RetrogeneDB ID:

retro_meug_2166

Retrocopy
location
Organism:Wallaby (Macropus eugenii)
Coordinates:Scaffold97444:4898..5836(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPLP0
Ensembl ID:ENSMEUG00000016409
Aliases:None
Description:ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]


Retrocopy-Parental alignment summary:






>retro_meug_2166
ATGCCCAAGGAAGATAGGGGTACCTGGAAATCCAATTGCTTCCTCAAGATCATCCAACTTTTGTATGACTATCCAGAATA
TTTCATTGTGAGAGCAAACAATATGGGCTACAAGCAGATGCAGCAGATTTGGATGTCCCTCCATAGTAAGGCCATGGTAC
TGGTGGGAAAAAACCCATGATGGGCAGAGCCATTTGTGGTCATCTAGAGAACAACCGTGCCCTGGAGAAACTGCTGCTTC
ATATTCAGGGGAATGTGGGCTTTGTGTTCACCAAGAAAGATCTGACTGAGATTAGGGATATGCTTTTGGCCCATAAGGAG
CCAGTTGCTTCCCATGCTGGTTCCATTACCTCATGTGATGTCACTGTGACTGCCCAGAATACTGGTCTGAGTCCTGAGAA
GACTTCCTTCTTCCAGGATCTGGATATCATCACTAAGATTTCCAGGGGCACCATTAAAATCTTGAGTGATGTGCAGCCAA
TTGAGACCAGAGACAAAGTGGGTGCCAGCAAGGCCACTTTGTTGAACATGCTGAACATTTCCCTTTTCTCCTCTGGGCTG
ATCATTCATCAGTGTTTGACGATGGCTTCATCTACAACCCTGCAGTGCTGCACATCACAGAGTAGACTTTGCACCTTCCG
TTCCTTTAGGGTGTCAGTAAAGTTGCCAGCATCTGTCTGCAGATTGACTACCCAATTTTTGCAACAGTACCCTACTCAAT
CATCAGTGAATAAAAGTGGGTCTTGACTATAGCTGTGGAGACTGAGTACAACTTCCCACTTTCTGAAAAATGCAAAGGCC
TTCCTGGCCGAACTTTCAGCATTTGTAGTGGCCACCTCTGCAGCAGCTGCTCCAGCTGCTGCTGCACCTGCTGCTGCTGC
TCCAGCCAAGGAAGAATCAGAGGAGTCTGATGAAGATATGGGATTTGGTCTATTTGAT

ORF - retro_meug_2166 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 70.62 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 3


Retrocopy - Parental Gene Alignment:

ParentalMPREDRATWKSNYFLKIIQLLDDYPKCFIVGADNVGSKQMQQIRMSLRGKAVVLMGKNT-MMRKAIRGHL
MP.EDR.TWKSN.FLKIIQLL.DYP..FIV.A.N.G.KQMQQI.MSL..KA.VL.GKN..MM..AI.GHL
RetrocopyMPKEDRGTWKSNCFLKIIQLLYDYPEYFIVRANNMGYKQMQQIWMSLHSKAMVLVGKNP<MMGRAICGHL
ParentalENNPALEKLLPHIRGNVGFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCDVTVPAQNTGLGPEKTSFFQ
ENN.ALEKLL.HI.GNVGFVFTK.DLTEIRDMLLA.K.P.A..AG.I..CDVTV.AQNTGL.PEKTSFFQ
RetrocopyENNRALEKLLLHIQGNVGFVFTKKDLTEIRDMLLAHKEPVASHAGSITSCDVTVTAQNTGLSPEKTSFFQ
ParentalALGITTKISRGTIEILSDVQLIKTGDKVGASEATLLNMLNISPFSFGLIIQQ-VFDNGSIYNPEVLDITE
.L.I.TKISRGTI.ILSDVQ.I.T.DKVGAS.ATLLNMLNIS.FS.GLII.Q.VFD.G.IYNP.VL.ITE
RetrocopyDLDIITKISRGTIKILSDVQPIETRDKVGASKATLLNMLNISLFSSGLIIHQ<VFDDGFIYNPAVLHITE
ParentalETLHLRFLEGVRNVASVCLQIGYPTVASVPHSIINGYKRVLAVAVETEYTFPLAEK-VKAFLADPSAFAV
.TLHL.FL.GV..VAS.CLQI.YP..A.VP.SII...K.VL..AVETEY.FPL.EK..KAFLA..SAF.V
Retrocopy*TLHLPFL*GVSKVASICLQIDYPIFATVPYSIISE*KWVLTIAVETEYNFPLSEK>AKAFLAELSAFVV
ParentalAAPVAAAPAAAAPAAAAPAKVEAKEESEESDEDMGFGLFD
A................PAK....EESEESDEDMGFGLFD
RetrocopyATXXXXXXXXXXXXXXXPAK----EESEESDEDMGFGLFD

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Macropus eugenii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Macropus eugenii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_meug_2166 retrocopy.

TSS - click to see more details

Macropus eugenii was not studied using FANTOM5 data.

Lab - click to see more details

retro_meug_2166 was not experimentally validated.

Retrocopy orthology:
Macropus eugenii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 18 parental genes, and 71 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000037562 retrocopies
retro_acar_111, retro_acar_115,
Ailuropoda melanoleuca ENSAMEG000000051444 retrocopies
retro_amel_1179, retro_amel_1194, retro_amel_1377, retro_amel_847,
Canis familiaris ENSCAFG000000102275 retrocopies
retro_cfam_1580, retro_cfam_224, retro_cfam_487, retro_cfam_534, retro_cfam_693,
Callithrix jacchus ENSCJAG000000086773 retrocopies
retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
Cavia porcellus ENSCPOG000000218125 retrocopies
retro_cpor_298, retro_cpor_449, retro_cpor_475, retro_cpor_498, retro_cpor_601,
Equus caballus ENSECAG000000158162 retrocopies
retro_ecab_1090, retro_ecab_585,
Felis catus ENSFCAG000000133541 retrocopy
retro_fcat_441,
Gorilla gorilla ENSGGOG000000265825 retrocopies
retro_ggor_1088, retro_ggor_1771, retro_ggor_472, retro_ggor_649, retro_ggor_650,
Macropus eugenii ENSMEUG00000016409 12 retrocopies
retro_meug_1211, retro_meug_1245, retro_meug_1339, retro_meug_1410, retro_meug_1672, retro_meug_1689, retro_meug_1789, retro_meug_1800, retro_meug_1943, retro_meug_2166 , retro_meug_294, retro_meug_772,
Myotis lucifugus ENSMLUG0000000197011 retrocopies
retro_mluc_1016, retro_mluc_1460, retro_mluc_1503, retro_mluc_1806, retro_mluc_1966, retro_mluc_2293, retro_mluc_268, retro_mluc_497, retro_mluc_564, retro_mluc_565, retro_mluc_882,
Macaca mulatta ENSMMUG000000091572 retrocopies
retro_mmul_2245, retro_mmul_939,
Mus musculus ENSMUSG000000672742 retrocopies
retro_mmus_143, retro_mmus_2249,
Oryctolagus cuniculus ENSOCUG000000057492 retrocopies
retro_ocun_293, retro_ocun_376,
Otolemur garnettii ENSOGAG000000038434 retrocopies
retro_ogar_2184, retro_ogar_2294, retro_ogar_556, retro_ogar_713,
Petromyzon marinus ENSPMAG000000013391 retrocopy
retro_pmar_6,
Pongo abelii ENSPPYG000000050225 retrocopies
retro_pabe_2113, retro_pabe_3035, retro_pabe_568, retro_pabe_66, retro_pabe_749,
Rattus norvegicus ENSRNOG000000011483 retrocopies
retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
retro_shar_286, retro_shar_413,


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