RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_1312
TACTGTTATGACAAGAACATCATCAAGAAGGCGATCGGGCAGAAGTTTGTGCACCAGTTCGTCTCTTTCCCGGAGATCCC

GAAGATGGATCCGCGTGCGGTGGAGGTCGGCCTGGAGAGCCTTCTGCTGCAGGACAGCGACGGCAAGGCCTCTCCCGAGG

GCCGTGAGGCTCACAAACACGGCCTCGCCGCCCTCAAAAGCACCAGCCGCAATGAATACATCCACTCAGGCCTGTACTCG

TCCTTCACCATCAATTCCCTGCAGAGCCCACCGGACGCCTTCAAGGCCATCAAGATGGAGAAGCTGGAGGAGCCGCCCCA

AGACAGCCCCCCTACCCGCCCCGTGGAAGAAGTCAGGACTGTGATCAGGTTTGTGACCAATAAAACCGACAAGCGCGTCA

CCAGGCCGGCGGTGTCCCTGGCTTCCACATCAGAGGCTGCAGCGGCGACTGCCTTCCTGGCCTCGTCCGTCTCGGCCGAG

ACCTCTTTAATGTTGCCAAAGGCTGCCAGTATTTCGTCTGCCTCACCCTTCTCATCTCGGTCCCCGTCCCTGTCCCCCAA

CTCACCCCTCCCTTCTGATCACAGAAGCCTCTTCCTGGAGGCCGCCTGCCATGACGCCGATTCCCTGGAGCCCTTGAACC

TGTCATCGGGCTCCAAGACCAAGTCTCCATCTCTTTCCCCAAAGTCCAAAAAACCCAAAGGCTTGGAAATCTCAGCGTCC

CCACTGGTGCTCTCCGGCACTGACATTGGCTCCATCGCCCGCAACAGCCCAGCCCTCCCCTCGGGATCCCTCACCTCAGC

CTTCTTCAGCGCACAGACACCAAATGGATTGCTTCTGACTCCGAGTCCAGTGCTCTCCAGCATGCATTTCTGCAGCAGCC

TTAGTCCAGTTGCTCCACTGAGTCCTGCCAGGCTGCAAGGGCCAGGCACGCTGTTCCAGTTCCCCACACTGCTTAGCGGC

CACATGCCAGTGCCAATCCCCAGTCTGGACAGCTGCTTCTCCAGTACTGCTTTCTTCCAGCTCTCAGAAATCC

ORF - retro_cjac_1312 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.74 %
Parental protein coverage:	84.28 %
Number of stop codons detected:	0
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalYYYDKNIIKKVIGQKFVYKFVSFPEILKMDPHAVEISRESLLLQDSDCKASPEGREAHKHSLAALKSTSR
		Y.YDKNIIKK.IGQKFV..FVSFPEI.KMDP.AVE...ESLLLQDSD.KASPEGREAHKH.LAALKSTSR
RetrocopyYCYDKNIIKKAIGQKFVHQFVSFPEIPKMDPRAVEVGLESLLLQDSDGKASPEGREAHKHGLAALKSTSR
ParentalNEYIHSGLYSSFTINSLQNPPDAFKAIKTEKLEEPPEDSP---PVEEVRTVIRFVTNKTDKHVTRPVVSL
		NEYIHSGLYSSFTINSLQ.PPDAFKAIK.EKLEEPP.DSP...PVEEVRTVIRFVTNKTDK.VTRP.VSL
RetrocopyNEYIHSGLYSSFTINSLQSPPDAFKAIKMEKLEEPPQDSPPTRPVEEVRTVIRFVTNKTDKRVTRPAVSL
ParentalPSTSEAAAASAFLASSVSAKISSLMLPNAASISSASPFSSRSPSLSPNSPLPSEHRSLFLEAACHDSDSL
		.STSEAAAA.AFLASSVSA...SLMLP.AASISSASPFSSRSPSLSPNSPLPS.HRSLFLEAACHD.DSL
RetrocopyASTSEAAAATAFLASSVSAE-TSLMLPKAASISSASPFSSRSPSLSPNSPLPSDHRSLFLEAACHDADSL
ParentalEPLNLSSGSKTKSPSLPPKAKKPKGLEISAPPLVLSGTDIGSIALNSPALPSGSLTPAFFTAQTPNGLLL
		EPLNLSSGSKTKSPSL.PK.KKPKGLEISA.PLVLSGTDIGSIA.NSPALPSGSLT.AFF.AQTPNGLLL
RetrocopyEPLNLSSGSKTKSPSLSPKSKKPKGLEISASPLVLSGTDIGSIARNSPALPSGSLTSAFFSAQTPNGLLL
ParentalTPSPLLSSIHFWSSLSPVAPLSPARLQGPSTLFQFPTLLNGHMPVPIPSLD-RAASPVLLSSNSQKS
		TPSP.LSS.HF.SSLSPVAPLSPARLQGP.TLFQFPTLL.GHMPVPIPSLD..A....L.SS.SQKS
RetrocopyTPSPVLSSMHFCSSLSPVAPLSPARLQGPGTLFQFPTLLSGHMPVPIPSLD>AASPVLLSSS-SQKS

							

							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 .09 RPM	5 .59 RPM
SRP051959_heart	0 .11 RPM	5 .77 RPM
SRP051959_kidney	0 .11 RPM	2 .86 RPM
SRP051959_liver	0 .06 RPM	1 .56 RPM
SRP051959_lung	0 .37 RPM	7 .08 RPM
SRP051959_lymph_node	0 .18 RPM	5 .96 RPM
SRP051959_skeletal_muscle	0 .11 RPM	2 .49 RPM
SRP051959_spleen	0 .11 RPM	5 .59 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_1312 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1312 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_1312 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	ENSCJAG00000002592	1 retrocopy	retro_cjac_1312 ,
Callithrix jacchus	ENSCJAG00000008102	1 retrocopy	retro_cjac_4220,
Callithrix jacchus	ENSCJAG00000013817	1 retrocopy	retro_cjac_2487,

	RetrogeneDB ID:	retro_cjac_1312
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	14:105081444..105082477(-)
	Located in intron of:	ENSCJAG00000016447
Retrocopy information	Ensembl ID:	ENSCJAG00000016452
	Aliases:	None
	Status:	KNOWN_PSEUDOGENE
Parental gene information	Parental gene summary:
	Parental gene symbol:	ELK3
	Ensembl ID:	ENSCJAG00000002592
	Aliases:	None
	Description:	ELK3, ETS-domain protein (SRF accessory protein 2) [Source:HGNC Symbol;Acc:3325]

Parental	YYYDKNIIKKVIGQKFVYKFVSFPEILKMDPHAVEISRESLLLQDSDCKASPEGREAHKHSLAALKSTSR
	Y.YDKNIIKK.IGQKFV..FVSFPEI.KMDP.AVE...ESLLLQDSD.KASPEGREAHKH.LAALKSTSR
Retrocopy	YCYDKNIIKKAIGQKFVHQFVSFPEIPKMDPRAVEVGLESLLLQDSDGKASPEGREAHKHGLAALKSTSR

Parental	NEYIHSGLYSSFTINSLQNPPDAFKAIKTEKLEEPPEDSP---PVEEVRTVIRFVTNKTDKHVTRPVVSL
	NEYIHSGLYSSFTINSLQ.PPDAFKAIK.EKLEEPP.DSP...PVEEVRTVIRFVTNKTDK.VTRP.VSL
Retrocopy	NEYIHSGLYSSFTINSLQSPPDAFKAIKMEKLEEPPQDSPPTRPVEEVRTVIRFVTNKTDKRVTRPAVSL

Parental	PSTSEAAAASAFLASSVSAKISSLMLPNAASISSASPFSSRSPSLSPNSPLPSEHRSLFLEAACHDSDSL
	.STSEAAAA.AFLASSVSA...SLMLP.AASISSASPFSSRSPSLSPNSPLPS.HRSLFLEAACHD.DSL
Retrocopy	ASTSEAAAATAFLASSVSAE-TSLMLPKAASISSASPFSSRSPSLSPNSPLPSDHRSLFLEAACHDADSL

Parental	EPLNLSSGSKTKSPSLPPKAKKPKGLEISAPPLVLSGTDIGSIALNSPALPSGSLTPAFFTAQTPNGLLL
	EPLNLSSGSKTKSPSL.PK.KKPKGLEISA.PLVLSGTDIGSIA.NSPALPSGSLT.AFF.AQTPNGLLL
Retrocopy	EPLNLSSGSKTKSPSLSPKSKKPKGLEISASPLVLSGTDIGSIARNSPALPSGSLTSAFFSAQTPNGLLL

Parental	TPSPLLSSIHFWSSLSPVAPLSPARLQGPSTLFQFPTLLNGHMPVPIPSLD-RAASPVLLSSNSQKS
	TPSP.LSS.HF.SSLSPVAPLSPARLQGP.TLFQFPTLL.GHMPVPIPSLD..A....L.SS.SQKS
Retrocopy	TPSPVLSSMHFCSSLSPVAPLSPARLQGPGTLFQFPTLLSGHMPVPIPSLD>AASPVLLSSS-SQKS

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

RetrogeneDB ID:

retro_cjac_1312