RetrogeneDB - Retrocopy retro_rnor

                        
>retro_rnor_1397
ACTCCACTCCATGACTTCCACCTAGCCCATGGAGGGAAAATGGTGGCATTTGCAGGGTGGAATCTGCCTGTGCAATACCG

GGACAGTCATGTTGATTCACACCTGCACACATGCTGGCACTGCTCTCTTTTTGATGTGTCCCACATGCTACAGACCAAGA

TATTTGGCTGTGTCCGAGTGAGGCTGATGGAGAGTATAGTGATTGGAGACACTGCAGAACTAAGGCCTAACCAGGGAGCA

CTATCTCTGTTTACCAATGAGGCTGGAGGCATCTTAGACGACTTGATTGTGACCAATACTTCTGAGGGGCACCTGTATGT

AGTATCCAATGCTGGCTGCTGGGACAAGGACTTGACTTTCATGCAGGACAAAGTCAAGGAGTTCCGGAACAGGGGCAGTG

ATGTGGGCCTGGAGGTGGTAGATAATGCTCTGTTGGCTCTGCAAGGACCCACGGCAGTACAGGTGTGAAAGGCTGGGATG

AGAGATGATAGGAGGAAACTGCCCTCCATTACTAGTGCTGTGATGGAGGTGTTTGGTGTGTTTGGCTGTCGTGTGACCTG

TTGTGGCTACACAGGAGAGGATGATGTTGAGATATCAGTGCCAGCAGTAGGAGCAGTCCACTTGGCGACTGCTCTGCTGA

AAAACGCAGAGGTAAAGCTGGCAGGACTAGCAGCCGGAGATACCCTGCTCCTGGAGGCTGGCCTCTGTCTGTATGGGAAT

GACATTGATAAACATACCACACCTGTGGAGGGCAGCCTCAGCTGGATGCTGGGAAAGCGCCGCCGAATTGCTATGGACTT

CCGGGGAGCCAAAATCATTGTTCCCCAGCTAAAGAGTAAGGTGCTGCGGAGATATGTGGGGTTGATATGCGAAGGGGCTC

CAATGAGAGCACACAGTCCTATTTTGAACACAGAAGGCGCTGTGATCGGTACAGTGACCAGTGACTGCCCTTCACCCAGC

CTGAAGAAGAATGTGGCGATGGGTTATGTGGCATTCAAGTACAGACGGCCAGGAACACAGCTGCTGGTAGAAGTTCGGCG

GAAGCAGCAAATAACCATGATTAGCAAAATGCCTTTTATGCTCACAAAGTACTATACTCTCAAG

ORF - retro_rnor_1397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.8 %
Parental protein coverage:	91.32 %
Number of stop codons detected:	1
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalTPLYDFHLAHGGKMVAFAGWSLPVQYRDSHVDSHLHTRRHCSLFDVSHMLQTKIFGCDRVRLMENIVVGD
TPL.DFHLAHGGKMVAFAGW.LPVQYRDSHVDSHLHT..HCSLFDVSHMLQTKIFGC.RVRLME.IV.GD
RetrocopyTPLHDFHLAHGGKMVAFAGWNLPVQYRDSHVDSHLHTCWHCSLFDVSHMLQTKIFGCVRVRLMESIVIGD
ParentalIAELRPNQGHFRIFRQLWRSTIPALLHWEARDHRLYSLTSHAAEVPDLARFQDKVKEFQNRGLDVGLEVV
.AELRPNQG....F..........L.........LY..........DL...QDKVKEF.NRG.DVGLEVV
RetrocopyTAELRPNQGALSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWDKDLTFMQDKVKEFRNRGSDVGLEVV
ParentalDNALLALQGPTAAQVLQAGVTDDMRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPAAGAVHLAT
DNALLALQGPTA.QV..AG..DD.RKLP..TSAVMEVFGV.GCRVT.CGYTGED.VEISVPA.GAVHLAT
RetrocopyDNALLALQGPTAVQV*KAGMRDDRRKLPSITSAVMEVFGVFGCRVTCCGYTGEDDVEISVPAVGAVHLAT
ParentalALLKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRVAMDFPGAKIIIPQLKGE
ALLKN.EVKLAGLAA.D.L.LEAGLCLYGNDID.HTTPVEGSLSW.LGKRRR.AMDF.GAKII.PQLK..
RetrocopyALLKNAEVKLAGLAAGDTLLLEAGLCLYGNDIDKHTTPVEGSLSWMLGKRRRIAMDFRGAKIIVPQLKSK
ParentalVQRRRVGLICEGAPMRAHSPILNTEGAVIGTVTSGCPSPSLKKNVAMGYVAFKYSRPGTQLLVEVRRKQQ
V.RR.VGLICEGAPMRAHSPILNTEGAVIGTVTS.CPSPSLKKNVAMGYVAFKY.RPGTQLLVEVRRKQQ
RetrocopyVLRRYVGLICEGAPMRAHSPILNTEGAVIGTVTSDCPSPSLKKNVAMGYVAFKYRRPGTQLLVEVRRKQQ
ParentalMTVVSKMPFVPTKYYTLK
.T..SKMPF..TKYYTLK
RetrocopyITMISKMPFMLTKYYTLK

                            

                            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 .22 RPM	21 .14 RPM
SRP017611_kidney	1 .05 RPM	63 .29 RPM
SRP017611_liver	0 .47 RPM	39 .20 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_1397 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1397 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_1397 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000011489	1 retrocopy	retro_cfam_1035,
Callithrix jacchus	ENSCJAG00000003962	1 retrocopy	retro_cjac_1895,
Homo sapiens	ENSG00000145020	1 retrocopy	retro_hsap_2953,
Monodelphis domestica	ENSMODG00000012973	1 retrocopy	retro_mdom_1809,
Pongo abelii	ENSPPYG00000013871	1 retrocopy	retro_pabe_2449,
Rattus norvegicus	ENSRNOG00000050214	1 retrocopy	retro_rnor_1397 ,

	RetrogeneDB ID:	retro_rnor_1397
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	18:47343989..47345093(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Amt
	Ensembl ID:	ENSRNOG00000050214
	Aliases:	None
	Description:	aminomethyltransferase, mitochondrial [Source:RefSeq peptide;Acc:NP_001014026]

Parental	TPLYDFHLAHGGKMVAFAGWSLPVQYRDSHVDSHLHTRRHCSLFDVSHMLQTKIFGCDRVRLMENIVVGD
	TPL.DFHLAHGGKMVAFAGW.LPVQYRDSHVDSHLHT..HCSLFDVSHMLQTKIFGC.RVRLME.IV.GD
Retrocopy	TPLHDFHLAHGGKMVAFAGWNLPVQYRDSHVDSHLHTCWHCSLFDVSHMLQTKIFGCVRVRLMESIVIGD

Parental	IAELRPNQGHFRIFRQLWRSTIPALLHWEARDHRLYSLTSHAAEVPDLARFQDKVKEFQNRGLDVGLEVV
	.AELRPNQG....F..........L.........LY..........DL...QDKVKEF.NRG.DVGLEVV
Retrocopy	TAELRPNQGALSLFTNEAGGILDDLIVTNTSEGHLYVVSNAGCWDKDLTFMQDKVKEFRNRGSDVGLEVV

Parental	DNALLALQGPTAAQVLQAGVTDDMRKLPFMTSAVMEVFGVSGCRVTRCGYTGEDGVEISVPAAGAVHLAT
	DNALLALQGPTA.QV..AG..DD.RKLP..TSAVMEVFGV.GCRVT.CGYTGED.VEISVPA.GAVHLAT
Retrocopy	DNALLALQGPTAVQV*KAGMRDDRRKLPSITSAVMEVFGVFGCRVTCCGYTGEDDVEISVPAVGAVHLAT

Parental	ALLKNPEVKLAGLAARDSLRLEAGLCLYGNDIDEHTTPVEGSLSWTLGKRRRVAMDFPGAKIIIPQLKGE
	ALLKN.EVKLAGLAA.D.L.LEAGLCLYGNDID.HTTPVEGSLSW.LGKRRR.AMDF.GAKII.PQLK..
Retrocopy	ALLKNAEVKLAGLAAGDTLLLEAGLCLYGNDIDKHTTPVEGSLSWMLGKRRRIAMDFRGAKIIVPQLKSK

Parental	VQRRRVGLICEGAPMRAHSPILNTEGAVIGTVTSGCPSPSLKKNVAMGYVAFKYSRPGTQLLVEVRRKQQ
	V.RR.VGLICEGAPMRAHSPILNTEGAVIGTVTS.CPSPSLKKNVAMGYVAFKY.RPGTQLLVEVRRKQQ
Retrocopy	VLRRYVGLICEGAPMRAHSPILNTEGAVIGTVTSDCPSPSLKKNVAMGYVAFKYRRPGTQLLVEVRRKQQ

Parental	MTVVSKMPFVPTKYYTLK
	.T..SKMPF..TKYYTLK
Retrocopy	ITMISKMPFMLTKYYTLK

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

RetrogeneDB ID:

retro_rnor_1397