RetrogeneDB - Retrocopy retro_cjac

						
>retro_cjac_1476
ATGGGGCTCTGGGAGAGCCCGAGCTCCTGGTGTGGCACCCAGAGGCGGTAGCTTTAGAGCCTCCAGTGCCTGTGGGGCTG

GAGGTGAAGTTGGGGTCCCTGGTGCTGCTGCTGGTGCTCACCCTTCTCGGCAGCCTGGTGCCCGTCTGTGTGCTGTGCCA

GCCAAGAGCTAACCATGAAGCCTCAGCTTCCTGCCAGAAAGCCCCAAGCCTAGTAAGCTGTTTTGTGGGGTGGCGTCTTT

TTGGCCACCTGTGTCCTTGACCTGCTGCCTGACCACCTGGCTGCTACAGGTGAGGCCCTGGCAGGCTTGCATGTGACGCT

CCGGTTCTCACTGCAAGAGTTCATCCTGGCCATGGGCTTCTCCCTCATCCTGGTGACAGAGCAGATCACATTGGCTTACA

AGCAGCAGTCAGGGCCGCCACCTCTGGAGGAAACAAGGGCTCTGCTGGGAACAGTGAATGGTGGGTCGCAGCATTGGCAT

GATGGACCAGGGATTCCACAGGCAAGTGGAGCCCCAGCAACCCCCTCAGCCTTGTGTGCCTGTGTCCTGCTCTTCTCCCT

GGCCCTCCACTCTGTGTTTGAGGGGCTGGCAGTAGGGCTTCAGTGAGACCAGACTCAGGCCACGGAGCTGTGCCTGGCTT

TGCTGCTCCACAAGGGGATCCTCGCTGTCAGTCTGTCCTTCCGGCTGCTGCAGAGCCACCTTGGGGCACAGGTGGTGGCT

GGCTGTGGGATCCTCTTCTCATGCATGACACCTCTAGGTGTTGGGCTGGGTGCAGCTCTGGGAGAGTGGGCAGGACCTCC

ACACCAGCTGGCCCAGTCTGTGCTAGAGGGCATGGCGGCTGACACTTTTCTCTATATCACCTTTCTGGAAATCCTGCCCC

AGGAGCTGGCCAGTTCTGAGCAAAGGATCCTCAAGGTCATTCTGCTCCTAGCAGACTTTGCCCTGCTCACTAACCTGCTC

TTCATCCAAATC

ORF - retro_cjac_1476 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	86.2 %
Parental protein coverage:	100. %
Number of stop codons detected:	1
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalMGPW-GEPELLVWRPEAVASEPPVLVGLEVKLGALVLLLVLTLLCSLVPICVLRRPGANHEASASRQKAL
		MG.W.GEPELLVW.PEAVA.EPPV.VGLEVKLG.LVLLLVLTLL.SLVP.CVL..P.ANHEASAS.QKA.
RetrocopyMGLW<GEPELLVWHPEAVALEPPVPVGLEVKLGSLVLLLVLTLLGSLVPVCVLCQPRANHEASASCQKAP
ParentalSLVSCFAG-GVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG
		SLVSCF.G.GVFLATC.LDLLPD.LAA..EALA.LHVTL.F.LQEFILAMGF.L.LV.EQITLAYK.QSG
RetrocopySLVSCFVG>GVFLATCVLDLLPDHLAATGEALAGLHVTLRFSLQEFILAMGFSLILVTEQITLAYKQQSG
ParentalPPPLEETRALLGTVNGGPQLWHDGPGVPQASGAPATPSALRACVLVFSLALHSVFEGLAVGLQRDRARAM
		PPPLEETRALLGTVNGG.Q.WHDGPG.PQASGAPATPSAL.ACVL.FSLALHSVFEGLAVGLQ.D...A.
RetrocopyPPPLEETRALLGTVNGGSQHWHDGPGIPQASGAPATPSALCACVLLFSLALHSVFEGLAVGLQ*DQTQAT
ParentalELCLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGM
		ELCLALLLHKGILAVSLS.RLLQSHL.AQVVAGCGILFSCMTPLG.GLGAAL.E.AGP.HQLAQSVLEGM
RetrocopyELCLALLLHKGILAVSLSFRLLQSHLGAQVVAGCGILFSCMTPLGVGLGAALGEWAGPPHQLAQSVLEGM
ParentalAAGTFLYITFLEILPQELASSEQRILKVILLLAGFALLTGLLFIQI
		AA.TFLYITFLEILPQELASSEQRILKVILLLA.FALLT.LLFIQI
RetrocopyAADTFLYITFLEILPQELASSEQRILKVILLLADFALLTNLLFIQI

							

							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	23 .14 RPM
SRP051959_heart	0 .00 RPM	17 .91 RPM
SRP051959_kidney	0 .00 RPM	23 .96 RPM
SRP051959_liver	0 .00 RPM	21 .53 RPM
SRP051959_lung	0 .00 RPM	21 .96 RPM
SRP051959_lymph_node	0 .00 RPM	12 .78 RPM
SRP051959_skeletal_muscle	0 .00 RPM	9 .35 RPM
SRP051959_spleen	0 .00 RPM	19 .62 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_1476 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1476 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cjac_1476 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010006	1 retrocopy	retro_cjac_1476 ,
Macropus eugenii	ENSMEUG00000006754	1 retrocopy	retro_meug_1551,
Microcebus murinus	ENSMICG00000010310	1 retrocopy	retro_mmur_162,
Myotis lucifugus	ENSMLUG00000013282	1 retrocopy	retro_mluc_2366,
Macaca mulatta	ENSMMUG00000005007	1 retrocopy	retro_mmul_28,
Mus musculus	ENSMUSG00000052310	1 retrocopy	retro_mmus_1899,
Oryctolagus cuniculus	ENSOCUG00000003045	1 retrocopy	retro_ocun_1792,

	RetrogeneDB ID:	retro_cjac_1476
Retrocopy location	Organism:	*Marmoset (Callithrix jacchus)*
	Coordinates:	16:67024811..67025783(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SLC39A1
	Ensembl ID:	ENSCJAG00000010006
	Aliases:	None
	Description:	solute carrier family 39 (zinc transporter), member 1 [Source:HGNC Symbol;Acc:12876]

Parental	MGPW-GEPELLVWRPEAVASEPPVLVGLEVKLGALVLLLVLTLLCSLVPICVLRRPGANHEASASRQKAL
	MG.W.GEPELLVW.PEAVA.EPPV.VGLEVKLG.LVLLLVLTLL.SLVP.CVL..P.ANHEASAS.QKA.
Retrocopy	MGLW<GEPELLVWHPEAVALEPPVPVGLEVKLGSLVLLLVLTLLGSLVPVCVLCQPRANHEASASCQKAP

Parental	SLVSCFAG-GVFLATCLLDLLPDYLAAIDEALAALHVTLQFPLQEFILAMGFFLVLVMEQITLAYKEQSG
	SLVSCF.G.GVFLATC.LDLLPD.LAA..EALA.LHVTL.F.LQEFILAMGF.L.LV.EQITLAYK.QSG
Retrocopy	SLVSCFVG>GVFLATCVLDLLPDHLAATGEALAGLHVTLRFSLQEFILAMGFSLILVTEQITLAYKQQSG

Parental	PPPLEETRALLGTVNGGPQLWHDGPGVPQASGAPATPSALRACVLVFSLALHSVFEGLAVGLQRDRARAM
	PPPLEETRALLGTVNGG.Q.WHDGPG.PQASGAPATPSAL.ACVL.FSLALHSVFEGLAVGLQ.D...A.
Retrocopy	PPPLEETRALLGTVNGGSQHWHDGPGIPQASGAPATPSALCACVLLFSLALHSVFEGLAVGLQ*DQTQAT

Parental	ELCLALLLHKGILAVSLSLRLLQSHLRAQVVAGCGILFSCMTPLGIGLGAALAESAGPLHQLAQSVLEGM
	ELCLALLLHKGILAVSLS.RLLQSHL.AQVVAGCGILFSCMTPLG.GLGAAL.E.AGP.HQLAQSVLEGM
Retrocopy	ELCLALLLHKGILAVSLSFRLLQSHLGAQVVAGCGILFSCMTPLGVGLGAALGEWAGPPHQLAQSVLEGM

Parental	AAGTFLYITFLEILPQELASSEQRILKVILLLAGFALLTGLLFIQI
	AA.TFLYITFLEILPQELASSEQRILKVILLLA.FALLT.LLFIQI
Retrocopy	AADTFLYITFLEILPQELASSEQRILKVILLLADFALLTNLLFIQI

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

RetrogeneDB ID:

retro_cjac_1476