RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_547
CCAAGAGTTCAAACAGACCCTCCCTCAGTTCCAGTATGTGACCTGTGTACTAAGGGTGTATTTCCCAAAGGACAAGAGTG

TGAATACCCACCCATCCAAGAGGGGCGGACAGCTGCTTGGAGAACCACAAGTGAAGAGAAAAAGTCGCTAGATCAGGCTA

GTGAGGAGATTTGGAACGACTTCCGAGAAGCTGCCGAAGCACACTGGCAAGATAGGAAATAATGTCATGAGCTGAATCAA

GCCTGGAATGACAATGATAGAAATATATGAGAAGTTGGAAGACTGTTCCCGAAAGCTCATAAAGGAGAATGGGTTAAATG

CAGGCCTGGCCTTTCCCACTGGGTGTTCTCTCAACAACTGTGCTGCACATTACACTCCCAATGCTGGTGACACGACAGTC

TTACAGTACGACGACATCTGTAAGACCGACTTTGGAACACATATAAGTGGTAGAATAATTGATTGTGCTTTTACTGTTAC

TTTTAATCCTAAATATGACATATTATTACAAGCTGTAAAAGATGCCACCAATACTGGAATGAAGTGTGCTGGGATTGATG

TCCGTCTCTGTGATGTTGGTGAGGCCATTCAAGAAGTTACGGAGTCCCGTGAAGTAGAAATAGATAAGAAGACATATCAA

GTGAAACCCATACGGAACTTAAATGGACATTCAATTGGGCCATATAGAATTCAAGCTAGAAAAACTGCCCATTGTGAAAG

GAGGGGAAGCTACAAGAATGGAGGAAGGAGAGGTGTATGCCATTGAGACCTTTGGTAGCACAGGGAAGGGCATGGTTCAT

GACGACATGGAATGTTCACACTACATGATAAATTTTGATGTGGGACACGTGCCAATAAGGCTTCCAAGAACAAAACACTT

GTTGAATGTCATCAACGAAAACTTCGGTACCCTTGCCTTCTGCCAAAGGTGACTGGATCACTTGGGAGAAAGTAAATACT

TAATGGCTCTGAAGAACCTGTGTGACTTGGGCATTGTAGATCCATATCCACCACTCTGTGACATTAAAGGACACAGCACA

GTTTGAACATACCATACTGCTGCGCCCAACCTGTAAAGAAGTTGTCAGCAGAGGAGATGAGTATTAAAACT

ORF - retro_rnor_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	89.33 %
Parental protein coverage:	86.28 %
Number of stop codons detected:	4
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalPRVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQ
		PRVQTDPPSVP.CDL...GVFPKGQECEYPP.Q.GRTAAWRTTSEEKK.LDQASEEIWNDFREAAEAH.Q
RetrocopyPRVQTDPPSVPVCDLCTKGVFPKGQECEYPPIQEGRTAAWRTTSEEKKSLDQASEEIWNDFREAAEAHWQ
ParentalVRK-YVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
		.RK..VMS.IKPGMTMIEI.EKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
RetrocopyDRK>NVMS*IKPGMTMIEIYEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
ParentalCKIDFGTHISGRIIDCAFTVTFNPKYDILLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDG
		CK.DFGTHISGRIIDCAFTVTFNPKYDILL.AVKDATNTG.KCAGIDVRLCDVGEAIQEV.ES.EVEID.
RetrocopyCKTDFGTHISGRIIDCAFTVTFNPKYDILLQAVKDATNTGMKCAGIDVRLCDVGEAIQEVTESREVEIDK
ParentalKTYQVKPIRNLNGHSIGPYRIHAGKTV-PIVK-GGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMK
		KTYQVKPIRNLNGHSIGPYRI.A.KT..P..K.GGEATRMEEGEVYAIETFGSTGKG.VHDDMECSHYM.
RetrocopyKTYQVKPIRNLNGHSIGPYRIQARKTA<PL*K<GGEATRMEEGEVYAIETFGSTGKGMVHDDMECSHYMI
ParentalNFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYT
		NFDVGHVPIRLPRTKHLLNVINENFGTLAFC.R.LD.LGESKYLMALKNLCDLGIVDPYPPLCDIKG..T
RetrocopyNFDVGHVPIRLPRTKHLLNVINENFGTLAFCQR*LDHLGESKYLMALKNLCDLGIVDPYPPLCDIKGHST
ParentalAQFEHT-ICAQPVKKLSAEEMTIKT
		....HT..CAQPVKKLSAEEM.IKT
RetrocopyV*TYHT<CCAQPVKKLSAEEMSIKT

							

							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	25 .31 RPM
SRP017611_kidney	0 .00 RPM	36 .98 RPM
SRP017611_liver	0 .00 RPM	15 .94 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_547 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_547 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_547 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006353	1 retrocopy	retro_cfam_1330,
Monodelphis domestica	ENSMODG00000008173	1 retrocopy	retro_mdom_297,
Mus musculus	ENSMUSG00000036112	2 retrocopies	retro_mmus_3689, retro_mmus_770,
Otolemur garnettii	ENSOGAG00000008469	1 retrocopy	retro_ogar_2163,
Rattus norvegicus	ENSRNOG00000021881	2 retrocopies	retro_rnor_1707, retro_rnor_547 ,

	RetrogeneDB ID:	retro_rnor_547
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	1:261237123..261238234(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Metap2
	Ensembl ID:	ENSRNOG00000021881
	Aliases:	Metap2, Amp2, Mnpep, p67
	Description:	methionine aminopeptidase 2 [Source:RefSeq peptide;Acc:NP_071984]

Parental	PRVQTDPPSVPICDLYPNGVFPKGQECEYPPTQDGRTAAWRTTSEEKKALDQASEEIWNDFREAAEAHRQ
	PRVQTDPPSVP.CDL...GVFPKGQECEYPP.Q.GRTAAWRTTSEEKK.LDQASEEIWNDFREAAEAH.Q
Retrocopy	PRVQTDPPSVPVCDLCTKGVFPKGQECEYPPIQEGRTAAWRTTSEEKKSLDQASEEIWNDFREAAEAHWQ

Parental	VRK-YVMSWIKPGMTMIEICEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
	.RK..VMS.IKPGMTMIEI.EKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI
Retrocopy	DRK>NVMS*IKPGMTMIEIYEKLEDCSRKLIKENGLNAGLAFPTGCSLNNCAAHYTPNAGDTTVLQYDDI

Parental	CKIDFGTHISGRIIDCAFTVTFNPKYDILLKAVKDATNTGIKCAGIDVRLCDVGEAIQEVMESYEVEIDG
	CK.DFGTHISGRIIDCAFTVTFNPKYDILL.AVKDATNTG.KCAGIDVRLCDVGEAIQEV.ES.EVEID.
Retrocopy	CKTDFGTHISGRIIDCAFTVTFNPKYDILLQAVKDATNTGMKCAGIDVRLCDVGEAIQEVTESREVEIDK

Parental	KTYQVKPIRNLNGHSIGPYRIHAGKTV-PIVK-GGEATRMEEGEVYAIETFGSTGKGVVHDDMECSHYMK
	KTYQVKPIRNLNGHSIGPYRI.A.KT..P..K.GGEATRMEEGEVYAIETFGSTGKG.VHDDMECSHYM.
Retrocopy	KTYQVKPIRNLNGHSIGPYRIQARKTA<PL*K<GGEATRMEEGEVYAIETFGSTGKGMVHDDMECSHYMI

Parental	NFDVGHVPIRLPRTKHLLNVINENFGTLAFCRRWLDRLGESKYLMALKNLCDLGIVDPYPPLCDIKGSYT
	NFDVGHVPIRLPRTKHLLNVINENFGTLAFC.R.LD.LGESKYLMALKNLCDLGIVDPYPPLCDIKG..T
Retrocopy	NFDVGHVPIRLPRTKHLLNVINENFGTLAFCQR*LDHLGESKYLMALKNLCDLGIVDPYPPLCDIKGHST

Parental	AQFEHT-ICAQPVKKLSAEEMTIKT
	....HT..CAQPVKKLSAEEM.IKT
Retrocopy	V*TYHT<CCAQPVKKLSAEEMSIKT

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

RetrogeneDB ID:

retro_rnor_547