RetrogeneDB ID:

retro_pabe_2167

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2b:128909998..128910899(-)
Located in intron of:ENSPPYG00000013305
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL3
Ensembl ID:ENSPPYG00000011837
Aliases:None
Description:ribosomal protein L3 [Source:HGNC Symbol;Acc:10332]


Retrocopy-Parental alignment summary:






>retro_pabe_2167
CCTCAAGGCCTCCAGACCTTCAAGACCATCTTCTCTAAGCACATCAGCGATGAGTGCAAAAAGCACTTCTCTAAGAACAG
GCATAAATCTAAGAAGAAGGCCTTTACCAATTACTGCAAGAAATGGCAGAATAAGGATGGCAAGAAGCAGCTGGAGCAGG
ACTTCAGCAGCGTGAAGAAGCACTGCCAAGTCATCCACGTCACTGCCCACACCCACATGCACCTGCTTCCTCCACGCCAG
AAGAAGGCCCGGCTGATGGAGATCTAGGTGAACAGAGGCACCGTGTCCAAGAAGCTGGAATGGGGCCGGGAGAGGCTAGA
GCAGCAGGTACCTATGAACCAAGTGTTTGGGCAGGACGAGATGATTGACGTCTTCAAGGTGACCAAGGGCAAAGACTACA
AAGGGGTCACGAGTCATTGACACACCAAGAAGCTACCCTGCAAGACCCACTGAGGCTTGTGCAAGGTGGCCTGGATTGGG
GCATGGCATACTGCCTGTGTGGCCTTCTCTGTGGCATGTGCTGGGCAGAAAGGGTACCATCACCGCACTGAGATCAACAA
GAAGATTGACCTGTAAGATCGGCCAGGGCTACCTTATCAAGGACGACCAACTGATCAAGAACAGTGCCTCCACTGACCAT
GACCTGCCTGACAAGAGCATCAACTCTCTGGGTGGCTTTGTCCTATATGGTGAAGTGACCAGTGGCTTTGTCATGCTGAA
GGAATGTGTGGTGGGAACCAAGAAGCGAGTGCTCACCCTCCACAAGTCTTTGCTGGCTGAGACCAAACGGCGAGCTCTGG
AGAAGACTGACCTTAAGTTCATTGACACCACTGCCAAGTTTGGCCATGGCTGCTCCCAGACCATGGAAGAGAAGAAAGTA
TTCATTGAAAGTATTCGTGAA

ORF - retro_pabe_2167 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 73.75 %
Parental protein coverage: 74.19 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalPRGLRTFKTVFAEHISDECKRRFYKNWHKSKKKAFTKYCKKWQDEDGKKQLEKDFSSMKKYCQVIRVIAH
P.GL.TFKT.F..HISDECK..F.KN.HKSKKKAFT.YCKKWQ..DGKKQLE.DFSS.KK.CQVI.V.AH
RetrocopyPQGLQTFKTIFSKHISDECKKHFSKNRHKSKKKAFTNYCKKWQNKDGKKQLEQDFSSVKKHCQVIHVTAH
ParentalTQMRLLPLRQKKAHLMEIQVNGGTVAEKLDWARERLEQQVPVNQVFGQDEMIDVIGVTKGKGYKGVTSRW
T.M.LLP.RQKKA.LMEI.VN.GTV..KL.W.RERLEQQVP.NQVFGQDEMIDV..VTKGK.YKGVTS..
RetrocopyTHMHLLPPRQKKARLMEI*VNRGTVSKKLEWGRERLEQQVPMNQVFGQDEMIDVFKVTKGKDYKGVTSH*
ParentalHTKKLPRKTHRGLRKVACIGAWHPARVAFSVARA-GQKGYHHRTEINKKIY-KIGQGYLIKDGKLIKNNA
HTKKLP.KTH.GL.KVA.IGAWH.A.VAFSVA.A.G.KG.............KIGQGYLIKD..LIKN.A
RetrocopyHTKKLPCKTH*GLCKVAWIGAWHTACVAFSVACA>GRKGTITALRSTRRLTCKIGQGYLIKDDQLIKNSA
ParentalSTDYDLSDKSINPLGGFVHYGEVTNDFVMLKGCVVGTKKRVLTLRKSLLVQTKRRALEKIDLKFIDTTSK
STD.DL.DKSIN.LGGFV.YGEVT..FVMLK.CVVGTKKRVLTL.KSLL..TKRRALEK.DLKFIDTT.K
RetrocopySTDHDLPDKSINSLGGFVLYGEVTSGFVMLKECVVGTKKRVLTLHKSLLAETKRRALEKTDLKFIDTTAK
ParentalFGHGRFQTMEEKKAFMGPLKK
FGHG..QTMEEKK.F......
RetrocopyFGHGCSQTMEEKKVFIESIRE

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_prefrontal_cortex 0 .17 RPM 169 .41 RPM
SRP007412_cerebellum 0 .36 RPM 139 .11 RPM
SRP007412_heart 0 .03 RPM 60 .51 RPM
SRP007412_kidney 0 .13 RPM 379 .03 RPM
SRP007412_liver 0 .03 RPM 256 .93 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_2167 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2167 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2167 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2403
Pan troglodytes retro_ptro_1753
Gorilla gorilla retro_ggor_1822
Macaca mulatta retro_mmul_973
Parental genes homology:
Parental genes homology involve 29 parental genes, and 143 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,
Equus caballus ENSECAG000000206651 retrocopy
retro_ecab_897,
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,
Homo sapiens ENSG000001003169 retrocopies
retro_hsap_1341, retro_hsap_2403, retro_hsap_2529, retro_hsap_3328, retro_hsap_3448, retro_hsap_3638, retro_hsap_3889, retro_hsap_4081, retro_hsap_4749,
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,
Microcebus murinus ENSMICG000000158321 retrocopy
retro_mmur_1307,
Myotis lucifugus ENSMLUG000000237111 retrocopy
retro_mluc_810,
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 ENSMUSG0000006003630 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,
Nomascus leucogenys ENSNLEG000000152342 retrocopies
retro_nleu_1038, retro_nleu_1449,
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 ENSPPYG000000069731 retrocopy
retro_pabe_2854,
Pongo abelii ENSPPYG00000011837 10 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,
Tursiops truncatus ENSTTRG000000108802 retrocopies
retro_ttru_1266, retro_ttru_1518,


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