RetrogeneDB ID:

retro_ogar_666

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873525.1:40409579..40410615(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NAP1L1
Ensembl ID:ENSOGAG00000010319
Aliases:None
Description:nucleosome assembly protein 1-like 1 [Source:HGNC Symbol;Acc:7637]


Retrocopy-Parental alignment summary:






>retro_ogar_666
ATGGCAGACATTGACAACAAAGAACAGTGTGAACTTGATCAGGATTTGGATGACGTTGTAGAAGTAGAAGAAGAAACTGG
TGAAGAAACAAAAATCAAAGTGTGTCAGCTAACTGTTCAGATGATGCAAAATCCTCAGATTCTTGCAGCCCTTCAAGAAA
GACTTGATGGTCTGGTAGAAACACCAACAGGATACACTGAAAGCTTGCGTAGGGTAGTTAAAAGACAAGTGAATGCTCTC
AAAAATCTTCAAGTTAAATGTGCACAGATAGAAGCCAAATTCTATGAGGAAGTTCATGGTCTTGAAAGGAAATATGCTGT
TCTCTATCAACCTCTATTTGACAAGTGATTTGAGATTATTAATGTGATTTATGAACCCACGGAAGAATGTGAATTGCAAG
CAGATGAAGAAGATGAAATTTCGGAGGAGCTGAAAAAAAAAAAAAGGCCAAGATTGAAGATGAGAAAAGGGATGAAGAAA
AAGAAGATCCCAAGGGAATTCCTGAATTTTGGTTGACTGTTTTTAAGAATGTTGACTTGCTCAGTGATATGGTTCAGGAA
CATGATGAACCTATTCTGAAGCACTTGAAAGATATTAAAGTCAAATTTTCAAATGCTGGCAAGCCTATTAGTTTCGTCTT
AGAATTTCACTTTGAACCCAATGAATATTTCACAAATGAAGTGTTGACAAAGACATATAGGATGAGGTCAGAACCAGATG
ATTCTGATCCCTTTTCTTTTGATGGACTAGAAATTATGGGTAGTACAGGGTGCCAGATAGATTAGAGAAAAGGAAGGAAT
GTCACTTTGAAAACCATTAAGAAGAAGCAGAAACATAAGGGATGTGGGACAGTTGGTACTGTGACTAAAACAGTTTCCAA
TGACTCCTTCTTTAATTTTTTGCACTTCCTGAAGTTCCTGAAAGTGGAGATCTGGACGATGATGCTGAAGCTATTCTTGC
TGCAGACCTTGAAATTGGTCACTTTTTATGTGAGTGTATAATCCCAAGATCAGTGTTATACTTTACTGGAGAAGCT

ORF - retro_ogar_666 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.71 %
Parental protein coverage: 88.49 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalLSDLENKEQCELDQDLDDVEEVEEEETGEETKIKARQLTVQMMQNPQILAALQERLDGLVETPTGYIESL
..D..NKEQCELDQDLDDV.EVEEE.TGEETKIK..QLTVQMMQNPQILAALQERLDGLVETPTGY.ESL
RetrocopyMADIDNKEQCELDQDLDDVVEVEEE-TGEETKIKVCQLTVQMMQNPQILAALQERLDGLVETPTGYTESL
ParentalPRVVKRRVNALKNLQVKCAQIEAKFYEEVHDLERKYAVLYQPLFDKRFEIINAIYEPTEEECEWKADEED
.RVVKR.VNALKNLQVKCAQIEAKFYEEVH.LERKYAVLYQPLFDK.FEIIN.IYEPT.EECE..ADEED
RetrocopyRRVVKRQVNALKNLQVKCAQIEAKFYEEVHGLERKYAVLYQPLFDK*FEIINVIYEPT-EECELQADEED
ParentalEISEEL--KEKAKIEDEKKDEEKEDP-KGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSDAG
EISEEL...........K....K..P.KGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFS.AG
RetrocopyEISEELXXXXXPRLKMRKGMKKKKIP<KGIPEFWLTVFKNVDLLSDMVQEHDEPILKHLKDIKVKFSNAG
ParentalQPMSFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGPEIMGCTGCQIDWKKGKNVTLKTIKKKQ
.P.SFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDG.EIMG.TGCQID..KG.NVTLKTIKKKQ
RetrocopyKPISFVLEFHFEPNEYFTNEVLTKTYRMRSEPDDSDPFSFDGLEIMGSTGCQID*RKGRNVTLKTIKKKQ
ParentalKHKGRGTVRTVTKTVSNDSFFN-FFAPPEVPESGDLDDDAEAILAADFEIGHFLRERIIPRSVLYFTGEA
KHKG.GTV.TVTKTVSNDSFFN.FFA.PEVPESGDLDDDAEAILAAD.EIGHFL.E.IIPRSVLYFTGEA
RetrocopyKHKGCGTVGTVTKTVSNDSFFN<FFALPEVPESGDLDDDAEAILAADLEIGHFLCECIIPRSVLYFTGEA

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






RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_666 was not experimentally validated.

Retrocopy orthology:
Otolemur garnettii 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 17 parental genes, and 45 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000209088 retrocopies
retro_btau_1319, retro_btau_1324, retro_btau_1462, retro_btau_1487, retro_btau_474, retro_btau_652, retro_btau_70, retro_btau_935,
Callithrix jacchus ENSCJAG000000011151 retrocopy
retro_cjac_534,
Felis catus ENSFCAG000000002791 retrocopy
retro_fcat_1037,
Homo sapiens ENSG000001871093 retrocopies
retro_hsap_1199, retro_hsap_2696, retro_hsap_833,
Gorilla gorilla ENSGGOG000000038833 retrocopies
retro_ggor_1879, retro_ggor_686, retro_ggor_934,
Macropus eugenii ENSMEUG000000137022 retrocopies
retro_meug_1031, retro_meug_604,
Macaca mulatta ENSMMUG000000155831 retrocopy
retro_mmul_233,
Monodelphis domestica ENSMODG000000204564 retrocopies
retro_mdom_1476, retro_mdom_1638, retro_mdom_520, retro_mdom_724,
Mustela putorius furoENSMPUG000000174741 retrocopy
retro_mputfur_505,
Mus musculus ENSMUSG000000587991 retrocopy
retro_mmus_263,
Nomascus leucogenys ENSNLEG000000046824 retrocopies
retro_nleu_1192, retro_nleu_2085, retro_nleu_265, retro_nleu_2766,
Otolemur garnettii ENSOGAG00000010319 4 retrocopies
retro_ogar_1278, retro_ogar_1281, retro_ogar_3357, retro_ogar_666 ,
Pan troglodytes ENSPTRG000000052404 retrocopies
retro_ptro_1820, retro_ptro_582, retro_ptro_694, retro_ptro_819,
Pteropus vampyrus ENSPVAG000000160322 retrocopies
retro_pvam_1282, retro_pvam_306,
Rattus norvegicus ENSRNOG000000038901 retrocopy
retro_rnor_150,
Ictidomys tridecemlineatus ENSSTOG000000030462 retrocopies
retro_itri_1007, retro_itri_416,
Vicugna pacos ENSVPAG000000072903 retrocopies
retro_vpac_435, retro_vpac_441, retro_vpac_601,


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