RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_214
ATGGCGCAATACAAAGGTACCATGCGGGAGGCTGGCCGGGCCATGCATCTGATCAAGAAGCGCGAGAAGCAGAAGGAGCA

GATGGAGGTGCTGAAGCAACGCATTGCAGAGGAGACCATCATGAAGTCAAAAGTGGACAAGAAGTTCTCGGCACACTACG

ACGCTGTGGAAGCCGAGCTGAAGTCCAGCACGGTGGGCCTGGTGACCCTGAATGACATGAAGGCCAAGCAGGAGGCCCTG

CTGAGGGAGCGGGAGATACAGCTGGCCAAGAGGGAGCAACTGGAGCAGCGTCGGCTACAGCTAGAGATCCTGCGTGAGAA

GGAGCGAAGGCGCGAACGCAAGCGCAAGATCTCCAACCTGTCTTTCACGCTGGATGAGGAAGAAGACGGTGACCAAGAGG

ATGGCCGCCAGGCCGAAGGTGCTGAGGTCCACAGTGGTGGGGCCAAGAAGAACTTGGGCAAGAACCCCGATGTGGACACG

AGCTTCCTGCCCGATCGCGAACGCGAGGAGGAGGAGAACCGGCTGCGGGAGGAACTGCGGCAGGAGTGGGAGGCGAAGCG

CGAGAAGGTGAAGGGCGAGGAGGTGGAGATCACCTTCAGCTACTGGGATGGCTCTGGCCACCGGCGCACAGTACGCATGC

GCAAGGGCAGCACTGTGCAGCAGTTCCTGAAGCGGGCGCTGCAGGGGCTGCGCAGGGACTTCCGGGAGCTGCGGGCGGCG

GGCGTGGAGCAGCTCATGTACGTCAAGGAGGATCTCATCCTGCCGCACTACCACACCTTTTACGACTTCATCGTGGCCAA

AGCGCGGGGCAAGAGTGGGCCGCTCTTCAGCTTCGACGTGCACGATGATGTGCGGCTGCTGAGCGATGCCACGATGGAGA

AAGACGAGTCACACGCGGGAAAGGTGGTGCTGCGCAGCTGGTATGAGAAGAACAAGCACATCTTCCCCGCCAGCCGCTGG

GAGCCCTACGACCCCGAGAAGAAGTGGGACAAGTACACCATCCGGTGA

ORF - retro_rnor_214 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	87.17 %
Parental protein coverage:	55.16 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalKKKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMKKGNT
		KK.LGKNPDVDTSFLPDR.REEEENRLREELRQEWEAK.EK.K.EE.EITFSYWDGSGHRRTV.M.KG.T
RetrocopyKKNLGKNPDVDTSFLPDREREEEENRLREELRQEWEAKREKVKGEEVEITFSYWDGSGHRRTVRMRKGST
ParentalMQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLS
		.QQFL..AL..LR.DF.ELR.AGVEQLMY.KEDLI.PH.H.FYDFIV.KARGKSGPLF.FDVHDDVRLLS
RetrocopyVQQFLKRALQGLRRDFRELRAAGVEQLMYVKEDLILPHYHTFYDFIVAKARGKSGPLFSFDVHDDVRLLS
ParentalDATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
		DAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
RetrocopyDATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR

							

							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	0 .00 RPM
SRP017611_kidney	0 .00 RPM	0 .00 RPM
SRP017611_liver	0 .07 RPM	0 .00 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_214 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_214 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_214 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 12 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000273	1 retrocopy	retro_amel_15,
Felis catus	ENSFCAG00000011399	1 retrocopy	retro_fcat_100,
Homo sapiens	ENSG00000071859	1 retrocopy	retro_hsap_94,
Loxodonta africana	ENSLAFG00000008766	1 retrocopy	retro_lafr_43,
Myotis lucifugus	ENSMLUG00000022234	1 retrocopy	retro_mluc_7,
Mustela putorius furo	ENSMPUG00000009476	1 retrocopy	retro_mputfur_145,
Mus musculus	ENSMUSG00000001962	1 retrocopy	retro_mmus_103,
Nomascus leucogenys	ENSNLEG00000014266	1 retrocopy	retro_nleu_109,
Rattus norvegicus	ENSRNOG00000045790	1 retrocopy	retro_rnor_214 ,
Sorex araneus	ENSSARG00000006465	1 retrocopy	retro_sara_554,
Sus scrofa	ENSSSCG00000025303	1 retrocopy	retro_sscr_56,
Ictidomys tridecemlineatus	ENSSTOG00000004448	10 retrocopies	retro_itri_105, retro_itri_1563, retro_itri_1688, retro_itri_1691, retro_itri_1693, retro_itri_1758, retro_itri_1760, retro_itri_1762, retro_itri_1780, retro_itri_184,

	RetrogeneDB ID:	retro_rnor_214
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	17:32764499..32765507(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSRNOG00000017083
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	Fam50a
	Ensembl ID:	ENSRNOG00000045790
	Aliases:	None
	Description:	Protein Fam50a; Similar to XAP-5 protein (Predicted), isoform CRA_a [Source:UniProtKB/TrEMBL;Acc:G3V9M8]

Parental	KKKLGKNPDVDTSFLPDRDREEEENRLREELRQEWEAKQEKIKSEEIEITFSYWDGSGHRRTVKMKKGNT
	KK.LGKNPDVDTSFLPDR.REEEENRLREELRQEWEAK.EK.K.EE.EITFSYWDGSGHRRTV.M.KG.T
Retrocopy	KKNLGKNPDVDTSFLPDREREEEENRLREELRQEWEAKREKVKGEEVEITFSYWDGSGHRRTVRMRKGST

Parental	MQQFLQKALEILRKDFSELRSAGVEQLMYIKEDLIIPHHHSFYDFIVTKARGKSGPLFNFDVHDDVRLLS
	.QQFL..AL..LR.DF.ELR.AGVEQLMY.KEDLI.PH.H.FYDFIV.KARGKSGPLF.FDVHDDVRLLS
Retrocopy	VQQFLKRALQGLRRDFRELRAAGVEQLMYVKEDLILPHYHTFYDFIVAKARGKSGPLFSFDVHDDVRLLS

Parental	DATVEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
	DAT.EKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR
Retrocopy	DATMEKDESHAGKVVLRSWYEKNKHIFPASRWEPYDPEKKWDKYTIR

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

RetrogeneDB ID:

retro_rnor_214