RetrogeneDB - Retrocopy retro_rnor

						
>retro_rnor_2540
ACCAACCAGACAGATGCACGGCTCCAGTATGGCCCCCAGTATGGTGCTGCTGTCTCTGTCCTTCTACAGGAAGTGTTCCG

TTTTGCCTCCTGCAAGCTCCTTAAGAAGGCTTCTGAGGGCTTAGCATCACTAACTGGGGACGAAGATCACCCATCTCCAT

CTGACGGATGGCCTATGTTTCTGGTCTGTCCTACGGTGTCATCAGTGGTGTCTTCCCTGTTACCAATATTGTGGCTGATG

CACTTGGGCCAGGTGTGGTTGGGATCCATGGAGACTCACCCTATTACTTCCTGACTTCAGCCTTTCTGACAGTAACCAGC

CATTATCCTGCTGCATAACTTTTGGGAAGTTGTGTTCTTTGATGCCTATGAGAGGAGACAGTACTGGGCTTTGGGCCTGG

TAGTTGAGAGTCATCTTTTGACTTCAGGACTGACATTCCTGAACCCCTGGTATGAGCCCAGCCTGCTGCCCATCTATGCA

GTCACTGTTTCCATGGGGCTCTGGGCTTTCGACACAGCCAGAGGCCCCCTCCGGAGTAGCCAGCGCAGCCTTTCGTGTAA

GGAC

ORF - retro_rnor_2540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.49 %
Parental protein coverage:	76.11 %
Number of stop codons detected:	1
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalTDRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDG-RSPISIRQMAYVSGLSFGII
		T...DARLQYG....GAAVSVLLQEVFRFA..KLLKKA.EGLASL..D..RSPISI..MAYVSGLS.G.I
RetrocopyTNQTDARLQYGPQ-YGAAVSVLLQEVFRFASCKLLKKASEGLASLTGDE<RSPISI*RMAYVSGLSYGVI
ParentalSGVFSVINILADALGPGVVGIHGDSP-YYFLTSAFLTA-AIILLHTFWGVVFFDACERRRYWALGLVVGS
		SGVF.V.NI.ADALGPGVVGIHGDSP.Y...........AIILLH.FW.VVFFDA.ERR.YWALGLVV.S
RetrocopySGVFPVTNIVADALGPGVVGIHGDSPYYFLTSAFLTVT>AIILLHNFWEVVFFDAYERRQYWALGLVVES
ParentalHLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFVTAGGSLRSIQRSLSCKD
		HLLTSGLTFLNPWYE.SLLPIYAVTVSMGLWAF.TA.G.LRS.QRSLSCKD
RetrocopyHLLTSGLTFLNPWYEPSLLPIYAVTVSMGLWAFDTARGPLRSSQRSLSCKD

							

							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	37 .67 RPM
SRP017611_kidney	0 .00 RPM	96 .44 RPM
SRP017611_liver	0 .00 RPM	51 .71 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_2540 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_2540 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_rnor_2540 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Myotis lucifugus	ENSMLUG00000013692	1 retrocopy	retro_mluc_783,
Rattus norvegicus	ENSRNOG00000023816	1 retrocopy	retro_rnor_2540 ,

	RetrogeneDB ID:	retro_rnor_2540
Retrocopy location	Organism:	*Rat (Rattus norvegicus)*
	Coordinates:	7:131726804..131727368(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	Aph1a
	Ensembl ID:	ENSRNOG00000023816
	Aliases:	Aph1a, RGD1311546
	Description:	anterior pharynx defective 1 homolog A [Source:RefSeq peptide;Acc:NP_001014277]

Parental	TDRSDARLQYGLLIFGAAVSVLLQEVFRFAYYKLLKKADEGLASLSEDG-RSPISIRQMAYVSGLSFGII
	T...DARLQYG....GAAVSVLLQEVFRFA..KLLKKA.EGLASL..D..RSPISI..MAYVSGLS.G.I
Retrocopy	TNQTDARLQYGPQ-YGAAVSVLLQEVFRFASCKLLKKASEGLASLTGDE<RSPISI*RMAYVSGLSYGVI

Parental	SGVFSVINILADALGPGVVGIHGDSP-YYFLTSAFLTA-AIILLHTFWGVVFFDACERRRYWALGLVVGS
	SGVF.V.NI.ADALGPGVVGIHGDSP.Y...........AIILLH.FW.VVFFDA.ERR.YWALGLVV.S
Retrocopy	SGVFPVTNIVADALGPGVVGIHGDSPYYFLTSAFLTVT>AIILLHNFWEVVFFDAYERRQYWALGLVVES

Parental	HLLTSGLTFLNPWYEASLLPIYAVTVSMGLWAFVTAGGSLRSIQRSLSCKD
	HLLTSGLTFLNPWYE.SLLPIYAVTVSMGLWAF.TA.G.LRS.QRSLSCKD
Retrocopy	HLLTSGLTFLNPWYEPSLLPIYAVTVSMGLWAFDTARGPLRSSQRSLSCKD

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

RetrogeneDB ID:

retro_rnor_2540