RetrogeneDB - Retrocopy retro_cfam

						
>retro_cfam_2185
GATACAGATGAATATAGACCTCCTGTTTGGAAATCTTACTTGTATCAGTTGCAACAGGAAGCCCCTCATCCTCGAAGAAT

CACTTGTACTAATGAGGTGGAAAACAGACCAAAGTACTATGGAAGAGAATTTCATGGCATGATCTCCCGAGAAGAAGCAG

ACCAGCTCTTGAGTGTGGCTGAGGAGAGTTACCTTATTCGTGAGAGCCAGCGTCAGCCGGGAACCTACACTTTGGCTTTA

AGATTTGGAAGTCAAACCAGAAACTTCAGGCTGTACTACGATGGAAAGCACTTCGTTGGGGAGAAGCGCTTTGAGTCCAT

CCATCATCTGGTGACTGATGGATTGATTACCCTCTATATTGAAACCAAGGCAGCAGAATACATTGCCAAGATGACAATAA

ACCCAATTTATGAGCACATAGGATACACAACCTTAAACAGAGAGCCAGCATACCAAAAACATATGCCAGTCCTGAAAGAG

ACACATGATGAGAGATATTCTACAGGCCAGGATGGGGTGTCAGAGTAAAGGTTGACATCACTTGTTAAAAGAGCAACTCT

GAAAGAAAACGAGCAAATTCCAAAATATGAAAAGGTTCACAATTTCAAGGTCCATACATTCCGAGGGCCACACTGGTGTG

AATACTGTGCTAACTTCATGTGGGGTCTCATTGCTCAGGGAGTGAAATGTGCAGATTGTGGTTTGAATGTTCATAAGCAG

TGTTCCAAGATGGTCCCAAATGACTGTAAGCCAGGCTTGAAACATGTCAAGAAGGTATACAGTTGTGACCTTACAACACT

CGTGAAAGCCCATATCACTAAGTGACCAATGGTGGTGGACATGTGCATCAGGGAAATTGAACCTAGAAGTCTTAATTCTG

AAGGACTGTATCTAGTATCAGGATTTAGTGACTTAATTGAAGATGTCAAGATGGCTTTTCACAGAGATGGCGAGAAAGCA

GATATTTCCCTGAACATATATGAAGACAGTAACATTATCACCGGCCCGCTGAAACTGTACTTCAGGGATCTACCAATTCC

ACTCATCATGTATGACGCCTACCCCAAGTTTATAGAGTCCGCCAAAATTCTGGATCCTGACGAGCAGTTGGAAACCCTTC

ACGAGGCACTGAAGCTGCTGCCCCCCACCCCCGCCGGCTCACTGCGA

ORF - retro_cfam_2185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.47 %
Parental protein coverage:	82.91 %
Number of stop codons detected:	2
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalDAEEYQPPIWKSYLYQLQQEAPRPKRIICPGEVENRPKYYGREFHGIISREQADELLGGVEGAYILRESQ
		D..EY.PP.WKSYLYQLQQEAP.P.RI.C..EVENRPKYYGREFHG.ISRE.AD.LL...E..Y..RESQ
RetrocopyDTDEYRPPVWKSYLYQLQQEAPHPRRITCTNEVENRPKYYGREFHGMISREEADQLLSVAEESYLIRESQ
ParentalRQPGCYTLALRFGNQTLNYRLFYDGKHFVGEKRFESIHDLVTDGLITLYIETKASEYISKMTTNPIYEHI
		RQPG.YTLALRFG.QT.N.RL.YDGKHFVGEKRFESIH.LVTDGLITLYIETKA.EYI.KMT.NPIYEHI
RetrocopyRQPGTYTLALRFGSQTRNFRLYYDGKHFVGEKRFESIHHLVTDGLITLYIETKAAEYIAKMTINPIYEHI
ParentalGYATLLREKV-SRRLSRSKNESRKTSVTNEEHTTVEKISSLVRRAALTHNDNHFNYEKTHNFKVHTFRGP
		GY.TL.RE..........K........T...........SLV.RA.L..N.....YEK.HNFKVHTFRGP
RetrocopyGYTTLNREPAYQKHMPVLKETHDERYSTGQDGVSE*RLTSLVKRATLKENEQIPKYEKVHNFKVHTFRGP
ParentalHWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAHNTQRPMVVD
		HWCEYCANFMWGLIAQGV.C.DCGLNVHKQCSK.VPNDC.P.LK..KKVY.CDLTTLVKAH.T..PMVVD
RetrocopyHWCEYCANFMWGLIAQGVKCADCGLNVHKQCSKMVPNDCKPGLKHVKKVYSCDLTTLVKAHITK*PMVVD
ParentalICIREIEARGLKSEGLYRVSGFTEHIEDVKMAFDRDGEKADISANIYPDINIITGALKLYFRDLPIPVIT
		.CIREIE.R.L.SEGLY.VSGF...IEDVKMAF.RDGEKADIS.NIY.D.NIITG.LKLYFRDLPIP.I.
RetrocopyMCIREIEPRSLNSEGLYLVSGFSDLIEDVKMAFHRDGEKADISLNIYEDSNIITGPLKLYFRDLPIPLIM
ParentalYDTYPKFIEAAKISNADERLEAVHDVLMLLPPAHYETLR
		YD.YPKFIE.AKI...DE.LE..H..L.LLPP.....LR
RetrocopyYDAYPKFIESAKILDPDEQLETLHEALKLLPPTPAGSLR

							

							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
SRP012049_cerebellum	7 .77 RPM	395 .80 RPM
SRP017611_brain	60 .81 RPM	55 .57 RPM
SRP017611_kidney	0 .53 RPM	7 .59 RPM
SRP017611_liver	0 .00 RPM	34 .37 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_2185 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_2185 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_2185 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003023	1 retrocopy	retro_cfam_2185 ,
Macaca mulatta	ENSMMUG00000008329	1 retrocopy	retro_mmul_1926,
Oryctolagus cuniculus	ENSOCUG00000009401	1 retrocopy	retro_ocun_440,
Sus scrofa	ENSSSCG00000016687	1 retrocopy	retro_sscr_939,

	RetrogeneDB ID:	retro_cfam_2185
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	X:77481324..77482491(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CHN2
	Ensembl ID:	ENSCAFG00000003023
	Aliases:	None
	Description:	chimerin 2 [Source:HGNC Symbol;Acc:1944]

Parental	DAEEYQPPIWKSYLYQLQQEAPRPKRIICPGEVENRPKYYGREFHGIISREQADELLGGVEGAYILRESQ
	D..EY.PP.WKSYLYQLQQEAP.P.RI.C..EVENRPKYYGREFHG.ISRE.AD.LL...E..Y..RESQ
Retrocopy	DTDEYRPPVWKSYLYQLQQEAPHPRRITCTNEVENRPKYYGREFHGMISREEADQLLSVAEESYLIRESQ

Parental	RQPGCYTLALRFGNQTLNYRLFYDGKHFVGEKRFESIHDLVTDGLITLYIETKASEYISKMTTNPIYEHI
	RQPG.YTLALRFG.QT.N.RL.YDGKHFVGEKRFESIH.LVTDGLITLYIETKA.EYI.KMT.NPIYEHI
Retrocopy	RQPGTYTLALRFGSQTRNFRLYYDGKHFVGEKRFESIHHLVTDGLITLYIETKAAEYIAKMTINPIYEHI

Parental	GYATLLREKV-SRRLSRSKNESRKTSVTNEEHTTVEKISSLVRRAALTHNDNHFNYEKTHNFKVHTFRGP
	GY.TL.RE..........K........T...........SLV.RA.L..N.....YEK.HNFKVHTFRGP
Retrocopy	GYTTLNREPAYQKHMPVLKETHDERYSTGQDGVSE*RLTSLVKRATLKENEQIPKYEKVHNFKVHTFRGP

Parental	HWCEYCANFMWGLIAQGVRCSDCGLNVHKQCSKHVPNDCQPDLKRIKKVYCCDLTTLVKAHNTQRPMVVD
	HWCEYCANFMWGLIAQGV.C.DCGLNVHKQCSK.VPNDC.P.LK..KKVY.CDLTTLVKAH.T..PMVVD
Retrocopy	HWCEYCANFMWGLIAQGVKCADCGLNVHKQCSKMVPNDCKPGLKHVKKVYSCDLTTLVKAHITK*PMVVD

Parental	ICIREIEARGLKSEGLYRVSGFTEHIEDVKMAFDRDGEKADISANIYPDINIITGALKLYFRDLPIPVIT
	.CIREIE.R.L.SEGLY.VSGF...IEDVKMAF.RDGEKADIS.NIY.D.NIITG.LKLYFRDLPIP.I.
Retrocopy	MCIREIEPRSLNSEGLYLVSGFSDLIEDVKMAFHRDGEKADISLNIYEDSNIITGPLKLYFRDLPIPLIM

Parental	YDTYPKFIEAAKISNADERLEAVHDVLMLLPPAHYETLR
	YD.YPKFIE.AKI...DE.LE..H..L.LLPP.....LR
Retrocopy	YDAYPKFIESAKILDPDEQLETLHEALKLLPPTPAGSLR

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

RetrogeneDB ID:

retro_cfam_2185