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 symbol: SNRPB
• Ensembl ID: ENSOGAG00000016149
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptides B and B1 [Source:HGNC Symbol;Acc:11153]

Sequence

>retro_ogar_2918
ATGGCTGTGGGCAAGAGTAGCAAGATACTGCTGCACATGGACTATAGAATGAGATGTATCCTTCAAGACCGCCCGATCTT
CATTGGCACTTCAAGGCTTTTGACAAACCTGTGAATTTGATCCTCTATGATTGTGATGAGTTCAGGAAGATCAAGCCAAA
GAATGCGAAGCAGCCATAAGGTGAAGAAAAGCGGGTTTGGGGTCTGGTGTTGCTGCGTGGGGAGAACTTGGTATCCATGA
CTGTGGAGGGGCCACCCCTCAAAGATACTGGCATTGCTCAAGTACCACTTGCTGGAGCTGCAGGAGGCCCTGGAGTTGGT
AGGGCAGCTGGCAGAGGAGTGCCAGCTGGTGTACCAATTCCTCAGGCTCCTGCTGGGTTAGCAGGCCCAGTCTGAGGAGT
TGGGGGACCATCCCAGCAGGTAATGACTCCACAGGGGACAGGCACTGTAGAGGCTGCTGCCATTGCTGCTACTGTATGCC
CCAGGACAAGGGACCCCACCTCCGCCTGTAGGCAGAGGAACACCACCTCCAGGCATTATGGTTCCTCCGCCTGGTGTGAG
ACCACCCATGGGCCCACCAGTTGGACTCCCTCCTGCTCGAGTGACACCAATAGGTATGCTCCCTCCAGGAATGAGACCCC
CTTCACCAGGAATTAGAGGTCCACCTCCCCCAGGAATGCGTTCTCCCAGACCT

Alignment

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:

Parental  MTVGKSSKMLQHIDYRMRCILQDGRIFIGT-FKAFDKHMNLILCDCDEFRKIKPKNSKQAEREEKRVLGL
          M.VGKSSK.L.H.DYRMRCILQD..IFIGT.FKAFDK..NLIL.DCDEFRKIKPKN.KQ...EEKRV.GL
Retrocopy MAVGKSSKILLHMDYRMRCILQDRPIFIGT<FKAFDKPVNLILYDCDEFRKIKPKNAKQP*GEEKRVWGL

Parental  VLLRGENLVSMTVEGPPPKDTGIARVPLAGAAGGPGIGRAAGRGIPAGVPMPQAPAGLAGPVRGVGGPSQ
          VLLRGENLVSMTVEGPP.KDTGIA.VPLAGAAGGPG.GRAAGRG.PAGVP.PQAPAGLAGPV.GVGGPSQ
Retrocopy VLLRGENLVSMTVEGPPLKDTGIAQVPLAGAAGGPGVGRAAGRGVPAGVPIPQAPAGLAGPV*GVGGPSQ

Parental  QVMTPQGRGTV-AAAAAAAT-ASIAGAPTQYPPGRGGPPPPMGRGAPPPGM---MGPPPGMRPPMGPPMG
          QVMTPQG.GTV.AAA.AA...A...G.P...P.GRG.PPP..G...PPPG....MGPP.G..P....P.G
Retrocopy QVMTPQGTGTVEAAAIAATV>APGQGTPPP-PVGRGTPPP--GIMVPPPGVRPPMGPPVGLPPARVTPIG

Parental  -IPPGRGTPM----GMPPPGMRPPPP
          ..PPG...P.....G.PPPGMR.P.P
Retrocopy MLPPGMRPPSPGIRGPPPPGMRSPRP

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2918 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011353	1 retrocopy	retro_amel_1403,
Canis familiaris	ENSCAFG00000006693	3 retrocopies	retro_cfam_1268, retro_cfam_1773, retro_cfam_461,
Callithrix jacchus	ENSCJAG00000020971	2 retrocopies	retro_cjac_172, retro_cjac_1739,
Dasypus novemcinctus	ENSDNOG00000007896	2 retrocopies	retro_dnov_2060, retro_dnov_2471,
Erinaceus europaeus	ENSEEUG00000015568	3 retrocopies	retro_eeur_312, retro_eeur_434, retro_eeur_6,
Felis catus	ENSFCAG00000014447	2 retrocopies	retro_fcat_1788, retro_fcat_1960,
Microcebus murinus	ENSMICG00000016519	4 retrocopies	retro_mmur_1012, retro_mmur_1478, retro_mmur_546, retro_mmur_861,
Myotis lucifugus	ENSMLUG00000016951	1 retrocopy	retro_mluc_1725,
Mustela putorius furo	ENSMPUG00000009283	1 retrocopy	retro_mputfur_1153,
Mus musculus	ENSMUSG00000027404	3 retrocopies	retro_mmus_2938, retro_mmus_3450, retro_mmus_554,
Nomascus leucogenys	ENSNLEG00000009206	1 retrocopy	retro_nleu_761,
Otolemur garnettii	ENSOGAG00000007392	5 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	ENSOPRG00000007459	2 retrocopies	retro_opri_697, retro_opri_72,
Pongo abelii	ENSPPYG00000010841	1 retrocopy	retro_pabe_2265,
Pteropus vampyrus	ENSPVAG00000017013	1 retrocopy	retro_pvam_289,
Rattus norvegicus	ENSRNOG00000006961	2 retrocopies	retro_rnor_2825, retro_rnor_474,
Tupaia belangeri	ENSTBEG00000010040	3 retrocopies	retro_tbel_1117, retro_tbel_1171, retro_tbel_2839,
Tarsius syrichta	ENSTSYG00000014498	2 retrocopies	retro_tsyr_45, retro_tsyr_719,