RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_1289
GAAACTCCAAAAGCAAGAAAAAGAAACCTCAAGCAACAGAACAAAAAAAAAAAAAAAAAAACACAGCAGAACCCAAAAAA

CCTGCTAAGGTTAAAAAAAAAAAGGCAAATCTGCCAATTCAAAGGAAAAGCAAGAAAAAATGATAGACATGTTTAAAGTG

AAAAAGGAAAGTAGACCATTAATGGTGTTTCAGAGGCCAAACTTCTGACCAAGACTCTCCCTGATGTTTTGACCTTCAAC

CTGGGCATTGTAATTTTTGGCATAAATCCAAGACTAAAGGCTGCTTACCAAGGACATCACTATCCTGGACCTGGAAACCA

TTTTTGAAAGTGTCTGTTCATGTCAGGGCCGAGTGAGGTCCAGCTGAACCACGTGGACGATCACACTTTACCAGGGAAGT

ATGGTATTGGATTTACCAACATGGTGGAGAGGATGACACCGGGCAGCAAGGTCTTTTCCAGTAAAGAATTTCATGAAAGA

GGATGTATTCTAGTACAGAAATATCAGCCATGATAGCAGTGTTTCATGGAAAATGTATTTGTGAAATTTTTAGTAAAGAA

GTCTTTGGAGTGAAGGTTAAGAACTTGGAATTTGGGCTTCAACCCCACAAGATTCCAGACACAGACACTCTCGGCTATAT

GATGCCATCATCTGGTGCAAGGTGTGCTCAGTTTCCTTGCACCCAGGACAAAGTTCATTGCTACATTAAGTTAAAGGACT

TAAGAGATCAGTTGAAAGGCACTGAATGAAACACAGACGTTCAAGAAGTGCAGAACACATTTGACCTACAGCTTGCCCAA

GAGAATGCAGAGAAGATGGTTGTTAAGAAAAATACTATCCTGGCTATGAAGCAGCCTATGGTGGTGCTTACAGGGAAAAC

CCATGTAATAGTGAACCTTGCAGCTTCTTGTCAAATGGGCTCGCTGCTGACAGGGTGGAGTTAAGAGAATCAAGTCTCAG

TGACATCCCAGATGGACAGTGGATAGCCCAGCCATTACAGATCAGAGTCCTTCCCTTAACAATCACTGTGGAGCACAAGA

GCAG

ORF - retro_ocun_1289 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	74.86 %
Parental protein coverage:	99.43 %
Number of stop codons detected:	2
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalEAPKGR----KRKTRATEPKKPAEPKKPAEAKKS-GKSAKSKEKQEKITDAFKVKRKVD-RFNGVSEAEL
		E.PK.R....K........K....PK.....KK..GKSA.SKEKQEK..D.FKVK.......NGVSEA.L
RetrocopyETPKARKRNLKQQNKKKKKKTQQNPKNLLRLKKK>GKSANSKEKQEKMIDMFKVKKESR<TINGVSEAKL
ParentalLTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGF
		LTKTLPD.LTFNL.IVI.GINP.L.AAY.GHHYPGPGNHF.KCLFMSG.SEVQLNH.DDHTLPGKYGIGF
RetrocopyLTKTLPDVLTFNLGIVIFGINPRLKAAYQGHHYPGPGNHF*KCLFMSGPSEVQLNHVDDHTLPGKYGIGF
ParentalTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP-RIAVFNGKCIYEIFSREVFGVKVKNLEFGLQPHK
		TNMVER.TPGSK..SSKEF.E.G.ILV...QKYQP..IAVF.GKCI.EIFS.EVFGVKVKNLEFGLQPHK
RetrocopyTNMVERMTPGSKVFSSKEFHERGCILV---QKYQP<MIAVFHGKCICEIFSKEVFGVKVKNLEFGLQPHK
ParentalIPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNTDVQEVRYTFDLQLAQEDAKKMA
		IPDT.TL.Y.MPSS.ARCAQFP..QDKVH.YIKLKDLRDQLKG.E.NTDVQEV..TFDLQLAQE.A.KM.
RetrocopyIPDTDTLGYMMPSSGARCAQFPCTQDKVHCYIKLKDLRDQLKGTE*NTDVQEVQNTFDLQLAQENAEKMV
ParentalVK-EEKYDPGYEAAYGGAYSDNPCNSEPCSFPSNGLAADSAELRESALNAIPDGQWMAQP-FTDQIPSLN
		VK.E..Y.PGYEAAYGGAY..NPCNSEPCSF.SNGLAAD..ELRES.L..IPDGQW.AQP..TDQ.PSLN
RetrocopyVK<EKYY-PGYEAAYGGAYRENPCNSEPCSFLSNGLAADRVELRESSLSDIPDGQWIAQP<ITDQSPSLN
ParentalNHCGAQEQ
		NHCGAQEQ
RetrocopyNHCGAQEQ

							

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

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0 .00 RPM	9 .66 RPM
SRP017611_kidney	0 .00 RPM	6 .89 RPM
SRP017611_liver	0 .00 RPM	5 .16 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_1289 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_1289 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_1289 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013722	1 retrocopy	retro_dnov_1749,
Echinops telfairi	ENSETEG00000019930	1 retrocopy	retro_etel_2184,
Homo sapiens	ENSG00000139372	1 retrocopy	retro_hsap_980,
Loxodonta africana	ENSLAFG00000003813	1 retrocopy	retro_lafr_460,
Mus musculus	ENSMUSG00000034674	4 retrocopies	retro_mmus_1125, retro_mmus_1363, retro_mmus_3040, retro_mmus_637,
Oryctolagus cuniculus	ENSOCUG00000016313	1 retrocopy	retro_ocun_1289 ,
Rattus norvegicus	ENSRNOG00000027124	1 retrocopy	retro_rnor_2286,

	RetrogeneDB ID:	retro_ocun_1289
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	7:8655860..8656904(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TDG
	Ensembl ID:	ENSOCUG00000016313
	Aliases:	None
	Description:	thymine-DNA glycosylase [Source:HGNC Symbol;Acc:11700]

Parental	EAPKGR----KRKTRATEPKKPAEPKKPAEAKKS-GKSAKSKEKQEKITDAFKVKRKVD-RFNGVSEAEL
	E.PK.R....K........K....PK.....KK..GKSA.SKEKQEK..D.FKVK.......NGVSEA.L
Retrocopy	ETPKARKRNLKQQNKKKKKKTQQNPKNLLRLKKK>GKSANSKEKQEKMIDMFKVKKESR<TINGVSEAKL

Parental	LTKTLPDILTFNLDIVIIGINPGLMAAYKGHHYPGPGNHFWKCLFMSGLSEVQLNHMDDHTLPGKYGIGF
	LTKTLPD.LTFNL.IVI.GINP.L.AAY.GHHYPGPGNHF.KCLFMSG.SEVQLNH.DDHTLPGKYGIGF
Retrocopy	LTKTLPDVLTFNLGIVIFGINPRLKAAYQGHHYPGPGNHF*KCLFMSGPSEVQLNHVDDHTLPGKYGIGF

Parental	TNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQP-RIAVFNGKCIYEIFSREVFGVKVKNLEFGLQPHK
	TNMVER.TPGSK..SSKEF.E.G.ILV...QKYQP..IAVF.GKCI.EIFS.EVFGVKVKNLEFGLQPHK
Retrocopy	TNMVERMTPGSKVFSSKEFHERGCILV---QKYQP<MIAVFHGKCICEIFSKEVFGVKVKNLEFGLQPHK

Parental	IPDTETLCYVMPSSSARCAQFPRAQDKVHYYIKLKDLRDQLKGIERNTDVQEVRYTFDLQLAQEDAKKMA
	IPDT.TL.Y.MPSS.ARCAQFP..QDKVH.YIKLKDLRDQLKG.E.NTDVQEV..TFDLQLAQE.A.KM.
Retrocopy	IPDTDTLGYMMPSSGARCAQFPCTQDKVHCYIKLKDLRDQLKGTE*NTDVQEVQNTFDLQLAQENAEKMV

Parental	VK-EEKYDPGYEAAYGGAYSDNPCNSEPCSFPSNGLAADSAELRESALNAIPDGQWMAQP-FTDQIPSLN
	VK.E..Y.PGYEAAYGGAY..NPCNSEPCSF.SNGLAAD..ELRES.L..IPDGQW.AQP..TDQ.PSLN
Retrocopy	VK<EKYY-PGYEAAYGGAYRENPCNSEPCSFLSNGLAADRVELRESSLSDIPDGQWIAQP<ITDQSPSLN

Parental	NHCGAQEQ
	NHCGAQEQ
Retrocopy	NHCGAQEQ

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

RetrogeneDB ID:

retro_ocun_1289