RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_2478
TCCAACGAGCTCTTCTCCACATGTGTCAGCAACGGCCCGCTTCATCATGAGCAGCTCGGCCTCAGCAGCCAATGGAAATG

ATAGCAAGAAGTTCAAAGGTGACCACAGGAGCATAGGAGTTCCTTCTAGAGACATCCATGTCTGCAAGCTGCCTAGTGAT

GTCACTGAGGGTGAGGTCATCTCTTTGGGGCTGCCCTTTGGGAAAGTTACCAACCTCCTTATGCTGAAGGGGAAGAACCA

GGCCTTCACTGAAATGAACACAGAGGAGGAGGATGCTAACACTGTGGTTAACTACTAAACATCGGTGGAGCCAGTGCTTT

GTAGACAGCCCACGTACATCTAGTTCTCCAACCACGAGGAGCTCAAAACCCACAGCTCGCCCAACCAGGCACGTGTCCAG

GCAGCCCTGCAGGCGGTGAACTCCATACAGTCAGGAAACCTGGCCTCGGCAGCCTCCACTGCTGCCGTGGATGCAAAAAT

GGTAATGGCAGGCCAGAGTTCAGTGCTCAGGATCATCGTGGAAAACCTCTTCTACCCAGTGACTCTAGACGTGCTGCACC

AGATCTTCTCTAAATTTGGCACAATCCTGAAGCTCATCATGTTCACCAAGAACAACCAGTTCCAGGCGCTGCTGCAGGAT

GCTGGCCCTGTGAGCACCCAGCATGCTAAGCTGTCCCTGGATGGCCAGAACATCTACAGTGCCTGCTGACACTGCACATC

GACTTCTCCAAGCTCACCAGTCTCAACGTCAAATACAACAACGACAAGAGCAGAGATTACAGGCAACCTGGCCTGCCCTC

TGGAGACAGCCAGCCTTCAGTGGACCAGACCATGGCAGCAGTCTTTGGTACACTCAGCATAATGTCAGTCTCTCAGTATG

CAGGA

ORF - retro_rnor_2478 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.51 %
Parental protein coverage:	53.07 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalSDELFSTCVSNGP-FIMSSSASAANGNDSKKFKGDNRSTGVPSRVIHVRKLPSDVTEGEVISLGLPFGKV
		S.ELFSTCVSNGP.FIMSSSASAANGNDSKKFKGD.RS.GVPSR.IHV.KLPSDVTEGEVISLGLPFGKV
RetrocopySNELFSTCVSNGP>FIMSSSASAANGNDSKKFKGDHRSIGVPSRDIHVCKLPSDVTEGEVISLGLPFGKV
ParentalTNLLMLKGKNQAFIEMSTEEA-ANTMVNYYTSVAPVLRGQPIYIQFSNHKELKTDSSPNQARAQAALQAV
		TNLLMLKGKNQAF.EM.TEE..ANT.VNY.TSV.PVL..QP.YI.FSNH.ELKT.SSPNQAR.QAALQAV
RetrocopyTNLLMLKGKNQAFTEMNTEEEDANTVVNY*TSVEPVLCRQPTYI*FSNHEELKTHSSPNQARVQAALQAV
ParentalNSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA
		NS.QSGNLA.AAS.AAVDA.M.MAGQS.VLRIIVENLFYPVTLDVLHQIFSKFGT.LK.I.FTKNNQFQA
RetrocopyNSIQSGNLASAASTAAVDAKMVMAGQSSVLRIIVENLFYPVTLDVLHQIFSKFGTILKLIMFTKNNQFQA
ParentalLLQYADPVSAQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTM
		LLQ.A.PVS.QHAKLSLDGQNIY.AC..TL.IDFSKLTSLNVKYNNDKSRDY..P.LPSGDSQPS.DQTM
RetrocopyLLQDAGPVSTQHAKLSLDGQNIYSAC<LTLHIDFSKLTSLNVKYNNDKSRDYRQPGLPSGDSQPSVDQTM
ParentalAAAFGAPGIMSASPYAG
		AA.FG...IMS.S.YAG
RetrocopyAAVFGTLSIMSVSQYAG

							

							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	33 .36 RPM
SRP017611_kidney	0 .00 RPM	189 .04 RPM
SRP017611_liver	0 .00 RPM	66 .90 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_2478 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2478 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_2478 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 14 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000020162	1 retrocopy	retro_cjac_1901,
Ciona savignyi	ENSCSAVG00000007421	1 retrocopy	retro_csav_17,
Dasypus novemcinctus	ENSDNOG00000000882	1 retrocopy	retro_dnov_982,
Equus caballus	ENSECAG00000018845	1 retrocopy	retro_ecab_330,
Echinops telfairi	ENSETEG00000006890	1 retrocopy	retro_etel_1573,
Homo sapiens	ENSG00000011304	1 retrocopy	retro_hsap_1354,
Gorilla gorilla	ENSGGOG00000005090	1 retrocopy	retro_ggor_1054,
Macropus eugenii	ENSMEUG00000006710	2 retrocopies	retro_meug_1447, retro_meug_67,
Myotis lucifugus	ENSMLUG00000003320	1 retrocopy	retro_mluc_755,
Mus musculus	ENSMUSG00000006498	1 retrocopy	retro_mmus_1072,
Nomascus leucogenys	ENSNLEG00000000864	1 retrocopy	retro_nleu_1834,
Pongo abelii	ENSPPYG00000009289	1 retrocopy	retro_pabe_1122,
Pan troglodytes	ENSPTRG00000010165	1 retrocopy	retro_ptro_928,
Rattus norvegicus	ENSRNOG00000010448	2 retrocopies	retro_rnor_1994, retro_rnor_2478 ,

	RetrogeneDB ID:	retro_rnor_2478
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	7:131646035..131646920(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Ptbp1
	Ensembl ID:	ENSRNOG00000010448
	Aliases:	Ptbp1, Ptb, Pybp, Pybp1, Pybp2
	Description:	polypyrimidine tract-binding protein 1 isoform b [Source:RefSeq peptide;Acc:NP_071961]

Parental	SDELFSTCVSNGP-FIMSSSASAANGNDSKKFKGDNRSTGVPSRVIHVRKLPSDVTEGEVISLGLPFGKV
	S.ELFSTCVSNGP.FIMSSSASAANGNDSKKFKGD.RS.GVPSR.IHV.KLPSDVTEGEVISLGLPFGKV
Retrocopy	SNELFSTCVSNGP>FIMSSSASAANGNDSKKFKGDHRSIGVPSRDIHVCKLPSDVTEGEVISLGLPFGKV

Parental	TNLLMLKGKNQAFIEMSTEEA-ANTMVNYYTSVAPVLRGQPIYIQFSNHKELKTDSSPNQARAQAALQAV
	TNLLMLKGKNQAF.EM.TEE..ANT.VNY.TSV.PVL..QP.YI.FSNH.ELKT.SSPNQAR.QAALQAV
Retrocopy	TNLLMLKGKNQAFTEMNTEEEDANTVVNYTSVEPVLCRQPTYIFSNHEELKTHSSPNQARVQAALQAV

Parental	NSVQSGNLALAASAAAVDAGMAMAGQSPVLRIIVENLFYPVTLDVLHQIFSKFGTVLKIITFTKNNQFQA
	NS.QSGNLA.AAS.AAVDA.M.MAGQS.VLRIIVENLFYPVTLDVLHQIFSKFGT.LK.I.FTKNNQFQA
Retrocopy	NSIQSGNLASAASTAAVDAKMVMAGQSSVLRIIVENLFYPVTLDVLHQIFSKFGTILKLIMFTKNNQFQA

Parental	LLQYADPVSAQHAKLSLDGQNIYNAC-CTLRIDFSKLTSLNVKYNNDKSRDYTRPDLPSGDSQPSLDQTM
	LLQ.A.PVS.QHAKLSLDGQNIY.AC..TL.IDFSKLTSLNVKYNNDKSRDY..P.LPSGDSQPS.DQTM
Retrocopy	LLQDAGPVSTQHAKLSLDGQNIYSAC<LTLHIDFSKLTSLNVKYNNDKSRDYRQPGLPSGDSQPSVDQTM

Parental	AAAFGAPGIMSASPYAG
	AA.FG...IMS.S.YAG
Retrocopy	AAVFGTLSIMSVSQYAG

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

RetrogeneDB ID:

retro_rnor_2478