RetrogeneDB ID: retro_ocun_1057

Retrocopy location

• Organism: Rabbit (Oryctolagus cuniculus)
• Coordinates: 2:98199941..98200321(+)
• Located in intron of: ENSOCUG00000023257

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: MRPS36
• Ensembl ID: ENSOCUG00000005261
• Aliases: None
• Description: mitochondrial ribosomal protein S36 [Source:HGNC Symbol;Acc:16631]

Sequence

>retro_ocun_1057
CCCACAGCAGCCCACAACTACAGAGGTGGCTGCGGCTTGCTCGCTCCCCGGAAGCTGCCCCTTCCCTGGGGTCATCATGG
ACAGTAAGATGGTGTCTGCCAGCCGGGTCGTTCAGGTAGTCAAACCACATACCCCATCAATAAGGTTCCCTGCCAGAAGA
GACGATCCTAAACCCAATGTGTCTGAAGTTTGAGATCAGCTGGACTGCCGTGTCACTCTTCTGCAGTTGCACAGCAGGCT
AAGGAAGTAGACCACCGGATTTGCTGATGGATCAGGGGCCACCGGACACTGCCGAAATCATTAAATCATTGCCTCAGAAG
TACAGAAGGAAACCTGTACCTCAAGAAGAAATGGAATTTGTCCAACGTGGAGGTCCCGAG

Alignment

ORF - retro_ocun_1057 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80. %
• Parental protein coverage: 71.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PTEAHDSRDRRGSLAPRKLPLP-GVMMGSKMASASRVVQVVKPHTPLIRFPDRRDNPKPNVSE-ALRSAG
          PT.AH..R...G.LAPRKLPLP.GV.M.SKM.SASRVVQVVKPHTP.IRFP.RRD.PKPNVSE..LRSAG
Retrocopy PTAAHNYRGGCGLLAPRKLPLP>GVIMDSKMVSASRVVQVVKPHTPSIRFPARRDDPKPNVSE<SLRSAG

Parental  LPSHTSTVAQHAK-GSKSPDLLMYQGPPDTAEIIKSLPQKYRRKPVPPEEMEFIQRGGPE
          LP.H.S.VAQ.AK.GS..PDLLM.QGPPDTAEIIKSLPQKYRRKPVP.EEMEF.QRGGPE
Retrocopy LPCHSSAVAQQAK<GSRPPDLLMDQGPPDTAEIIKSLPQKYRRKPVPQEEMEFVQRGGPE

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	16.34 RPM
SRP017611_kidney	0.00 RPM	33.65 RPM
SRP017611_liver	0.00 RPM	7.78 RPM

ChIP-Seq

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ocun_1057 retrocopy.

TSS

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab

retro_ocun_1057 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ocun_1057 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003161	2 retrocopies	retro_amel_1838, retro_amel_565,
Callithrix jacchus	ENSCJAG00000016092	2 retrocopies	retro_cjac_3202, retro_cjac_45,
Dipodomys ordii	ENSDORG00000007063	1 retrocopy	retro_dord_110,
Echinops telfairi	ENSETEG00000019493	2 retrocopies	retro_etel_1624, retro_etel_625,
Felis catus	ENSFCAG00000031782	1 retrocopy	retro_fcat_724,
Homo sapiens	ENSG00000134056	2 retrocopies	retro_hsap_2750, retro_hsap_823,
Loxodonta africana	ENSLAFG00000007932	2 retrocopies	retro_lafr_1243, retro_lafr_598,
Monodelphis domestica	ENSMODG00000019701	1 retrocopy	retro_mdom_1559,
Mus musculus	ENSMUSG00000061474	4 retrocopies	retro_mmus_105, retro_mmus_123, retro_mmus_3223, retro_mmus_753,
Nomascus leucogenys	ENSNLEG00000004071	4 retrocopies	retro_nleu_1545, retro_nleu_196, retro_nleu_2243, retro_nleu_257,
Oryctolagus cuniculus	ENSOCUG00000005261	2 retrocopies	retro_ocun_1057 , retro_ocun_1109,
Otolemur garnettii	ENSOGAG00000024260	9 retrocopies	retro_ogar_1166, retro_ogar_1716, retro_ogar_2238, retro_ogar_2363, retro_ogar_2629, retro_ogar_3382, retro_ogar_711, retro_ogar_790, retro_ogar_869,
Ochotona princeps	ENSOPRG00000011392	1 retrocopy	retro_opri_587,
Pongo abelii	ENSPPYG00000015524	3 retrocopies	retro_pabe_2219, retro_pabe_735, retro_pabe_917,
Pan troglodytes	ENSPTRG00000016944	4 retrocopies	retro_ptro_1858, retro_ptro_2038, retro_ptro_573, retro_ptro_690,
Pteropus vampyrus	ENSPVAG00000010843	1 retrocopy	retro_pvam_174,
Rattus norvegicus	ENSRNOG00000048862	2 retrocopies	retro_rnor_1792, retro_rnor_2014,
Ictidomys tridecemlineatus	ENSSTOG00000021863	2 retrocopies	retro_itri_1039, retro_itri_938,
Tupaia belangeri	ENSTBEG00000012048	22 retrocopies	retro_tbel_1313, retro_tbel_1494, retro_tbel_1527, retro_tbel_224, retro_tbel_2404, retro_tbel_2661, retro_tbel_2755, retro_tbel_2762, retro_tbel_2924, retro_tbel_2934, retro_tbel_3239, retro_tbel_3240, retro_tbel_359, retro_tbel_3891, retro_tbel_3893, retro_tbel_3941, retro_tbel_4124, retro_tbel_4429, retro_tbel_4515, retro_tbel_4543, retro_tbel_4592, retro_tbel_702,