RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_904
ATAGTTACCTCCCACCTTGCCCTATTCAGTGTGTCTGACAAAACTGGCCTTGTGGAATTCATCAGAAACATTGTGTTTCT

TGGTGTGAGTCCAGTCACTTGCAGAGGCATGGAAAAGGTGATCAGGGATGCTAGCCTGGAAGTCAGAGGTATGTTTAAGC

TAATGGGATTCCCTGAAATGTTAGGAGAACTTGTACAAACCTTATATTCTGCTGGCCATGCCGGAATCTTTACAAACAAT

ATTCCAGAAAATGCTGCTGACATCACCAGGCTTGATTTCAACTTTCTAAGAGTTGTTGTCTGTAACCTGTACCACTTCAT

GAGGACTATGTCTTCCCCAGATGTAACTGTTGAGGCAACTGTTTAGCAAATTAACATTGGTGGCATGACCTTACTGACAA

CTGCATCCAAAACACATGTTCAAGTGACAGTAGTCTATAAAACAGAGAACTATGCTGTGGTGGCTACAGAGATGCAGGGC

TGTGATAATAAGGACACTTCCCTGGAGACGAGATGCCACTTGGCATTGAAGGCATTCACTCATACCACTCAAAATGATAA

AGTAATATCAGATTATTTCAGGAAACTGTACAGTAATGGAAATTCTCAGATGCCCTTGAGGTATGGGATGAACCCCCATC

AGACTCTTGCTCATCTGTGTACAGTGATGCCCAAGCATCCCATAAAAGTTCTGATCAGAGCCCCACGATCCATAAACTTG

CGTAATGCTTTGAATGTCTGGCAGCTGGTGAAAAAACTCTGAGGAGCAGTAGATATTCCAGCATTGGCTTCTTTCATGCA

AGTCAGTCCAGCAGGTGCTGCTGTTGAGTTTCCACTTAGGGAGGACAAAGCTAGAGTTTGCGTGGTTTATGACCTCTATC

TGACCCTTACTCCCTCCCCAGCCATTGCATAT

ORF - retro_rnor_904 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	67.76 %
Parental protein coverage:	51.18 %
Number of stop codons detected:	2
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMASSQLALFSVSDKTGLVEFARNLASLGLSLVASGGTAKAIRDAGLAVRDVSELTGFPEMLGGRVKTLHP
		...S.LALFSVSDKTGLVEF.RN...LG.S.V...G..K.IRDA.L.VR....L.GFPEMLG..V.TL..
RetrocopyIVTSHLALFSVSDKTGLVEFIRNIVFLGVSPVTCRGMEKVIRDASLEVRGMFKLMGFPEMLGELVQTLYS
ParentalAVHAGILARNIPEDAADMARLDFNLIRVVVCNLYPFVKTVASPDVTVEAAVEQIDIGGVTLLRAAAKNHA
		A.HAGI...NIPE.AAD..RLDFN..RVVVCNLY.F..T..SPDVTVEA.V.QI.IGG.TLL..A.K.H.
RetrocopyAGHAGIFTNNIPENAADITRLDFNFLRVVVCNLYHFMRTMSSPDVTVEATV*QINIGGMTLLTTASKTHV
ParentalRVTVVCEPEDYGAVAAEMQGSGNKDTSLETRRHLALKAFTHTAQYDEAISDYFRRQYSKGISQMPLRYGM
		.VTVV...E.Y..VA.EMQG..NKDTSLETR.HLALKAFTHT.Q.D..ISDYFR..YS.G.SQMPLRYGM
RetrocopyQVTVVYKTENYAVVATEMQGCDNKDTSLETRCHLALKAFTHTTQNDKVISDYFRKLYSNGNSQMPLRYGM
ParentalNPHQTPAQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVTELRGAVDIPAAASFKHVSPAGAAVGVPLS
		NPHQT.A.L.T..PK.PI.VL..AP..INL..ALN.WQLV..L.GAVDIPA.ASF..VSPAGAAV..PL.
RetrocopyNPHQTLAHLCTVMPKHPIKVLIRAPRSINLRNALNVWQLVKKL*GAVDIPALASFMQVSPAGAAVEFPLR
ParentalEDEARVCMVYDLYPTLTPL-AIAY
		ED.ARVC.VYDLY.TLTP..AIAY
RetrocopyEDKARVCVVYDLYLTLTPSPAIAY

							

							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	20 .63 RPM
SRP017611_kidney	0 .00 RPM	34 .40 RPM
SRP017611_liver	0 .00 RPM	12 .37 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_904 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_904 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_904 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
Callithrix jacchus	ENSCJAG00000011695	4 retrocopies	retro_cjac_1538, retro_cjac_2185, retro_cjac_3116, retro_cjac_706,
Microcebus murinus	ENSMICG00000014573	1 retrocopy	retro_mmur_1591,
Myotis lucifugus	ENSMLUG00000001830	1 retrocopy	retro_mluc_1370,
Monodelphis domestica	ENSMODG00000015612	1 retrocopy	retro_mdom_1074,
Mustela putorius furo	ENSMPUG00000007676	1 retrocopy	retro_mputfur_1609,
Mus musculus	ENSMUSG00000026192	1 retrocopy	retro_mmus_2729,
Rattus norvegicus	ENSRNOG00000015511	1 retrocopy	retro_rnor_904 ,

	RetrogeneDB ID:	retro_rnor_904
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	13:17740587..17741499(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Atic
	Ensembl ID:	ENSRNOG00000015511
	Aliases:	None
	Description:	Bifunctional purine biosynthesis protein PURH Phosphoribosylaminoimidazolecarboxamide formyltransferase IMP cyclohydrolase [Source:UniProtKB/Swiss-Prot;Acc:O35567]

Parental	MASSQLALFSVSDKTGLVEFARNLASLGLSLVASGGTAKAIRDAGLAVRDVSELTGFPEMLGGRVKTLHP
	...S.LALFSVSDKTGLVEF.RN...LG.S.V...G..K.IRDA.L.VR....L.GFPEMLG..V.TL..
Retrocopy	IVTSHLALFSVSDKTGLVEFIRNIVFLGVSPVTCRGMEKVIRDASLEVRGMFKLMGFPEMLGELVQTLYS

Parental	AVHAGILARNIPEDAADMARLDFNLIRVVVCNLYPFVKTVASPDVTVEAAVEQIDIGGVTLLRAAAKNHA
	A.HAGI...NIPE.AAD..RLDFN..RVVVCNLY.F..T..SPDVTVEA.V.QI.IGG.TLL..A.K.H.
Retrocopy	AGHAGIFTNNIPENAADITRLDFNFLRVVVCNLYHFMRTMSSPDVTVEATV*QINIGGMTLLTTASKTHV

Parental	RVTVVCEPEDYGAVAAEMQGSGNKDTSLETRRHLALKAFTHTAQYDEAISDYFRRQYSKGISQMPLRYGM
	.VTVV...E.Y..VA.EMQG..NKDTSLETR.HLALKAFTHT.Q.D..ISDYFR..YS.G.SQMPLRYGM
Retrocopy	QVTVVYKTENYAVVATEMQGCDNKDTSLETRCHLALKAFTHTTQNDKVISDYFRKLYSNGNSQMPLRYGM

Parental	NPHQTPAQLYTLKPKLPITVLNGAPGFINLCDALNAWQLVTELRGAVDIPAAASFKHVSPAGAAVGVPLS
	NPHQT.A.L.T..PK.PI.VL..AP..INL..ALN.WQLV..L.GAVDIPA.ASF..VSPAGAAV..PL.
Retrocopy	NPHQTLAHLCTVMPKHPIKVLIRAPRSINLRNALNVWQLVKKL*GAVDIPALASFMQVSPAGAAVEFPLR

Parental	EDEARVCMVYDLYPTLTPL-AIAY
	ED.ARVC.VYDLY.TLTP..AIAY
Retrocopy	EDKARVCVVYDLYLTLTPSPAIAY

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

RetrogeneDB ID:

retro_rnor_904