RetrogeneDB - Retrocopy retro_cfam

						
>retro_cfam_147
ATGGAGGAGCCGCCGAAGGAGGGCGAGGCCGAGGTCGCCGAGCAGTGGTTCTCCAAGTGGGAGCGCCAGTGCCTGGCCGA

GGCCGAGCAGCAAGAGCAGCTGGCCCCCGAGCTGCGGGAGGAGGCGAGCGCCGAGGCGGCGGGGCTCCGGAGCGAGCAGC

AGAAGCTGTGGCACCTCTTCCAGATCTCGGCCACCGCCGTGGCCCAGCTCTACAAGGATGCTGGGTGCCAACAGCCAGAA

CTGTCCATGTGGGACCCCTTCCAGAACGCGGCCATGGCCGTGACCAGTCTGTACAAAGAGAGCGGGGACGCCCACCAACG

AAGTTTTGACCTGGGCGTCCAGGTGGGCTACCAGCGGCGCATCCGGGATGTCCTGGAGTGGGCGAAGCAGGGCCGCAGCA

CCATTCTCCGCGAAGACCTGATCAGCTTCCTGTGTGGCAAAGTGCCCCCCGCGCCTCCCCCGCCGCGCGCCCCGCGGACG

CCCCCGAAGCCGCCCGCCGCGGCCGCCGGCCAGGCCGCGGCCCCCGAGCCCGGCTCGGCCGTGGACGTCGACCTGCAGCC

GTTCCACGAGGCCATCGCCGTGCATGGCCTGAGCGGAGCCATGGCGAGCATCAGCGTGAGGTCCGGCGCCCCCGGCTCCC

CGCCCCAGGCCAGCGGCGTCGCGGGCGCGGTGCCCGGCGGCGGGCGCCGGAATAGTAGCTTCCTCGACGACGACTCGAGC

CCCTTCACCTCCGAAGAGCAGGCCCCGCGCCCGGACAGCGGGGGCACCCGCAAGCGCACCTCGGCCCGGTGCGGTGACAG

TGTCACAGACTCCCCGACCGCCAAGCGCAACCGGATGCTCTGA

ORF - retro_cfam_147 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.54 %
Parental protein coverage:	80.97 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalDRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLIS
		D..CQQP.LS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.GYQRR..DVL.W.K..R.TI.REDLIS
RetrocopyDAGCQQPELSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGYQRRIRDVLEWAKQGRSTILREDLIS
ParentalFLCGKVPP----PRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPG
		FLCGKVPP....PR..R.PP.........A...E..S.V..DLQPF.EAIA.HGLSGAMASISVRS..PG
RetrocopyFLCGKVPPAPPPPRAPRTPPKPPAAAAGQAAAPEPGSAVDVDLQPFHEAIAVHGLSGAMASISVRSGAPG
ParentalSPTHVSSGSNA----SRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
		SP...S....A.....RR.....D.D...F.SEE.A...D.GGTRKRTSA.CGD..TDSPT.KRNRM.
RetrocopySPPQASGVAGAVPGGGRRNSSFLDDDSSPFTSEEQAPRPDSGGTRKRTSARCGDSVTDSPTAKRNRML

							

							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
SRP012049_cerebellum	2 .44 RPM	27 .68 RPM
SRP017611_brain	2 .46 RPM	26 .68 RPM
SRP017611_kidney	0 .40 RPM	16 .11 RPM
SRP017611_liver	0 .15 RPM	10 .01 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_147 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_147 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_cfam_147 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4765
Pan troglodytes	retro_ptro_3172
Gorilla gorilla	retro_ggor_2968
Pongo abelii	retro_pabe_163
Mus musculus	retro_mmus_3460
Rattus norvegicus	retro_rnor_156
Sus scrofa	retro_sscr_1177
Equus caballus	retro_ecab_1091

Parental genes homology:

Parental genes homology involve 17 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010719	2 retrocopies	retro_amel_1715, retro_amel_88,
Canis familiaris	ENSCAFG00000018981	1 retrocopy	retro_cfam_147 ,
Cavia porcellus	ENSCPOG00000010925	1 retrocopy	retro_cpor_101,
Dasypus novemcinctus	ENSDNOG00000015893	3 retrocopies	retro_dnov_1575, retro_dnov_2266, retro_dnov_827,
Equus caballus	ENSECAG00000009430	1 retrocopy	retro_ecab_1091,
Homo sapiens	ENSG00000182831	1 retrocopy	retro_hsap_4765,
Gorilla gorilla	ENSGGOG00000010744	1 retrocopy	retro_ggor_2968,
Monodelphis domestica	ENSMODG00000005378	2 retrocopies	retro_mdom_1716, retro_mdom_299,
Mustela putorius furo	ENSMPUG00000014707	1 retrocopy	retro_mputfur_44,
Mus musculus	ENSMUSG00000022507	1 retrocopy	retro_mmus_3460,
Nomascus leucogenys	ENSNLEG00000010106	1 retrocopy	retro_nleu_2348,
Otolemur garnettii	ENSOGAG00000003909	1 retrocopy	retro_ogar_74,
Pongo abelii	ENSPPYG00000007088	1 retrocopy	retro_pabe_163,
Pan troglodytes	ENSPTRG00000007751	1 retrocopy	retro_ptro_3172,
Rattus norvegicus	ENSRNOG00000002545	2 retrocopies	retro_rnor_156, retro_rnor_1928,
Sus scrofa	ENSSSCG00000028454	1 retrocopy	retro_sscr_1177,
Ictidomys tridecemlineatus	ENSSTOG00000009324	1 retrocopy	retro_itri_137,

	RetrogeneDB ID:	retro_cfam_147
Retrocopy location	Organism:	*Dog (Canis familiaris)*
	Coordinates:	X:110022561..110023404(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSCAFG00000019025
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	C16orf72
	Ensembl ID:	ENSCAFG00000018981
	Aliases:	None
	Description:	chromosome 16 open reading frame 72 [Source:HGNC Symbol;Acc:30103]

Parental	DRVCQQPGLSLWVPFQNAATAVTNLYKESVDTHQRSFDIGIQIGYQRRNKDVLAWVKKRRRTIRREDLIS
	D..CQQP.LS.W.PFQNAA.AVT.LYKES.D.HQRSFD.G.Q.GYQRR..DVL.W.K..R.TI.REDLIS
Retrocopy	DAGCQQPELSMWDPFQNAAMAVTSLYKESGDAHQRSFDLGVQVGYQRRIRDVLEWAKQGRSTILREDLIS

Parental	FLCGKVPP----PRNSRAPPRLTVVSPNRATSTETSSSVETDLQPFREAIALHGLSGAMASISVRSSTPG
	FLCGKVPP....PR..R.PP.........A...E..S.V..DLQPF.EAIA.HGLSGAMASISVRS..PG
Retrocopy	FLCGKVPPAPPPPRAPRTPPKPPAAAAGQAAAPEPGSAVDVDLQPFHEAIAVHGLSGAMASISVRSGAPG

Parental	SPTHVSSGSNA----SRRRNGLHDVDLNTFISEEMALHLDNGGTRKRTSAQCGDVITDSPTHKRNRMI
	SP...S....A.....RR.....D.D...F.SEE.A...D.GGTRKRTSA.CGD..TDSPT.KRNRM.
Retrocopy	SPPQASGVAGAVPGGGRRNSSFLDDDSSPFTSEEQAPRPDSGGTRKRTSARCGDSVTDSPTAKRNRML

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

RetrogeneDB ID:

retro_cfam_147