RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_797
CTGGGACTCTCCATGGGCTGCTGCTGGCACTGGTGCTGGCGTTCAGGGCCAAGAGCATGATGAGCAAGGAGCACATAGTT

TGTCCCGATTCAGAGCTGGGCCAGTGGCCACCAGAGGACAAGCACAGCTTCCTGTACGATCATGAGGTCTTCCTGGGCAA

GGAGGACTCCAAGACCTTTGATAGCTAAGCCTGGATGAGAGCAAGGAGAGGCTGGGGAAAATTGTTGATTCAATTGACAG

TGATGGAGGCAGCCTTGTTACTACTGAGCAGCTGAAAGTTTGGATCAAACAGGTACAAAAAAGATACATCTACCATAATG

TGGCTAAACTCTGGAGGATTATGATAGGGACATAGACGAAAAGATCTCCTGGGAAGAATACAAGCAGTCTACTTTTGGCT

ACTACCTGGGAAACCTTGCTGAATCCCAAGATAGCTCTGATCTTCACACCTTTAAAAAAATGCCTCCATGAGATGAGGAG

GTTTAAGGCTTCAGTCATTGACAGCAACCTGACAGCTACTCGAGAGGGATTCATTGCCTGTCTGAACCAGAGGAGTTGAA

ACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCGACAAGAACAGGGAAGGACTTGTGGACCAGGATGAGT

ATATTGTGGACATGTTTTTCCCACGAGGACAATGCCCCTGAGCCAGATTGGGTTTTGTCCAAATGGGAGCAGTTCAATGA

TTTCCCAGATCTGAACAAGGATGGGAAGCTGGACAAGGATGAGATTGGACACTGAATCCTCCCTCACAACTATGACCATG

CAGGGGCTGAGGCCCGGCGTCTGGTGTATGAGTCAGACAAAAACAAGGATGAGATGCTAACCAAGGAGGAGATTCTACAA

AACTGGAACATGTTTGTGGGAAGTCAAGCCATCAATTACAAGGAAGATCTTACCAAAAATCATGATGAACTT

ORF - retro_rnor_797 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.46 %
Parental protein coverage:	98.15 %
Number of stop codons detected:	1
Number of frameshifts detected	6

Retrocopy - Parental Gene Alignment:

									ParentalLGLALG-LLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDES
		LGL..G.LLLALVLA.RAK....KE..V.PDSELG..PPED..SF.YDHE.FLGKEDSKTFD..LS.DES
RetrocopyLGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSELGQWPPEDKHSFLYDHEVFLGKEDSKTFDS<LSLDES
ParentalKERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWK-DYDRDKDEKISWEEYKQATYGYYL
		KERLGKIVD.IDSDG..LVTTE.LKVWIK.VQKRYIY.NVAK.W..DYDRD.DEKISWEEYKQ.T.GYYL
RetrocopyKERLGKIVDSIDSDGGSLVTTEQLKVWIKQVQKRYIYHNVAKLWR<DYDRDIDEKISWEEYKQSTFGYYL
ParentalGNPAEFQDSSDHHTFKKMLP-RDERRFKASDLDGDLTATREEFTAFLH-PEEFEHMKEIVVLETLEDIDK
		GN.AE.QDSSD.HTFKK..P....RRFKAS..D..LTATRE.F.A.L..PEE..HMKEIVVLETLEDIDK
RetrocopyGNLAESQDSSDLHTFKK-MP>HEMRRFKASVIDSNLTATREGFIACLN<PEELKHMKEIVVLETLEDIDK
ParentalNGDGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEAR
		N..G.VDQDEYI.DM.FSHEDN.PEPDWVLS..EQFNDF.DLNKDGKLDKDEI.H.ILP..YDHA.AEAR
RetrocopyNREGLVDQDEYIVDM>FSHEDNAPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIGH*ILPHNYDHAGAEAR
ParentalHLVYESDKNKDEMLTKEEILDNWNMFVGSQATNYGEDLTKNHDEL
		.LVYESDKNKDEMLTKEEIL.NWNMFVGSQA.NY.EDLTKNHDEL
RetrocopyRLVYESDKNKDEMLTKEEILQNWNMFVGSQAINYKEDLTKNHDEL

							

							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 .07 RPM	46 .66 RPM
SRP017611_kidney	0 .00 RPM	28 .40 RPM
SRP017611_liver	0 .00 RPM	8 .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_797 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_797 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_797 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 3 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000049449	2 retrocopies	retro_hsap_1259, retro_hsap_3629,
Pongo abelii	ENSPPYG00000003385	1 retrocopy	retro_pabe_2976,
Rattus norvegicus	ENSRNOG00000013452	28 retrocopies	retro_rnor_1207, retro_rnor_1224, retro_rnor_2111, retro_rnor_2112, retro_rnor_2113, retro_rnor_2352, retro_rnor_2353, retro_rnor_2354, retro_rnor_2355, retro_rnor_2408, retro_rnor_2409, retro_rnor_2410, retro_rnor_2434, retro_rnor_2435, retro_rnor_2436, retro_rnor_2437, retro_rnor_2438, retro_rnor_2486, retro_rnor_2508, retro_rnor_2509, retro_rnor_2510, retro_rnor_2511, retro_rnor_2513, retro_rnor_2664, retro_rnor_2711, retro_rnor_2716, retro_rnor_2760, retro_rnor_797 ,

	RetrogeneDB ID:	retro_rnor_797
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	11:42438090..42439042(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Rcn1
	Ensembl ID:	ENSRNOG00000013452
	Aliases:	Rcn1, Rcn
	Description:	reticulocalbin-1 precursor [Source:RefSeq peptide;Acc:NP_001102056]

Parental	LGLALG-LLLALVLALRAKPTVRKERVVRPDSELGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDES
	LGL..G.LLLALVLA.RAK....KE..V.PDSELG..PPED..SF.YDHE.FLGKEDSKTFD..LS.DES
Retrocopy	LGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSELGQWPPEDKHSFLYDHEVFLGKEDSKTFDS<LSLDES

Parental	KERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWK-DYDRDKDEKISWEEYKQATYGYYL
	KERLGKIVD.IDSDG..LVTTE.LKVWIK.VQKRYIY.NVAK.W..DYDRD.DEKISWEEYKQ.T.GYYL
Retrocopy	KERLGKIVDSIDSDGGSLVTTEQLKVWIKQVQKRYIYHNVAKLWR<DYDRDIDEKISWEEYKQSTFGYYL

Parental	GNPAEFQDSSDHHTFKKMLP-RDERRFKASDLDGDLTATREEFTAFLH-PEEFEHMKEIVVLETLEDIDK
	GN.AE.QDSSD.HTFKK..P....RRFKAS..D..LTATRE.F.A.L..PEE..HMKEIVVLETLEDIDK
Retrocopy	GNLAESQDSSDLHTFKK-MP>HEMRRFKASVIDSNLTATREGFIACLN<PEELKHMKEIVVLETLEDIDK

Parental	NGDGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEAR
	N..G.VDQDEYI.DM.FSHEDN.PEPDWVLS..EQFNDF.DLNKDGKLDKDEI.H.ILP..YDHA.AEAR
Retrocopy	NREGLVDQDEYIVDM>FSHEDNAPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIGH*ILPHNYDHAGAEAR

Parental	HLVYESDKNKDEMLTKEEILDNWNMFVGSQATNYGEDLTKNHDEL
	.LVYESDKNKDEMLTKEEIL.NWNMFVGSQA.NY.EDLTKNHDEL
Retrocopy	RLVYESDKNKDEMLTKEEILQNWNMFVGSQAINYKEDLTKNHDEL

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

RetrogeneDB ID:

retro_rnor_797