RetrogeneDB ID:

retro_ogar_2918

Retrocopy
location
Organism:Bushbaby (Otolemur garnettii)
Coordinates:GL873681.1:131221..131914(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SNRPB
Ensembl ID:ENSOGAG00000016149
Aliases:None
Description:small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]


Retrocopy-Parental alignment summary:






>retro_ogar_2918
ATGGCTGTGGGCAAGAGTAGCAAGATACTGCTGCACATGGACTATAGAATGAGATGTATCCTTCAAGACCGCCCGATCTT
CATTGGCACTTCAAGGCTTTTGACAAACCTGTGAATTTGATCCTCTATGATTGTGATGAGTTCAGGAAGATCAAGCCAAA
GAATGCGAAGCAGCCATAAGGTGAAGAAAAGCGGGTTTGGGGTCTGGTGTTGCTGCGTGGGGAGAACTTGGTATCCATGA
CTGTGGAGGGGCCACCCCTCAAAGATACTGGCATTGCTCAAGTACCACTTGCTGGAGCTGCAGGAGGCCCTGGAGTTGGT
AGGGCAGCTGGCAGAGGAGTGCCAGCTGGTGTACCAATTCCTCAGGCTCCTGCTGGGTTAGCAGGCCCAGTCTGAGGAGT
TGGGGGACCATCCCAGCAGGTAATGACTCCACAGGGGACAGGCACTGTAGAGGCTGCTGCCATTGCTGCTACTGTATGCC
CCAGGACAAGGGACCCCACCTCCGCCTGTAGGCAGAGGAACACCACCTCCAGGCATTATGGTTCCTCCGCCTGGTGTGAG
ACCACCCATGGGCCCACCAGTTGGACTCCCTCCTGCTCGAGTGACACCAATAGGTATGCTCCCTCCAGGAATGAGACCCC
CTTCACCAGGAATTAGAGGTCCACCTCCCCCAGGAATGCGTTCTCCCAGACCT

ORF - retro_ogar_2918 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.03 %
Parental protein coverage: 93.75 %
Number of stop codons detected: 2
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalMTVGKSSKMLQHIDYRMRCILQDGRIFIGT-FKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL
M.VGKSSK.L.H.DYRMRCILQD..IFIGT.FKAFDK..NLIL.DCDEFRKIKPKN.KQ...EEKRV.GL
RetrocopyMAVGKSSKILLHMDYRMRCILQDRPIFIGT<FKAFDKPVNLILYDCDEFRKIKPKNAKQP*GEEKRVWGL
ParentalVLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQ
VLLRGENLVSMTVEGPP.KDTGIA.VPLAGAAGGPG.GRAAGRG.PAGVP.PQAPAGLAGPV.GVGGPSQ
RetrocopyVLLRGENLVSMTVEGPPLKDTGIAQVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPV*GVGGPSQ
ParentalQVMTPQGRGTV-AAAAAAAT-ASIAGAPTQYPPGRGGPPPPMGRGAPPPGM---MGPPPGMRPPMGPPMG
QVMTPQG.GTV.AAA.AA...A...G.P...P.GRG.PPP..G...PPPG....MGPP.G..P....P.G
RetrocopyQVMTPQGTGTVEAAAIAATV>APGQGTPPP-PVGRGTPPP--GIMVPPPGVRPPMGPPVGLPPARVTPIG
Parental-IPPGRGTPM----GMPPPGMRPPPP
..PPG...P.....G.PPPGMR.P.P
RetrocopyMLPPGMRPPSPGIRGPPPPGMRSPRP

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_2918 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 19 parental genes, and 43 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000113531 retrocopy
retro_amel_1403,
Canis familiaris ENSCAFG000000066933 retrocopies
retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus ENSCJAG000000209712 retrocopies
retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus ENSDNOG000000078962 retrocopies
retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus ENSEEUG000000155683 retrocopies
retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus ENSFCAG000000144472 retrocopies
retro_fcat_1788, retro_fcat_1960,
Microcebus murinus ENSMICG000000165194 retrocopies
retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus ENSMLUG000000169511 retrocopy
retro_mluc_1725,
Mustela putorius furoENSMPUG000000092831 retrocopy
retro_mputfur_1153,
Mus musculus ENSMUSG000000274043 retrocopies
retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Nomascus leucogenys ENSNLEG000000092061 retrocopy
retro_nleu_761,
Otolemur garnettii ENSOGAG000000073925 retrocopies
retro_ogar_1179, retro_ogar_3042, retro_ogar_3060, retro_ogar_475, retro_ogar_722,
Otolemur garnettii ENSOGAG00000016149 4 retrocopies
retro_ogar_2197, retro_ogar_2841, retro_ogar_2918 , retro_ogar_3236,
Ochotona princeps ENSOPRG000000074592 retrocopies
retro_opri_697, retro_opri_72,
Pongo abelii ENSPPYG000000108411 retrocopy
retro_pabe_2265,
Pteropus vampyrus ENSPVAG000000170131 retrocopy
retro_pvam_289,
Rattus norvegicus ENSRNOG000000069612 retrocopies
retro_rnor_2825, retro_rnor_474,
Tupaia belangeri ENSTBEG000000100403 retrocopies
retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta ENSTSYG000000144982 retrocopies
retro_tsyr_45, retro_tsyr_719,


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