RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_2661
ATGGGGATCTTAGAGAAGATCTTGGAGATCAAGAAGGAGATTGCTCGGACACGGAAGAACAAAGCCACTGAGTATCATCT

GGGCCTGCTGAATGCTAAACTCGCCAAGTATCGGGCCCAGCTCCTGGAACCATCCAAATCCACCTCATCCAAAGGAGAGG

GCTTTGATGTCATGAATTTTGGCGATGCCCACATGGAGCTAATTGGATTTCCCTCTGTGGGTAAGTCCACATTCTTGAGT

CTGATGACCTCCACGGCCATCGAGGCGGCGTCCTATGAGTTCACCACTCTGACATGTGTTCCTGGGGTCGTTGAATACAA

AGGTAGCAACATCCAGCTCCTGGACCTTCCCGGAATCATTGAAGGCACAGCACAAGGAAAAAGGCCATGGCCAGCAGGTG

ATTGCTGTGGCATGCACGGCCGATGTCGTCATCATGTTGCTGGATGCCACCAAGGGAGAGGTGCAGAGGTCTCTGCTGGA

GAAGGAGCTGGAGTCCATGGGCATCCACCTCAGCGAGCACAAGCCTAACATCTACTTCAAGCCCAAGAGAGGCGGCGGCA

ACTCCTTTAACTCGACAGTCACACTGACCCAATGCTCGGAAAAGCTGGTGCAGCTCATCCTGCACGAATACAAGATCTTC

AATGCAGACGTGCTCTTCCAAGAAGACTGTTCCCCAGATGAGTTCATCGATGTGATCATGGGCAACTGGGTGTACATGCC

TTGCATGTATGTTTATAACAAAATCGACCAGATCTCCATGGAAGAGGTGGACCGCCTGGCCCAAAAACCCAACAGTGTGG

TCACCAGCTATGGCATGAAGCTGAACTTGGTCTACCTGCTGGAGATGCTTTGGGAGTACTTGGCCCTGACCTGCATCTAC

ACCAAGAAGATAGGAGAGAGGCCAGACTTCCCAGACACTATCATTCTCCAGAAAGGGGCCTCAGTGGAGCACGTGTGCCA

CCGCATCCACCGGTCACTTGCCAGCCAGTTCCAGTATGCCCTGGTGTGGGGCACCAGCACAAAGTACAGTCCGCAGTGGG

TGGGCCTGACCCACACCATGGAGCCTGAGGACGTCATCCAGATCGTGAAGAAG

ORF - retro_cjac_2661 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	87.95 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMGILEKISEIEKEIARTQKNKATEYHLGLLKAKLAKYRAQLLEPSKSASSKGEGFDVMKSGDARVALIGF
		MGILEKI.EI.KEIART.KNKATEYHLGLL.AKLAKYRAQLLEPSKS.SSKGEGFDVM..GDA...LIGF
RetrocopyMGILEKILEIKKEIARTRKNKATEYHLGLLNAKLAKYRAQLLEPSKSTSSKGEGFDVMNFGDAHMELIGF
ParentalPSVGKSTFLSLMTSTASEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGK-GRGRQVIAVART
		PSVGKSTFLSLMTSTA.EAASYEFTTLTC.PGV.EYKG.NIQLLDLPGIIEG.AQGK.G.G.QVIAVA.T
RetrocopyPSVGKSTFLSLMTSTAIEAASYEFTTLTCVPGVVEYKGSNIQLLDLPGIIEGTAQGK>GHGQQVIAVACT
ParentalADVVIMMLDATKGEVQRSLLEKELESVGIRLNKHKPNIYFKPKKGGGISFNSTVTLTQCSEKLVQLILHE
		ADVVIM.LDATKGEVQRSLLEKELES.GI.L..HKPNIYFKPK.GGG.SFNSTVTLTQCSEKLVQLILHE
RetrocopyADVVIMLLDATKGEVQRSLLEKELESMGIHLSEHKPNIYFKPKRGGGNSFNSTVTLTQCSEKLVQLILHE
ParentalYKIFNAEVLFREDCSPDEFIDVIVGNRVYMPCLYVYNKIDQISMEEVDCLARKPNSVVISCGMKLNLDYL
		YKIFNA.VLF.EDCSPDEFIDVI.GN.VYMPC.YVYNKIDQISMEEVD.LA.KPNSVV.S.GMKLNL.YL
RetrocopyYKIFNADVLFQEDCSPDEFIDVIMGNWVYMPCMYVYNKIDQISMEEVDRLAQKPNSVVTSYGMKLNLVYL
ParentalLEMLWEYLALTCIYTKKRGQRPDFTDAIILRKGASVEHVCHRIHRSLASQFKYALVWGTSTKYSPQRVGL
		LEMLWEYLALTCIYTKK.G.RPDF.D.IIL.KGASVEHVCHRIHRSLASQF.YALVWGTSTKYSPQ.VGL
RetrocopyLEMLWEYLALTCIYTKKIGERPDFPDTIILQKGASVEHVCHRIHRSLASQFQYALVWGTSTKYSPQWVGL
ParentalTHTMEHEDVIQIVKK
		THTME.EDVIQIVKK
RetrocopyTHTMEPEDVIQIVKK

							

							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 .07 RPM	11 .58 RPM
SRP051959_heart	0 .09 RPM	9 .19 RPM
SRP051959_kidney	0 .09 RPM	18 .41 RPM
SRP051959_liver	0 .04 RPM	11 .96 RPM
SRP051959_lung	0 .03 RPM	13 .40 RPM
SRP051959_lymph_node	0 .00 RPM	15 .20 RPM
SRP051959_skeletal_muscle	0 .13 RPM	10 .57 RPM
SRP051959_spleen	0 .04 RPM	14 .41 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_2661 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2661 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_2661 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014953	1 retrocopy	retro_cjac_2661 ,
Mus musculus	ENSMUSG00000020537	1 retrocopy	retro_mmus_974,
Otolemur garnettii	ENSOGAG00000033863	1 retrocopy	retro_ogar_822,

	RetrogeneDB ID:	retro_cjac_2661
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	5:122540501..122541594(-)
	Located in intron of:	ENSCJAG00000019883
Retrocopy information	Ensembl ID:	ENSCJAG00000019907
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	DRG2
	Ensembl ID:	ENSCJAG00000014953
	Aliases:	None
	Description:	developmentally regulated GTP binding protein 2 [Source:HGNC Symbol;Acc:3030]

Parental	MGILEKISEIEKEIARTQKNKATEYHLGLLKAKLAKYRAQLLEPSKSASSKGEGFDVMKSGDARVALIGF
	MGILEKI.EI.KEIART.KNKATEYHLGLL.AKLAKYRAQLLEPSKS.SSKGEGFDVM..GDA...LIGF
Retrocopy	MGILEKILEIKKEIARTRKNKATEYHLGLLNAKLAKYRAQLLEPSKSTSSKGEGFDVMNFGDAHMELIGF

Parental	PSVGKSTFLSLMTSTASEAASYEFTTLTCIPGVIEYKGANIQLLDLPGIIEGAAQGK-GRGRQVIAVART
	PSVGKSTFLSLMTSTA.EAASYEFTTLTC.PGV.EYKG.NIQLLDLPGIIEG.AQGK.G.G.QVIAVA.T
Retrocopy	PSVGKSTFLSLMTSTAIEAASYEFTTLTCVPGVVEYKGSNIQLLDLPGIIEGTAQGK>GHGQQVIAVACT

Parental	ADVVIMMLDATKGEVQRSLLEKELESVGIRLNKHKPNIYFKPKKGGGISFNSTVTLTQCSEKLVQLILHE
	ADVVIM.LDATKGEVQRSLLEKELES.GI.L..HKPNIYFKPK.GGG.SFNSTVTLTQCSEKLVQLILHE
Retrocopy	ADVVIMLLDATKGEVQRSLLEKELESMGIHLSEHKPNIYFKPKRGGGNSFNSTVTLTQCSEKLVQLILHE

Parental	YKIFNAEVLFREDCSPDEFIDVIVGNRVYMPCLYVYNKIDQISMEEVDCLARKPNSVVISCGMKLNLDYL
	YKIFNA.VLF.EDCSPDEFIDVI.GN.VYMPC.YVYNKIDQISMEEVD.LA.KPNSVV.S.GMKLNL.YL
Retrocopy	YKIFNADVLFQEDCSPDEFIDVIMGNWVYMPCMYVYNKIDQISMEEVDRLAQKPNSVVTSYGMKLNLVYL

Parental	LEMLWEYLALTCIYTKKRGQRPDFTDAIILRKGASVEHVCHRIHRSLASQFKYALVWGTSTKYSPQRVGL
	LEMLWEYLALTCIYTKK.G.RPDF.D.IIL.KGASVEHVCHRIHRSLASQF.YALVWGTSTKYSPQ.VGL
Retrocopy	LEMLWEYLALTCIYTKKIGERPDFPDTIILQKGASVEHVCHRIHRSLASQFQYALVWGTSTKYSPQWVGL

Parental	THTMEHEDVIQIVKK
	THTME.EDVIQIVKK
Retrocopy	THTMEPEDVIQIVKK

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

RetrogeneDB ID:

retro_cjac_2661