RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_233
GCGGGTGTTTGAGGGAACGAGTTTAGTTCTTGGTCTGTTATTTTCAGAAATGGAAATTGGCCTATACCAGGAGAGTGAAT

CCCGGACGTGGCTGCATTGTCCATGGCCTTCTCTGTGAAGGAAAACCTTTCTTGGCCAGGACTTGCAGTAGGTGACCTAT

TTCATCGTCCTCGGGCTACCGTCATGGTGATGGTGAAGGGAGTGGACAAACTGGCTCTACTACCAGGCAGTGTCTTTTCA

TACCCTTTGGAGAATGCAGTTCCGTTTGGTCTTGGCAGTGTTGCAAATTCCATTCGCTCTTTATTTTCTGAGGAAACTCC

TGTTGTTTTGCAGTTGGCTCCTAGTGAGGAAAGAGTGTATTTGGTAGGGAAGGCAAACTCAGTGTTTGAAGACCTTTCAG

TCACCTTAGGACAGCTCCATAATTACTTGTTTCAGGAAAACTCCATTCTCAGTTCATTTCCCCTGAATTCTCTGAGTAGG

AACAATGGAGTTGACTTGCTCTTTCTTTCTGAACTCCAAGTGCTACATGATATTTCAAGCTTGGTGTCTTGTCATAAGCA

TCTAGCCAAGGATCATTCTCCTGATTTATATTCACTGGAGCTGGCAGGTTTGGATGAAATTGGGAAGCATTACAGGGAAG

ACTCTGAACAATTCAGAGTTGCTTCTAAAATCCTGTTGACGCTCTGCAAGAGTTTGCAGATAACATGTACAGTCTTTACA

GTGGGAATGCAGTGGTAGAGTTAGTCACTATTAAGTCATTTGACACCTCCCTTATGAGGAAGACAAGGACTATCTTTGAG

GCAAAATAAGTGAAGAACCCAGCAAGTCCCTATAACCTTGCGTATAATTTTGAATATTCAGTGATTTTCAACATGATACT

TTGGATAATGATTGCCTTGGCCCTGGCTGTGATTATCACTTCTTACAATATTTGGAACATGGATCCTGGATATAATAGCA

TCATTTATAGGATTACAAACCAGAAGATTCGAATAGAT

ORF - retro_ptro_233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	85.88 %
Parental protein coverage:	97.98 %
Number of stop codons detected:	3
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalSGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVK
.GV.GNEF....S..SV.FRNGNWPIPGE.IPDVAALSM.FSVKE.LSWPGLAVG.LFHRPRATVMVMVK
RetrocopyAGV*GNEF----SSWSVIFRNGNWPIPGE*IPDVAALSMAFSVKENLSWPGLAVGDLFHRPRATVMVMVK
ParentalGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTL
GV.KLAL.PGSV.SYPLENAVPF.L.SVANSI.SLFSEETPVVLQLAPSEERVY.VGKANSVFEDLSVTL
RetrocopyGVDKLALLPGSVFSYPLENAVPFGLGSVANSIRSLFSEETPVVLQLAPSEERVYLVGKANSVFEDLSVTL
ParentalRQLRNRLFQENSVLSSLPINSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDE
.QL.N.LFQENS.LSS.P.NSLSRNN.VDLLFLSELQVLHDISSL.S.HKHLAKDHSPDLYSLELAGLDE
RetrocopyGQLHNYLFQENSILSSFPLNSLSRNNGVDLLFLSELQVLHDISSLVSCHKHLAKDHSPDLYSLELAGLDE
ParentalIGKRYGEDSEQFRDASKIL-VDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRTILEAKQAKNPA
IGK.Y.EDSEQFR.ASKIL.VDALQ.FAD.MYSLY.GNAVVELVT.KSFDTSL.RKTRTI.EAK..KNPA
RetrocopyIGKHYREDSEQFRVASKIL<VDALQEFADNMYSLYSGNAVVELVTIKSFDTSLMRKTRTIFEAK*VKNPA
ParentalSPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD
SPYNLA..YNFEYSV.FNM.LWIMIALALAVIITSYNIWNMDPGY.SIIYR.TNQKIR.D
RetrocopySPYNLA--YNFEYSVIFNMILWIMIALALAVIITSYNIWNMDPGYNSIIYRITNQKIRID

                            

                            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
SRP007412_brain_prefrontal_cortex	0 .00 RPM	86 .21 RPM
SRP007412_cerebellum	0 .00 RPM	70 .37 RPM
SRP007412_heart	0 .09 RPM	18 .77 RPM
SRP007412_kidney	0 .08 RPM	153 .69 RPM
SRP007412_liver	0 .00 RPM	36 .79 RPM
SRP007412_testis	0 .11 RPM	22 .13 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_233 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_233 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_233 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_280
Gorilla gorilla	retro_ggor_323
Pongo abelii	retro_pabe_389
Macaca mulatta	retro_mmul_561

Parental genes homology:

Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006109	1 retrocopy	retro_dnov_2102,
Homo sapiens	ENSG00000182220	1 retrocopy	retro_hsap_280,
Gorilla gorilla	ENSGGOG00000000532	1 retrocopy	retro_ggor_323,
Myotis lucifugus	ENSMLUG00000001159	1 retrocopy	retro_mluc_1613,
Macaca mulatta	ENSMMUG00000012762	1 retrocopy	retro_mmul_561,
Nomascus leucogenys	ENSNLEG00000001441	1 retrocopy	retro_nleu_1491,
Pongo abelii	ENSPPYG00000020251	1 retrocopy	retro_pabe_389,
Pan troglodytes	ENSPTRG00000021803	1 retrocopy	retro_ptro_233 ,

	RetrogeneDB ID:	retro_ptro_233
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	1:175919466..175920464(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ATP6AP2
	Ensembl ID:	ENSPTRG00000021803
	Aliases:	None
	Description:	ATPase, H+ transporting, lysosomal accessory protein 2 [Source:HGNC Symbol;Acc:18305]

Parental	SGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFHRPRATVMVMVK
	.GV.GNEF....S..SV.FRNGNWPIPGE.IPDVAALSM.FSVKE.LSWPGLAVG.LFHRPRATVMVMVK
Retrocopy	AGVGNEF----SSWSVIFRNGNWPIPGEIPDVAALSMAFSVKENLSWPGLAVGDLFHRPRATVMVMVK

Parental	GVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKANSVFEDLSVTL
	GV.KLAL.PGSV.SYPLENAVPF.L.SVANSI.SLFSEETPVVLQLAPSEERVY.VGKANSVFEDLSVTL
Retrocopy	GVDKLALLPGSVFSYPLENAVPFGLGSVANSIRSLFSEETPVVLQLAPSEERVYLVGKANSVFEDLSVTL

Parental	RQLRNRLFQENSVLSSLPINSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPDLYSLELAGLDE
	.QL.N.LFQENS.LSS.P.NSLSRNN.VDLLFLSELQVLHDISSL.S.HKHLAKDHSPDLYSLELAGLDE
Retrocopy	GQLHNYLFQENSILSSFPLNSLSRNNGVDLLFLSELQVLHDISSLVSCHKHLAKDHSPDLYSLELAGLDE

Parental	IGKRYGEDSEQFRDASKIL-VDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRTILEAKQAKNPA
	IGK.Y.EDSEQFR.ASKIL.VDALQ.FAD.MYSLY.GNAVVELVT.KSFDTSL.RKTRTI.EAK..KNPA
Retrocopy	IGKHYREDSEQFRVASKIL<VDALQEFADNMYSLYSGNAVVELVTIKSFDTSLMRKTRTIFEAK*VKNPA

Parental	SPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRMD
	SPYNLA..YNFEYSV.FNM.LWIMIALALAVIITSYNIWNMDPGY.SIIYR.TNQKIR.D
Retrocopy	SPYNLA--YNFEYSVIFNMILWIMIALALAVIITSYNIWNMDPGYNSIIYRITNQKIRID

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

RetrogeneDB ID:

retro_ptro_233