RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_2113
CTGGGACTCTCCATGGGCTGCTGCTGGCACTGGTGCTGGCGTTCAGGGCCAAGAGCATGATGAGCAAGGAGCACATAGTT

TGTCCCGATTCAGACTGGGCCAGTGGCCACCAGAGGACAAGCACAGCTTCCTGTACGATCATGAGGTCTTCCTGGGCAAG

GAGGACTCCAAGAACTTTGATAGCTAAGCCTGGATGAGAGCAAGGAGAGGCTGGGGAAAATTGTTGATTCAATTGACAGT

GATGGAGGCAGCCTTGTTACTACTGAGCAGCTGAAAGTTTGGATCAAACAGGTACAAAAAAGATACATCTACCATAATGT

GGCTAAACTCTGGAAGGATTATGATAGGGACATAGACGAAAAAATCTCCTGGGAAGAATACAAGCAGTCTACTTTTGGCT

ACTACCTGGGAAACCTTGCTGAATCCCAAGATAGCTCTGATCTTCACACCTTTAAAAAAATGCCTCCATGAGATGAGAGG

AGGTTTAAGGCTTCAGACATTGACAGCAACCTGACAGCCACTCGAGAGGGATTCATTGCATTTCTGAACCCAGAGGAGTT

GAAACATATGAAGGAGATTGTAGTTCTGGAAACCCTGGAGGATATCGACAAGAACAGGGAAGGACTTGTGGACCAGGATG

AGTATATTGTGGACATGTTTTTCCCACGAGGACAATGCCCCTGAGCCAGACTGGGTTTTGTCCAAATGGGAGCAGTTCAA

TGATTTCCCAGATCTGAACAAGGATGGGAAGCTAGACAAGGATGAGATTCGCCACTGAATCCTCCCTCACAACTATGACC

ATGCAGGGGCTGAGGCCCGGCGTCTGGTGTATGAGTCAGACAAAAACAAGGATGAGATGCTAACCAAGGAGGAGATTCTA

CAAAACTGGAACATGTTTGTGGGAAGTCAAGCCATCAATTACAAGGAAGATCTTACCAAAAATCATGATGAACTT

ORF - retro_rnor_2113 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.5 %
Parental protein coverage:	98.15 %
Number of stop codons detected:	2
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalLGLALG-LLLALVLALRAKPTVRKERVVRPDSE-LGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDE
		LGL..G.LLLALVLA.RAK....KE..V.PDS..LG..PPED..SF.YDHE.FLGKEDSK.FD..LS.DE
RetrocopyLGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSD<LGQWPPEDKHSFLYDHEVFLGKEDSKNFDS<LSLDE
ParentalSKERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGYYL
		SKERLGKIVD.IDSDG..LVTTE.LKVWIK.VQKRYIY.NVAK.WKDYDRD.DEKISWEEYKQ.T.GYYL
RetrocopySKERLGKIVDSIDSDGGSLVTTEQLKVWIKQVQKRYIYHNVAKLWKDYDRDIDEKISWEEYKQSTFGYYL
ParentalGNPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNG
		GN.AE.QDSSD.HTFKKM.P.DERRFKASD.D..LTATRE.F.AFL.PEE..HMKEIVVLETLEDIDKN.
RetrocopyGNLAESQDSSDLHTFKKMPP*DERRFKASDIDSNLTATREGFIAFLNPEELKHMKEIVVLETLEDIDKNR
ParentalDGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHL
		.G.VDQDEYI.DM.FSHEDN.PEPDWVLS..EQFNDF.DLNKDGKLDKDEIRH.ILP..YDHA.AEAR.L
RetrocopyEGLVDQDEYIVDM>FSHEDNAPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIRH*ILPHNYDHAGAEARRL
ParentalVYESDKNKDEMLTKEEILDNWNMFVGSQATNYGEDLTKNHDEL
		VYESDKNKDEMLTKEEIL.NWNMFVGSQA.NY.EDLTKNHDEL
RetrocopyVYESDKNKDEMLTKEEILQNWNMFVGSQAINYKEDLTKNHDEL

							

							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	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_2113 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2113 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_2113 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_2113
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	4:229160334..229161289(-)
	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-LLLALVLALRAKPTVRKERVVRPDSE-LGERPPEDNQSFQYDHEAFLGKEDSKTFDQ-LSPDE
	LGL..G.LLLALVLA.RAK....KE..V.PDS..LG..PPED..SF.YDHE.FLGKEDSK.FD..LS.DE
Retrocopy	LGLSMG<LLLALVLAFRAKSMMSKEHIVCPDSD<LGQWPPEDKHSFLYDHEVFLGKEDSKNFDS<LSLDE

Parental	SKERLGKIVDRIDSDGDGLVTTEELKVWIKRVQKRYIYDNVAKVWKDYDRDKDEKISWEEYKQATYGYYL
	SKERLGKIVD.IDSDG..LVTTE.LKVWIK.VQKRYIY.NVAK.WKDYDRD.DEKISWEEYKQ.T.GYYL
Retrocopy	SKERLGKIVDSIDSDGGSLVTTEQLKVWIKQVQKRYIYHNVAKLWKDYDRDIDEKISWEEYKQSTFGYYL

Parental	GNPAEFQDSSDHHTFKKMLPRDERRFKASDLDGDLTATREEFTAFLHPEEFEHMKEIVVLETLEDIDKNG
	GN.AE.QDSSD.HTFKKM.P.DERRFKASD.D..LTATRE.F.AFL.PEE..HMKEIVVLETLEDIDKN.
Retrocopy	GNLAESQDSSDLHTFKKMPP*DERRFKASDIDSNLTATREGFIAFLNPEELKHMKEIVVLETLEDIDKNR

Parental	DGFVDQDEYIADM-FSHEDNGPEPDWVLSEREQFNDFRDLNKDGKLDKDEIRHWILPQDYDHAQAEARHL
	.G.VDQDEYI.DM.FSHEDN.PEPDWVLS..EQFNDF.DLNKDGKLDKDEIRH.ILP..YDHA.AEAR.L
Retrocopy	EGLVDQDEYIVDM>FSHEDNAPEPDWVLSKWEQFNDFPDLNKDGKLDKDEIRH*ILPHNYDHAGAEARRL

Parental	VYESDKNKDEMLTKEEILDNWNMFVGSQATNYGEDLTKNHDEL
	VYESDKNKDEMLTKEEIL.NWNMFVGSQA.NY.EDLTKNHDEL
Retrocopy	VYESDKNKDEMLTKEEILQNWNMFVGSQAINYKEDLTKNHDEL

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

RetrogeneDB ID:

retro_rnor_2113