RetrogeneDB - Retrocopy retro_btau

						
>retro_btau_820
CCTGGTTGGGTCCGATAGGCTGAGCAGATGCTGTGACACCCCGTCACCCCCCACCTCTGCACTGTCACGTCTTCCTAGCA

GATCATGGGATCCCTGGTGAAGTACTACATTGCCAGACCACAGAATCTGTCCCCTGACAAGGTTTTCCATGTTATCGTGG

CTCCATGCTATGACAAGAAGCTGGAGGCTCTTCAGGAAGACATCCTCATGTCTCTCGGGTTTCCCGGGGCACTGACTGAC

TAGTGCTGACCTCAGGTAAAATAGCTCAGATGATGGAACAGAGTTACCTCTCGATGAGACATGCTGCCCTGCGCACTCTG

GAGATGTGAAAGAGGAGGAGCTGAGGCACCACGATGGAGTCAGCTCTGACGGGTACCTGGCACATATCTTCAGACATGCA

GGCAAGGAGCTGTTCAGTGAGGACGTGGGGGAGGTCACCTACCATGCTCTGAGGAACAAAGACTTCCAGGAGGTCACCCT

CGAGAAGAGCAGAGAGGTCTTCTTGCACTTTGCTGCAGCTTATGGCTTTTGAAACATCCAGAACGGGGTCCTAAAATGGA

AGGGCAAATTCCCTTATCACTTTGTGGAGGTTCTTGTTTGTGTTGGGGTATGCCTCAATGGCAGAGGCCAAGCTCAGACC

GAGGATGGGCACATAGAAAAGGCCCTGCTGCAGAAGATGAAAGGCCTCTACACTGACATCTCCGTGCAGCTCCTGGAGGC

CAGAACACACGTGCAGGAGTTATACAGGGAGTGGCTGGAAGGCACGACTCCCTCCACGTCCAGGAAGCCCTGCACACCTC

TTACTAGGGCTCAGGGCAACCCGCTGACAGCAGAGACATCAAG

ORF - retro_btau_820 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	73.08 %
Parental protein coverage:	62.06 %
Number of stop codons detected:	6
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalPGWVRYAERVLGHPVTPHLCTAKSPQQIMGSLVKDYFARRQNLSPDKIFHVIVAPCYDKKLEALQEDVLT
		PGWVR.AE..L.HPVTPHLCT..S..QIMGSLVK.Y.AR.QNLSPDK.FHVIVAPCYDKKLEALQED.L.
RetrocopyPGWVR*AEQML*HPVTPHLCTVTSS*QIMGSLVKYYIARPQNLSPDKVFHVIVAPCYDKKLEALQEDILM
ParentalA-SRGSRGTDCVLTSGEIAQMMEQ-SDVSVREAALDTLFGDVKEEELRRHDGAGSDGYLAHIFRHAAKEL
		..SR.SRGTD...........M.........E.......GDVKEEELR.HDG..SDGYLAHIFRHA.KEL
RetrocopyS<SRVSRGTD*LVLTSGKIAQMME<TELPLDETCCPAHSGDVKEEELRHHDGVSSDGYLAHIFRHAGKEL
ParentalFNEDVGEVTYRALRNKDFQEVTLEKSGEVLLRFAAAYGFRNIQNVVLKLKKGKFPYHFVEVLACAGGCLN
		F.EDVGEVTY.ALRNKDFQEVTLEKS.EV.L.FAAAYGF.NIQN.VLK..KGKFPYHFVEVL.C.G.CLN
RetrocopyFSEDVGEVTYHALRNKDFQEVTLEKSREVFLHFAAAYGF*NIQNGVLKW-KGKFPYHFVEVLVCVGVCLN
ParentalGRGQAQTADGRTDKALLQKMKGIYADIPVQLPEASTHVQELYQEWLDGT-DSPRVQEALHTAYQGPGQPA
		GRGQAQT.DG...KALLQKMKG.Y.DI.VQL.EA.THVQELY.EWL.GT.DS..VQEALHT.Y.G.GQPA
RetrocopyGRGQAQTEDGHIEKALLQKMKGLYTDISVQLLEARTHVQELYREWLEGT<DSLHVQEALHTSY*GSGQPA
ParentalDSRDIK
		DSRDIK
RetrocopyDSRDIK

							

							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
ERP005899_liver	0 .00 RPM	6 .20 RPM
ERP005899_muscle	0 .00 RPM	31 .88 RPM
SRP017611_brain	0 .00 RPM	29 .19 RPM
SRP017611_kidney	0 .00 RPM	24 .66 RPM
SRP017611_liver	0 .00 RPM	10 .04 RPM
SRP030211_testis	0 .00 RPM	44 .09 RPM

ChIP-Seq - click to see more details

Bos taurus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_btau_820 retrocopy.

TSS - click to see more details

Bos taurus was not studied using FANTOM5 data.

Lab - click to see more details

retro_btau_820 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_btau_820 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018178	1 retrocopy	retro_btau_820 ,
Canis familiaris	ENSCAFG00000012976	1 retrocopy	retro_cfam_659,
Dasypus novemcinctus	ENSDNOG00000011246	1 retrocopy	retro_dnov_1757,
Echinops telfairi	ENSETEG00000009329	1 retrocopy	retro_etel_999,
Myotis lucifugus	ENSMLUG00000017740	23 retrocopies	retro_mluc_1006, retro_mluc_1012, retro_mluc_1083, retro_mluc_1091, retro_mluc_1124, retro_mluc_1256, retro_mluc_1282, retro_mluc_1457, retro_mluc_1573, retro_mluc_1622, retro_mluc_1632, retro_mluc_1700, retro_mluc_1718, retro_mluc_1898, retro_mluc_1973, retro_mluc_2365, retro_mluc_671, retro_mluc_688, retro_mluc_817, retro_mluc_825, retro_mluc_877, retro_mluc_879, retro_mluc_982,

	RetrogeneDB ID:	retro_btau_820
Retrocopy location	Organism:	*Cow (Bos taurus)*
	Coordinates:	2:57212220..57213063(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NARF
	Ensembl ID:	ENSBTAG00000018178
	Aliases:	None
	Description:	nuclear prelamin A recognition factor [Source:RefSeq peptide;Acc:NP_001095788]

Parental	PGWVRYAERVLGHPVTPHLCTAKSPQQIMGSLVKDYFARRQNLSPDKIFHVIVAPCYDKKLEALQEDVLT
	PGWVR.AE..L.HPVTPHLCT..S..QIMGSLVK.Y.AR.QNLSPDK.FHVIVAPCYDKKLEALQED.L.
Retrocopy	PGWVRAEQMLHPVTPHLCTVTSS*QIMGSLVKYYIARPQNLSPDKVFHVIVAPCYDKKLEALQEDILM

Parental	A-SRGSRGTDCVLTSGEIAQMMEQ-SDVSVREAALDTLFGDVKEEELRRHDGAGSDGYLAHIFRHAAKEL
	..SR.SRGTD...........M.........E.......GDVKEEELR.HDG..SDGYLAHIFRHA.KEL
Retrocopy	S<SRVSRGTD*LVLTSGKIAQMME<TELPLDETCCPAHSGDVKEEELRHHDGVSSDGYLAHIFRHAGKEL

Parental	FNEDVGEVTYRALRNKDFQEVTLEKSGEVLLRFAAAYGFRNIQNVVLKLKKGKFPYHFVEVLACAGGCLN
	F.EDVGEVTY.ALRNKDFQEVTLEKS.EV.L.FAAAYGF.NIQN.VLK..KGKFPYHFVEVL.C.G.CLN
Retrocopy	FSEDVGEVTYHALRNKDFQEVTLEKSREVFLHFAAAYGF*NIQNGVLKW-KGKFPYHFVEVLVCVGVCLN

Parental	GRGQAQTADGRTDKALLQKMKGIYADIPVQLPEASTHVQELYQEWLDGT-DSPRVQEALHTAYQGPGQPA
	GRGQAQT.DG...KALLQKMKG.Y.DI.VQL.EA.THVQELY.EWL.GT.DS..VQEALHT.Y.G.GQPA
Retrocopy	GRGQAQTEDGHIEKALLQKMKGLYTDISVQLLEARTHVQELYREWLEGT<DSLHVQEALHTSY*GSGQPA

Parental	DSRDIK
	DSRDIK
Retrocopy	DSRDIK

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

RetrogeneDB ID:

retro_btau_820