RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_3816
ATGTACGCAGCCATTCCCCAGAGTGGCTCTCCATTTTCAGCCTCAGTGCAGGATCCAGGCCTGCATATGTGGAGGGTGGA

GAAGCTGAAGCCAGTTCCTGTGGCACAAGAGAACCAGGGTGTCTTCTTCTCCTCGGGGACTTCTACCTACTGCTGTACAG

TGGCCCAGAAGAGGTTTCCCATCTGCACCTGTGGATAGGCCAGCAGTCATCCTGGCATGAGCAGGGGTCCTGTGCTGTGC

TGGCTGTGTACCTCAACACACTGCTGGAAGAGCGGCCTGTGCAGCACTGTGAGGTGCAGGGCAGTGAGTCCAATCTCTTC

ATGAGCTACTTCCCACAGGGCCTCAAGTACCAGGAAGGTGGTGTGGAGTCAGCATTTCACAAGACCTCCTCAGGAGCCCC

AGCTGCCGTCAAGAAACTCTTCCAGGTGAAGGGGAGAAGAACATCCATGCCACTGAGTGGGCACTGAGCTGGGACAGCTT

CAACATGGGGGACTGCTTCATCCTGGACCTGGGCCAGAACATCTTTGCCTGGTGTGGTAGAAAGTCCAACATCCTGGAAC

GCAACAAGGCGAGGGACCTGGCCCTGGCCATCCGGGACAGTGAGCGATAGGGCAAGGCCCAGGTGGAGATTGTCACTGAT

GGGGAGGAGCCTGATGAGATGATCCAGGTTCTGGGCCCCAAGCCTTCTCTCAAGGAGGGCAACCCTGAGGAAGACCTCAC

AGCTGACCAGACAAATGCCCAGGCCACGGGTCTGTATAAGGTCTCTGATGCCACTGGACAGATGAACCTGACCAAGGTGG

CTAACTCCAGTCCCTTTGCCCCTGAAGTGCTGATGTCTGATGACTGCTCTGTGCTAAACAATGGGTTCTGTGGCAAGATC

TACATCTGGAAGGGACGAAAAGCGAATGAGAAGGAGCAGCAGGCAGCCCTGCAAGTGGCTGAGGGCTTCATCTTGCACAT

GTGGTATGCCCTCAACACTCAGGTGGAGATTCTGCCCCAGAGCCGTGAG

ORF - retro_cjac_3816 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.14 %
Parental protein coverage:	96.54 %
Number of stop codons detected:	1
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalMYTAIPQSGSPFSASVQDPGLHVWRVEKLKPVPVARENQGV-FFSG-DSYLVLHNGPEEVSHLHLWIGQQ
		MY.AIPQSGSPFSASVQDPGLH.WRVEKLKPVPVA.ENQGV.F.SG.D.YL.L..GPEEVSHLHLWIGQQ
RetrocopyMYAAIPQSGSPFSASVQDPGLHMWRVEKLKPVPVAQENQGVFFSSG<DFYLLLYSGPEEVSHLHLWIGQQ
ParentalSSRDEQGACAVLAVHLNTLLGERPVQHREVQGNESDLFMSYFPRGLKYQEGGVESAFHKTSSGAPAAIKK
		SS..EQG.CAVLAV.LNTLL.ERPVQH.EVQG.ES.LFMSYFP.GLKYQEGGVESAFHKTSSGAPAA.KK
RetrocopySSWHEQGSCAVLAVYLNTLLEERPVQHCEVQGSESNLFMSYFPQGLKYQEGGVESAFHKTSSGAPAAVKK
ParentalLYQVKGK-KNIRATERALSWDSFNTGDCFILDLGQNIFAWCGGKSNILERNKARDLALAIRDSERQGKAQ
		L.QVKG..KNI.ATE.ALSWDSFN.GDCFILDLGQNIFAWCG.KSNILERNKARDLALAIRDSER.GKAQ
RetrocopyLFQVKGR<KNIHATEWALSWDSFNMGDCFILDLGQNIFAWCGRKSNILERNKARDLALAIRDSER*GKAQ
ParentalVEIVTDGEEPAEMIQVLGPK-ALKEGNPEEDLTADQTNSQAAALYKVSDATGQMNLTKVADSSPFALELL
		VEIVTDGEEP.EMIQVLGPK..LKEGNPEEDLTADQTN.QA..LYKVSDATGQMNLTKVA.SSPFA.E.L
RetrocopyVEIVTDGEEPDEMIQVLGPKPSLKEGNPEEDLTADQTNAQATGLYKVSDATGQMNLTKVANSSPFAPEVL
ParentalISDDCFVLDNGLCGKIYIWKGRKANEKERQAALQVAEGFISRMRYAPNTQVEILPQGRE
		.SDDC.VL.NG.CGKIYIWKGRKANEKE.QAALQVAEGFI..M.YA.NTQVEILPQ.RE
RetrocopyMSDDCSVLNNGFCGKIYIWKGRKANEKEQQAALQVAEGFILHMWYALNTQVEILPQSRE

							

							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	2 .26 RPM	36 .70 RPM
SRP051959_heart	1 .81 RPM	5 .40 RPM
SRP051959_kidney	1 .82 RPM	6 .32 RPM
SRP051959_liver	1 .13 RPM	5 .18 RPM
SRP051959_lung	3 .01 RPM	14 .82 RPM
SRP051959_lymph_node	4 .16 RPM	14 .31 RPM
SRP051959_skeletal_muscle	1 .94 RPM	2 .36 RPM
SRP051959_spleen	3 .49 RPM	45 .55 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_3816 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3816 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_3816 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019705	2 retrocopies	retro_cjac_3816 , retro_cjac_459,
Macropus eugenii	ENSMEUG00000013559	1 retrocopy	retro_meug_1063,
Mus musculus	ENSMUSG00000056737	1 retrocopy	retro_mmus_3506,
Otolemur garnettii	ENSOGAG00000001084	1 retrocopy	retro_ogar_3277,
Rattus norvegicus	ENSRNOG00000013668	1 retrocopy	retro_rnor_840,

	RetrogeneDB ID:	retro_cjac_3816
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	GL284773.1:7139..8148(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CAPG
	Ensembl ID:	ENSCJAG00000019705
	Aliases:	None
	Description:	capping protein (actin filament), gelsolin-like [Source:HGNC Symbol;Acc:1474]

Parental	MYTAIPQSGSPFSASVQDPGLHVWRVEKLKPVPVARENQGV-FFSG-DSYLVLHNGPEEVSHLHLWIGQQ
	MY.AIPQSGSPFSASVQDPGLH.WRVEKLKPVPVA.ENQGV.F.SG.D.YL.L..GPEEVSHLHLWIGQQ
Retrocopy	MYAAIPQSGSPFSASVQDPGLHMWRVEKLKPVPVAQENQGVFFSSG<DFYLLLYSGPEEVSHLHLWIGQQ

Parental	SSRDEQGACAVLAVHLNTLLGERPVQHREVQGNESDLFMSYFPRGLKYQEGGVESAFHKTSSGAPAAIKK
	SS..EQG.CAVLAV.LNTLL.ERPVQH.EVQG.ES.LFMSYFP.GLKYQEGGVESAFHKTSSGAPAA.KK
Retrocopy	SSWHEQGSCAVLAVYLNTLLEERPVQHCEVQGSESNLFMSYFPQGLKYQEGGVESAFHKTSSGAPAAVKK

Parental	LYQVKGK-KNIRATERALSWDSFNTGDCFILDLGQNIFAWCGGKSNILERNKARDLALAIRDSERQGKAQ
	L.QVKG..KNI.ATE.ALSWDSFN.GDCFILDLGQNIFAWCG.KSNILERNKARDLALAIRDSER.GKAQ
Retrocopy	LFQVKGR<KNIHATEWALSWDSFNMGDCFILDLGQNIFAWCGRKSNILERNKARDLALAIRDSER*GKAQ

Parental	VEIVTDGEEPAEMIQVLGPK-ALKEGNPEEDLTADQTNSQAAALYKVSDATGQMNLTKVADSSPFALELL
	VEIVTDGEEP.EMIQVLGPK..LKEGNPEEDLTADQTN.QA..LYKVSDATGQMNLTKVA.SSPFA.E.L
Retrocopy	VEIVTDGEEPDEMIQVLGPKPSLKEGNPEEDLTADQTNAQATGLYKVSDATGQMNLTKVANSSPFAPEVL

Parental	ISDDCFVLDNGLCGKIYIWKGRKANEKERQAALQVAEGFISRMRYAPNTQVEILPQGRE
	.SDDC.VL.NG.CGKIYIWKGRKANEKE.QAALQVAEGFI..M.YA.NTQVEILPQ.RE
Retrocopy	MSDDCSVLNNGFCGKIYIWKGRKANEKEQQAALQVAEGFILHMWYALNTQVEILPQSRE

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

RetrogeneDB ID:

retro_cjac_3816