACCAAGAAGCGAGTACTTACTCT
TCGTAAGTCCTTGCTGGTTCAGACCAAACGTCGGGCCCTGGAGAAGATTGACCTGAAGTTCATTGACACCACCTCCAAAT
TTGGCCATGGTCGCTTCCAGACCATGGAGGAGAAGAAAGCATTTATGGGACCACTCAAGAAAGATCGCATTGCCAAGGAG
GAAGGAGCT

ORF - retro_mmus_3422 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 100.0 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
MSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
RetrocopyMSHRKFSAPRHGSLGFLPRKRSSRHRGKVKSFPKDDASKPVHLTAFLGYKAGMTHIVREVDRPGSKVNKK
ParentalEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDD
EVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDD
RetrocopyEVVEAVTIVETPPMVVVGIVGYVETPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDD
ParentalTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQV
TGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQV
RetrocopyTGKKQLEKDFNSMKKYCQVIRIIAHTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQV
ParentalFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
FGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
RetrocopyFGQDEMIDVIGVTKGKGYKGVTSRWHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARAGQKGYHHRTEI
ParentalNKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKS
NKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKS
RetrocopyNKKIYKIGQGYLIKDGKLIKNNASTDYDLSDKSINPLGGFVHYGEVTNDFIMLKGCVVGTKKRVLTLRKS
ParentalLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
LLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA
RetrocopyLLVQTKRRALEKIDLKFIDTTSKFGHGRFQTMEEKKAFMGPLKKDRIAKEEGA

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 1 .36 RPM 182 .07 RPM
SRP007412_cerebellum 4 .91 RPM 112 .33 RPM
SRP007412_heart 0 .19 RPM 83 .24 RPM
SRP007412_kidney 3 .73 RPM 150 .53 RPM
SRP007412_liver 2 .81 RPM 142 .14 RPM
SRP007412_testis 3 .11 RPM 55 .30 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_mmus_3422 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001YKA POLR2A X:13202601..13202801

EST - click to see more details

4 EST(s) were mapped to retro_mmus_3422 retrocopy
EST ID Start End Identity Match Mis-match Score
AV470695 13202859 13203369 99.9 509 1 508
AV472897 13202849 13203341 99.2 485 2 478
AV476197 13202915 13203341 100 426 0 426
AV573195 13202902 13203345 99.8 440 1 438

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_1551716 libraries 0 libraries 11 libraries 8 libraries 1047 libraries
TSS #2 TSS_155172731 libraries 223 libraries 116 libraries 2 libraries 0 libraries

The graphical summary, for retro_mmus_3422 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_3422 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3422 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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