RetrogeneDB - Retrocopy retro_ocun

						
>retro_ocun_807
CTTGGGGAAAGCTCAGATATAAAACCTGGTGTGAGCAGCAAAAAGGTTGCTGATCGGCCCAAAGGAAAGCATGCCTCGGC

TGTTGCCTCCAAGGAGGACCTGTGGACCCTATTGAAACCACCCCCAGTTTTTCCAGTGGACAATAGCAGTGCTAAAATCC

TTCCTAAAATAAGTTATGCAAGCAAAGTTAAGGAAAACCTCAATAAAACTAAACAGAACTCTGTGTCACCATCTTCGCCC

TCATCCTCTTCATCATCTACTGGAGAAACTCAGACACAATCTTCAAGTCGGTTATCCCAGCTTCCTCTGCCGGCACTGAA

ATCTGTTACTTCTGCCAGCTTTTCTAACGGGCCTGTCGAAGCAGGGACTGATGCAAGTGTGTATCCTCCAGGGGGCCAGC

CACTGCTAACTACTGCTGCTAATACTTTAACACCCATCTCTTCTGGGGCTGATTCAGTGCTCCAGGACGTGAGTCTAACT

TCAGCAGCTGTTAAACAAATAAAGCCTAGCCTTTTTATTTATCCTTCAAATATGCAAACTGTGCTTTTAAGCACAGCACA

AGTGGATCTGCCCTCTCAGACCGATCAACAAAACCTGGGGGATATCTTCCAGAATCACTGGGGTTTATGATTTATAAATG

AGCCCAGTGCTGGCCCTGAGGCTGTTACTGGGAAGTCATCTGATCATAAAGTGGTGGAGGTGACATTTCAAGGAGAATAT

CCTGCCACTTTGGTTTCACAGGGAGCTGAATAATCCCCTCAGGAACTGAGCATCCTGTGGTTCCCAAGGCTTATGAGCTG

GAGAAACGGACTAGTGCTCAAGTTCTGAGTAGCATTCTAAAATCTGGGACTACTGAGAGGGGAGCCTTATCCTTGGAACC

CAGTCATATAGGTGACCTGCAAAAAGCAGACACCAGTAGTCAAGGTGCTTTAGTGTTTCTCTCAAAGGACTATGAGATAG

AAAATCAAAATCCTCTGGCCTCTCCTGCGAACACTGTGTAGGGCTCCTCCAAAGAACAGAGATACCAGAGAGGCCTAGAA

AGGAAAAATAGCTGGGGTTCTTTTGACCTGAGGGCTGCTATTGTATCTCACACTAAAGAAATGGAATCTATTTGGAATTT

GCAGAAGCAAGATCCCAAAAGGATAATCACTTACAATGAAGCCATGGCTAGTCCAGATCAA

ORF - retro_ocun_807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.16 %
Parental protein coverage:	56.75 %
Number of stop codons detected:	2
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalLRKSSDIKPGVSSKKFDDRPKGKHASAVASKEDSWTLFKPPPVFPVDNSSAKIVPKISYASKVKENLNKT
		L..SSDIKPGVSSKK..DRPKGKHASAVASKED.WTL.KPPPVFPVDNSSAKI.PKISYASKVKENLNKT
RetrocopyLGESSDIKPGVSSKKVADRPKGKHASAVASKEDLWTLLKPPPVFPVDNSSAKILPKISYASKVKENLNKT
ParentalIQNSVSPSSSSSSSSSTGETQTQSSSRLSQVPMSALKSVTSASFSNGPVLAGTDANVYPPGGQPLLTTAA
		.QNSVSPSS.SSSSSSTGETQTQSSSRLSQ.P..ALKSVTSASFSNGPV.AGTDA.VYPPGGQPLLTTAA
RetrocopyKQNSVSPSSPSSSSSSTGETQTQSSSRLSQLPLPALKSVTSASFSNGPVEAGTDASVYPPGGQPLLTTAA
ParentalNTLTPISSGTDSVLQDVSLTSAAVEQIKSSLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQNQWGLS
		NTLTPISSG.DSVLQDVSLTSAAV.QIK.SLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQN.WGL.
RetrocopyNTLTPISSGADSVLQDVSLTSAAVKQIKPSLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQNHWGL*
ParentalFINEPSAGPETVIGKSSDHKVVEVTFQGEYPATLVSQGAE-IIPSGTEHPVFPKAYELEKRTSPQVLSNI
		FINEPSAGPE.V.GKSSDHKVVEVTFQGEYPATLVSQGAE.IIPSGTEHPV.PKAYELEKRTS.QVLS.I
RetrocopyFINEPSAGPEAVTGKSSDHKVVEVTFQGEYPATLVSQGAE<IIPSGTEHPVVPKAYELEKRTSAQVLSSI
ParentalLKSGTTNESGALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASPTNTLLGSAKEQRYQRGLER
		LKSGTT.E.GALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASP.NT..GS.KEQRYQRGLER
RetrocopyLKSGTT-ERGALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASPANTV*GSSKEQRYQRGLER
ParentalNDSWGSFDLRAAIVYHTKEMESIWNLQKQDPKRIITYNEAMDSPDQ
		..SWGSFDLRAAIV.HTKEMESIWNLQKQDPKRIITYNEAM.SPDQ
RetrocopyKNSWGSFDLRAAIVSHTKEMESIWNLQKQDPKRIITYNEAMASPDQ

							

							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 .06 RPM	25 .39 RPM
SRP017611_kidney	0 .00 RPM	31 .02 RPM
SRP017611_liver	0 .00 RPM	29 .06 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_807 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_807 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ocun_807 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033077	1 retrocopy	retro_btau_802,
Oryctolagus cuniculus	ENSOCUG00000016483	1 retrocopy	retro_ocun_807 ,

	RetrogeneDB ID:	retro_ocun_807
Retrocopy location	Organism:	*Rabbit (Oryctolagus cuniculus)*
	Coordinates:	15:65276021..65277202(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NUFIP2
	Ensembl ID:	ENSOCUG00000016483
	Aliases:	None
	Description:	nuclear fragile X mental retardation protein interacting protein 2 [Source:HGNC Symbol;Acc:17634]

Parental	LRKSSDIKPGVSSKKFDDRPKGKHASAVASKEDSWTLFKPPPVFPVDNSSAKIVPKISYASKVKENLNKT
	L..SSDIKPGVSSKK..DRPKGKHASAVASKED.WTL.KPPPVFPVDNSSAKI.PKISYASKVKENLNKT
Retrocopy	LGESSDIKPGVSSKKVADRPKGKHASAVASKEDLWTLLKPPPVFPVDNSSAKILPKISYASKVKENLNKT

Parental	IQNSVSPSSSSSSSSSTGETQTQSSSRLSQVPMSALKSVTSASFSNGPVLAGTDANVYPPGGQPLLTTAA
	.QNSVSPSS.SSSSSSTGETQTQSSSRLSQ.P..ALKSVTSASFSNGPV.AGTDA.VYPPGGQPLLTTAA
Retrocopy	KQNSVSPSSPSSSSSSTGETQTQSSSRLSQLPLPALKSVTSASFSNGPVEAGTDASVYPPGGQPLLTTAA

Parental	NTLTPISSGTDSVLQDVSLTSAAVEQIKSSLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQNQWGLS
	NTLTPISSG.DSVLQDVSLTSAAV.QIK.SLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQN.WGL.
Retrocopy	NTLTPISSGADSVLQDVSLTSAAVKQIKPSLFIYPSNMQTVLLSTAQVDLPSQTDQQNLGDIFQNHWGL*

Parental	FINEPSAGPETVIGKSSDHKVVEVTFQGEYPATLVSQGAE-IIPSGTEHPVFPKAYELEKRTSPQVLSNI
	FINEPSAGPE.V.GKSSDHKVVEVTFQGEYPATLVSQGAE.IIPSGTEHPV.PKAYELEKRTS.QVLS.I
Retrocopy	FINEPSAGPEAVTGKSSDHKVVEVTFQGEYPATLVSQGAE<IIPSGTEHPVVPKAYELEKRTSAQVLSSI

Parental	LKSGTTNESGALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASPTNTLLGSAKEQRYQRGLER
	LKSGTT.E.GALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASP.NT..GS.KEQRYQRGLER
Retrocopy	LKSGTT-ERGALSLEPSHIGDLQKADTSSQGALVFLSKDYEIENQNPLASPANTV*GSSKEQRYQRGLER

Parental	NDSWGSFDLRAAIVYHTKEMESIWNLQKQDPKRIITYNEAMDSPDQ
	..SWGSFDLRAAIV.HTKEMESIWNLQKQDPKRIITYNEAM.SPDQ
Retrocopy	KNSWGSFDLRAAIVSHTKEMESIWNLQKQDPKRIITYNEAMASPDQ

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

RetrogeneDB ID:

retro_ocun_807