RetrogeneDB ID:

retro_nleu_1365

Retrocopy
location
Organism:Gibbon (Nomascus leucogenys)
Coordinates:GL397291.1:12652864..12653761(+)
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:ENSNLEG00000000292
Aliases:None
Description:ribosomal protein, large, P0 [Source:HGNC Symbol;Acc:10371]


Retrocopy-Parental alignment summary:






>retro_nleu_1365
CAACTATTGGATGATTATCCGAAATGTTTCATCGTGGGAGCAGACAATGTGGGCTCCAAGCAGATGCGCAGATCCGCATG
TCCCTTTGCGGGAAGGCCGTGGTGCTGATGGGCAAGAACACCATGATGCACAAGGCCATCCGAGGGCACCTGGAAAACAA
CCCAGCTCTGGAGAAACTGCTGCCTCATTTCCGGGGGGATGTGGGCTTTGTGTTCACCAGGGAGCACCTCACTGAGATCA
GGGACATGTTGCTGGCCAATAAGGTGCCAGCTGCTGCCCATGCTGGTGTCATTGCCCCATGTGGAGTCATTGTGCCAGCC
CAGAACACTGGTCCCGGGCCCGAGAAGACCTCCTTTTTCCAGGCTTTAGGTATCACCACTAAAATCTCCAGGGGCACCAT
TGAAATCCTGAGTGAAGTGCAGCTGATCAAGACTGGAGACAAAGTGGGAGCCAGTGAAGCCACACTGCTGAACATGCCCA
ACATCTCCCCCTTCTCCTTTGGGCTGGTCATCCATCAGGTGTTCGACAATGGCAGCATCTACAACCCTGAAGTGCTTGAC
ATCACAGAGGAAACTCTGCATTCTCGCTTCCTGGAGGTTGTCCGCAATGTTGCCGGTGTCTGTCTGCAGATTGGCTACCC
AACTGTTGCATCAGTACCCCATTCTATCATCAACGGGTACAAAATGAGTCTTGGCCTTGTCTGTGGAGATGGATTACACC
TTCCCACTTGCTGAAAAGGTCAAGGCCTTCTTGGCTGGTCCATCTGCCTTTGTGGCTGCTGCCCCTGTGGCCGCTGCCAC
CACAGCTGCTCCTGCTGCTGCTGCAGCCCCAGCTAAGGTTGAAGCCAAGGAAGAGTCGGAGGAGTCGGATGAGGATATGG
GATTTGGTCTCTTTGAC

ORF - retro_nleu_1365 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.38 %
Parental protein coverage: 98.68 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQLLDDYPKCFIVGADNVGSKQMQ-QIRMSLRGKAVVLMGKNTMMRKAIRGHLENNPALEKLLPHIRGNVG
QLLDDYPKCFIVGADNVGSKQM..QIRMSL.GKAVVLMGKNTMM.KAIRGHLENNPALEKLLPH.RG.VG
RetrocopyQLLDDYPKCFIVGADNVGSKQMR<QIRMSLCGKAVVLMGKNTMMHKAIRGHLENNPALEKLLPHFRGDVG
ParentalFVFTKEDLTEIRDMLLANKVPAAARAGAIAPCEVTVPAQNTGLGPEKTSFFQALGITTKISRGTIEILSD
FVFT.E.LTEIRDMLLANKVPAAA.AG.IAPC.V.VPAQNTG.GPEKTSFFQALGITTKISRGTIEILS.
RetrocopyFVFTREHLTEIRDMLLANKVPAAAHAGVIAPCGVIVPAQNTGPGPEKTSFFQALGITTKISRGTIEILSE
ParentalVQLIKTGDKVGASEATLLNMLNISPFSFGLVIQQVFDNGSIYNPEVLDITEETLHSRFLEGVRNVASVCL
VQLIKTGDKVGASEATLLNM.NISPFSFGLVI.QVFDNGSIYNPEVLDITEETLHSRFLE.VRNVA.VCL
RetrocopyVQLIKTGDKVGASEATLLNMPNISPFSFGLVIHQVFDNGSIYNPEVLDITEETLHSRFLEVVRNVAGVCL
ParentalQIGYPTVASVPHSIINGYKR-VLALSVETDYTFPLAEKVKAFLADPSAFVAAAPVAAATTAAPAAAAAPA
QIGYPTVASVPHSIINGYK..VLALSVE.DYTFPLAEKVKAFLA.PSAFVA...................
RetrocopyQIGYPTVASVPHSIINGYKM>VLALSVEMDYTFPLAEKVKAFLAGPSAFVAXXXXXXXXXXXXXXXXXXX
ParentalKVEAKEESEESDEDMGFGLFD
KVEAKEESEESDEDMGFGLFD
RetrocopyKVEAKEESEESDEDMGFGLFD

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






RNA-Seq - click to see more details

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Nomascus leucogenys was not studied using ChIP-Seq data.

EST - click to see more details

Nomascus leucogenys was not studied using EST data.

TSS - click to see more details

Nomascus leucogenys was not studied using FANTOM5 data.

Lab - click to see more details

retro_nleu_1365 was not experimentally validated.

Retrocopy orthology:
Nomascus leucogenys 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 21 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
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,
Choloepus hoffmanni ENSCHOG000000027452 retrocopies
retro_chof_1115, retro_chof_2341,
Callithrix jacchus ENSCJAG000000086773 retrocopies
retro_cjac_1693, retro_cjac_2840, retro_cjac_786,
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,
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,
Mustela putorius furoENSMPUG000000030554 retrocopies
retro_mputfur_1632, retro_mputfur_362, retro_mputfur_426, retro_mputfur_910,
Mus musculus ENSMUSG000000672742 retrocopies
retro_mmus_143, retro_mmus_2249,
Nomascus leucogenys ENSNLEG00000000292 11 retrocopies
retro_nleu_1080, retro_nleu_1365 , retro_nleu_1419, retro_nleu_1470, retro_nleu_1551, retro_nleu_1639, retro_nleu_1686, retro_nleu_1722, retro_nleu_2058, retro_nleu_2927, retro_nleu_3095,
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,
Pteropus vampyrus ENSPVAG000000031103 retrocopies
retro_pvam_114, retro_pvam_62, retro_pvam_745,
Rattus norvegicus ENSRNOG000000011483 retrocopies
retro_rnor_1350, retro_rnor_2092, retro_rnor_2970,
Sarcophilus harrisii ENSSHAG000000016232 retrocopies
retro_shar_286, retro_shar_413,
Ictidomys tridecemlineatus ENSSTOG000000113274 retrocopies
retro_itri_1155, retro_itri_276, retro_itri_331, retro_itri_982,
Tarsius syrichta ENSTSYG000000097327 retrocopies
retro_tsyr_1133, retro_tsyr_130, retro_tsyr_1376, retro_tsyr_1429, retro_tsyr_727, retro_tsyr_75, retro_tsyr_84,
Vicugna pacos ENSVPAG000000121562 retrocopies
retro_vpac_234, retro_vpac_45,


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