RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_2472
GTGAAGCAGCTGCCAGTCTTGGAACCTGGACACAAGCCCAGGAAAGCAGTGTCGTACACCTTGACTCTCCCTGGAGACAG

CTCCTGTGCTTGAGCTGGCCACAGCTGTTCATAGTTACCCCCAGTTGGTAATGCCAAGAGAGGGAAGGTCTTCATTGTTG

GGGGAGCAAATCCAAACAGAAGCTTCTCAGATGTGCACACCATGAATCTCGGAAAACACCAGTGGGACTTAGTTACCTGC

AGGGACCTCTTGCCCCGGTATAAACATGCTAGCTTCATTCCCTCCTGCACACCTGACAGTATTTGGGTATTTGGAGGTGC

CAGCCAATCAGGAAATCTAAATTGTCTACAAGTCCTGAATCCTGAAACCAGGACATGGACCACGTCAGAAGTGACCAGCC

CCCTACCATCCCCAAGAACATTCTACACGTCATCGGCAGCCATTGGAAACCAGCTGTATGCCTTTGGGGTTGGAGAGAGA

GGTGTCTAGCCTGGTGCAGGACATGAAGCTGCATGTGTCTGATGCAAACACTCTGACCTGGTCACAGCCAGAGACACTTG

GAAATCCTCCATACCCCAGGCATGGTCATGTGATAGTGGCAGCAGGGACAAAGCTCTTCATCCATGGAGCCTTGGCGATA

GACAAATTCTATGTTAATCTCCATTACATTGATATAAGTGACATGAAACGGCAGAAACTAAGTCCCACGGAGGCTGCTCT

AGCAGGCTGTGCTGCCCACTCAGCTGTGGCCTTGGGAAAACACTTGTACATCTTTGGTGGAATGACTCCTGCAGGAGCGC

TGGACACAACGTACTAGTATCACACAGAAAAGCAGCATTGGACCTTGCTTAAGTTTGATACTTTTCCACGCCCTGGACGA

TTGGGCCACTCCTTGGGTATCATTCCGTGGCCAGTGACATGTGCTTCTGAGAAGGAAGATTCCAATTCTCTCACTCTGAA

TCATGAAGCTGAGGAAGGAGATTCAGCTGACACAGTAATGACCCACAGTAGTGACTCACACAAGGAAAGCCAGGCTGATA

CACTGCTCTGTTTTGTGTTTGGTGGGATGAGTACAGAAGGGGAAATCTATGATGATTGTGTTGTGACTGTAGTTGAC

ORF - retro_cjac_2472 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.45 %
Parental protein coverage:	100. %
Number of stop codons detected:	4
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMKQLPILEPGDKPRKASWYTLTLQGDSPCARVGHSCSYLPPVGNAKRGKVFIVGGANPNRSFSDVHAMDL
		.KQLP.LEPG.KPRKA..YTLTL.GDS.CA..GHSCS.LPPVGNAKRGKVFIVGGANPNRSFSDVH.M.L
RetrocopyVKQLPVLEPGHKPRKAVSYTLTLPGDSSCA*AGHSCS*LPPVGNAKRGKVFIVGGANPNRSFSDVHTMNL
ParentalGKHQWDLVTCKGLLPRYEHASFIPSCTPDSIWVFGGANQSGNRNCLQVLNPETRTWTMPEVTSPPPSPRT
		GKHQWDLVTC..LLPRY.HASFIPSCTPDSIWVFGGA.QSGN.NCLQVLNPETRTWT..EVTSP.PSPRT
RetrocopyGKHQWDLVTCRDLLPRYKHASFIPSCTPDSIWVFGGASQSGNLNCLQVLNPETRTWTTSEVTSPLPSPRT
ParentalFHTSSAAIGNQLYVFGGGERGAQP-VQDVKLHVFDASTLTWSQPETLGNPPSPRHGHVMVAAGTKLFIHG
		F.TSSAAIGNQLY.FG.GERG..P.VQD.KLHV.DA.TLTWSQPETLGNPP.PRHGHV.VAAGTKLFIHG
RetrocopyFYTSSAAIGNQLYAFGVGERGV*P>VQDMKLHVSDANTLTWSQPETLGNPPYPRHGHVIVAAGTKLFIHG
ParentalGLAGDKFYDDFHCIDISDMKWQKLSPTGATPAGCAAHSAVAVGKHLYIFGGMTPAGALDTMYQYHTEKQH
		.LA.DKFY...H.IDISDMK.QKLSPT.A..AGCAAHSAVA.GKHLYIFGGMTPAGALDT.Y.YHTEKQH
RetrocopyALAIDKFYVNLHYIDISDMKRQKLSPTEAALAGCAAHSAVALGKHLYIFGGMTPAGALDTTY*YHTEKQH
ParentalWTLLKFDTFLPPGRLDHSMCIIPWPVTCASEKEDSNSLSLNHEAEKVDSADTVMTHSGDSHEESRADTLL
		WTLLKFDTF..PGRL.HS..IIPWPVTCASEKEDSNSL.LNHEAE..DSADTVMTHS.DSH.ES.ADTLL
RetrocopyWTLLKFDTFPRPGRLGHSLGIIPWPVTCASEKEDSNSLTLNHEAEEGDSADTVMTHSSDSHKESQADTLL
ParentalCFVFGGMNTEGEIYDDCIVTAVD
		CFVFGGM.TEGEIYDDC.VT.VD
RetrocopyCFVFGGMSTEGEIYDDCVVTVVD

							

							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
SRP051959_colon	0 .00 RPM	3 .95 RPM
SRP051959_heart	0 .05 RPM	3 .32 RPM
SRP051959_kidney	0 .00 RPM	5 .06 RPM
SRP051959_liver	0 .00 RPM	4 .03 RPM
SRP051959_lung	0 .03 RPM	3 .58 RPM
SRP051959_lymph_node	0 .00 RPM	3 .49 RPM
SRP051959_skeletal_muscle	0 .00 RPM	2 .29 RPM
SRP051959_spleen	0 .02 RPM	3 .51 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_2472 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2472 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_2472 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
Canis familiaris	ENSCAFG00000020201	1 retrocopy	retro_cfam_1704,
Callithrix jacchus	ENSCJAG00000006849	1 retrocopy	retro_cjac_2472 ,

	RetrogeneDB ID:	retro_cjac_2472
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	4:122862202..122863319(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	RABEPK
	Ensembl ID:	ENSCJAG00000006849
	Aliases:	None
	Description:	Rab9 effector protein with kelch motifs [Source:HGNC Symbol;Acc:16896]

Parental	MKQLPILEPGDKPRKASWYTLTLQGDSPCARVGHSCSYLPPVGNAKRGKVFIVGGANPNRSFSDVHAMDL
	.KQLP.LEPG.KPRKA..YTLTL.GDS.CA..GHSCS.LPPVGNAKRGKVFIVGGANPNRSFSDVH.M.L
Retrocopy	VKQLPVLEPGHKPRKAVSYTLTLPGDSSCAAGHSCSLPPVGNAKRGKVFIVGGANPNRSFSDVHTMNL

Parental	GKHQWDLVTCKGLLPRYEHASFIPSCTPDSIWVFGGANQSGNRNCLQVLNPETRTWTMPEVTSPPPSPRT
	GKHQWDLVTC..LLPRY.HASFIPSCTPDSIWVFGGA.QSGN.NCLQVLNPETRTWT..EVTSP.PSPRT
Retrocopy	GKHQWDLVTCRDLLPRYKHASFIPSCTPDSIWVFGGASQSGNLNCLQVLNPETRTWTTSEVTSPLPSPRT

Parental	FHTSSAAIGNQLYVFGGGERGAQP-VQDVKLHVFDASTLTWSQPETLGNPPSPRHGHVMVAAGTKLFIHG
	F.TSSAAIGNQLY.FG.GERG..P.VQD.KLHV.DA.TLTWSQPETLGNPP.PRHGHV.VAAGTKLFIHG
Retrocopy	FYTSSAAIGNQLYAFGVGERGV*P>VQDMKLHVSDANTLTWSQPETLGNPPYPRHGHVIVAAGTKLFIHG

Parental	GLAGDKFYDDFHCIDISDMKWQKLSPTGATPAGCAAHSAVAVGKHLYIFGGMTPAGALDTMYQYHTEKQH
	.LA.DKFY...H.IDISDMK.QKLSPT.A..AGCAAHSAVA.GKHLYIFGGMTPAGALDT.Y.YHTEKQH
Retrocopy	ALAIDKFYVNLHYIDISDMKRQKLSPTEAALAGCAAHSAVALGKHLYIFGGMTPAGALDTTY*YHTEKQH

Parental	WTLLKFDTFLPPGRLDHSMCIIPWPVTCASEKEDSNSLSLNHEAEKVDSADTVMTHSGDSHEESRADTLL
	WTLLKFDTF..PGRL.HS..IIPWPVTCASEKEDSNSL.LNHEAE..DSADTVMTHS.DSH.ES.ADTLL
Retrocopy	WTLLKFDTFPRPGRLGHSLGIIPWPVTCASEKEDSNSLTLNHEAEEGDSADTVMTHSSDSHKESQADTLL

Parental	CFVFGGMNTEGEIYDDCIVTAVD
	CFVFGGM.TEGEIYDDC.VT.VD
Retrocopy	CFVFGGMSTEGEIYDDCVVTVVD

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

RetrogeneDB ID:

retro_cjac_2472