RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_2603
CTAGCAGACAAATTAATGAGAATTGCTATTGTCAATCATGACAAATGTAAACCTAAGAAATGTCAACAGGAATGCAGAAA

GAGTTGTCCTGTAGTTCAAATGGGAGAATTATGCATAGAAGTTACACTCCAGAACAAAATAGCATGGATTTCTGAAACTC

TTTGTATTGGTTGTGGTATCTGTATTAAGAAATGCCCCTTTGGCGCCTTATCAATTGACAATTTACCAAGCAACTTGGAA

AAAGAAACCACACATTGATATTGTGCCAATGTCATCTAAATTCACAGTTGCCTATCCCTCGTCCAGGTAAAGTTTTGGGA

TTAGTTGGAACTAATGGTATTGGAAAGTCAACTGCTTTAAAAATTTTTAGCAGGAAAACAAAAGCCAAACCTTGGAAAGT

ACGATGATCCTCCTGACTGGCAAGACATTTTGACTTATTTCCGTGAATCTGAATTACAGAATTACTTTACCAAGATTCTA

GAAGAGAACCTAAAAGCCATCATCAAATCTCAATATGTAGACCAGATTCCTAAGCCTGCAAAGGGGACAGTGGGATCTAT

TTTGGACTGAAAAGATGAAACAAAGACACAGGCAATTGTATGTCAGCAGCTTGAATTAACCCACCTAACAGAACGAAATG

TTGAAGATCTTTCAGGAGGAGAGTTGCAGAGATTTGCCTGTGCTGTCATTTGCATACAGAAAGCTGATATTTTCATGTTT

GGTGAGACTTCTAGTTACCTAGATGTCAAACAGCATTTAAAGCCTGCTATTACTATACAATCTCTGATAAATCCAGACAG

ATATATCATTGTAGTGGAATATGATCTAGGTGTATTAGACTATCTCTCTGATTTCAACTGCTGTTTATATGGTGTACCAA

GCACCTATGGAGTTGTCACTGTGCCTTTTAGTGTAAGAAAGGGCATAAACATTTTTTTGGATGGCTATGTTCCAACAGAA

AACTTGAGATTCCAAGATGCATCACTTGTTTTTAAAGTGGCTGAGACAGCAAATGAAGAAGAAGTCAAAATGATGTGTAT

GTATAAATATTCAGGAATGAATTAAAAATGGGAGAGTTTGAGCTAGCAATTGTAGCTGGAGAGTTTACAGATTCTGAAAT

CATGGTGATGATGCTAGGGGAAAATGGAATGGGTAAAACGACATTTATCAGAATGCTTGCTGGAAGACTTAAACCTGATG

AAGAAGAAGTACCAGTTCTAAATGTCAGTTATAAGTTACAGAAAATTAGTCCCAAATTAACTGGAAGTGTTCGCCAGTTA

CTACATGAAAAAATAAGAGATGCTTATACACATCCACAATTTGTGACTAATGTAATGAAGCCTCTGCAAATTGAAAACAT

CATCGATCAAGAGGTGCAGACATTATCGGGTGGTGAACTACAGCGAGTAGCTTTAGCCCTTTGTTTGGGCAAACCTGCTG

ATGTCTATTTAATTGATGAACCATCTGCATATTTGGATTCTGAGCAAAGACTGATGGCAGCTCGAGTTGTCAAACGTTTC

ATACTTCATGCAAAAAAGACAGCCTTTGTTGTGGAACATGACTTCATCATGGCCACCTATCTAGCGGATCATGTCATCAT

TTTTTATGGTCTTCCATCTACTAAGAACACAGTTGCAAACAGTCCTCAAACCCTTTTGGCTGGCATGAATACATTTTAGT

CTCAGCTTGAAACTACATTCAGAAGAGATCCAAACCACTATAGACCACGAATAAATAAATTTAATTTAATTAAGGATGTA

GAACAAAAGAAGAGTGGAAACTACTTTTTCTTG

ORF - retro_ptro_2603 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	89.53 %
Parental protein coverage:	99.67 %
Number of stop codons detected:	4
Number of frameshifts detected:	3

Retrocopy - Parental Gene Alignment:

                                ParentalMADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGAL
.ADKL.RIAIVNHDKCKPKKC.QEC.KSCPVV.MG.LCIEVT.Q.KIAWISETLCIGCGICIKKCPFGAL
RetrocopyLADKLMRIAIVNHDKCKPKKCQQECRKSCPVVQMGELCIEVTLQNKIAWISETLCIGCGICIKKCPFGAL
ParentalSIVNLPSNLEKETTHRYCANAFKLH-RLPIPRPGEVLGLVGTNGIGKSTALKI-LAGKQKPNLGKYDDPP
SI.NLPSNLEKETTH.YCAN....H..LPIPRPG.VLGLVGTNGIGKSTALKI.LAGKQKPNLGKYDDPP
RetrocopySIDNLPSNLEKETTH*YCANVI*IH<QLPIPRPGKVLGLVGTNGIGKSTALKI>LAGKQKPNLGKYDDPP
ParentalDWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTH
DWQ.ILTYFR.SELQNYFTKILE..LKAIIK.QYVDQIPK.AKGTVGSILD.KDETKTQAIVCQQL.LTH
RetrocopyDWQDILTYFRESELQNYFTKILEENLKAIIKSQYVDQIPKPAKGTVGSILD*KDETKTQAIVCQQLELTH
ParentalLKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSV
L.ERNVEDLSGGELQRFACAV.CIQKADIFMF.E.SSYLDVKQ.LK.AITI.SLINPDRYIIVVE.DL.V
RetrocopyLTERNVEDLSGGELQRFACAVICIQKADIFMFGETSSYLDVKQHLKPAITIQSLINPDRYIIVVEYDLGV
ParentalLDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMY
LDYLSDF.CCLYGVPS.YGVVT.PFSVR.GINIFLDGYVPTENLRF.DASLVFKVAETANEEEVK.MCMY
RetrocopyLDYLSDFNCCLYGVPSTYGVVTVPFSVRKGINIFLDGYVPTENLRFQDASLVFKVAETANEEEVKMMCMY
ParentalKYPGM-KKKMGEFELAIVAGEFTDSEIMV-MLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKI
KY.GM...KMGEFELAIVAGEFTDSEIMV.MLGENG.GKTTFIRMLAGRLKPDE..EVPVLNVSYK.QKI
RetrocopyKYSGM<ELKMGEFELAIVAGEFTDSEIMVMMLGENGMGKTTFIRMLAGRLKPDE-EEVPVLNVSYKLQKI
ParentalSPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
SPK.TGSVRQLLHEKIRDAYTHPQFVT.VMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
RetrocopySPKLTGSVRQLLHEKIRDAYTHPQFVTNVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
ParentalEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGVPS-KNTVANSPQTLLAGM
EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLAD.VI.F.G.PS.KNTVANSPQTLLAGM
RetrocopyEPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADHVIIFYGLPSTKNTVANSPQTLLAGM
ParentalNKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFL
N.F.SQLE.TFRRDPN.YRPRINK.N.IKDVEQKKSGNYFFL
RetrocopyNTF*SQLETTFRRDPNHYRPRINKFNLIKDVEQKKSGNYFFL

                            

                            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 .02 RPM	21 .31 RPM
SRP007412_cerebellum	0 .00 RPM	27 .82 RPM
SRP007412_heart	0 .00 RPM	24 .57 RPM
SRP007412_kidney	0 .00 RPM	22 .46 RPM
SRP007412_liver	0 .00 RPM	19 .12 RPM
SRP007412_testis	0 .00 RPM	39 .10 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_2603 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2603 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2603 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3826
Pongo abelii	retro_pabe_3067

Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004534	1 retrocopy	retro_chof_1280,
Cavia porcellus	ENSCPOG00000007367	1 retrocopy	retro_cpor_289,
Homo sapiens	ENSG00000164163	1 retrocopy	retro_hsap_3826,
Macaca mulatta	ENSMMUG00000004433	1 retrocopy	retro_mmul_1628,
Mus musculus	ENSMUSG00000058355	1 retrocopy	retro_mmus_1503,
Nomascus leucogenys	ENSNLEG00000005460	1 retrocopy	retro_nleu_2125,
Oryctolagus cuniculus	ENSOCUG00000001821	2 retrocopies	retro_ocun_1925, retro_ocun_668,
Procavia capensis	ENSPCAG00000006183	1 retrocopy	retro_pcap_90,
Pongo abelii	ENSPPYG00000015097	1 retrocopy	retro_pabe_3067,
Pan troglodytes	ENSPTRG00000016481	1 retrocopy	retro_ptro_2603 ,

	RetrogeneDB ID:	retro_ptro_2603
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	7:22181985..22183778(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	ABCE1
	Ensembl ID:	ENSPTRG00000016481
	Aliases:	None
	Description:	Pan troglodytes ATP-binding cassette, sub-family E (OABP), member 1 (ABCE1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246609]

Parental	MADKLTRIAIVNHDKCKPKKCRQECKKSCPVVRMGKLCIEVTPQSKIAWISETLCIGCGICIKKCPFGAL
	.ADKL.RIAIVNHDKCKPKKC.QEC.KSCPVV.MG.LCIEVT.Q.KIAWISETLCIGCGICIKKCPFGAL
Retrocopy	LADKLMRIAIVNHDKCKPKKCQQECRKSCPVVQMGELCIEVTLQNKIAWISETLCIGCGICIKKCPFGAL

Parental	SIVNLPSNLEKETTHRYCANAFKLH-RLPIPRPGEVLGLVGTNGIGKSTALKI-LAGKQKPNLGKYDDPP
	SI.NLPSNLEKETTH.YCAN....H..LPIPRPG.VLGLVGTNGIGKSTALKI.LAGKQKPNLGKYDDPP
Retrocopy	SIDNLPSNLEKETTHYCANVIIH<QLPIPRPGKVLGLVGTNGIGKSTALKI>LAGKQKPNLGKYDDPP

Parental	DWQEILTYFRGSELQNYFTKILEDDLKAIIKPQYVDQIPKAAKGTVGSILDRKDETKTQAIVCQQLDLTH
	DWQ.ILTYFR.SELQNYFTKILE..LKAIIK.QYVDQIPK.AKGTVGSILD.KDETKTQAIVCQQL.LTH
Retrocopy	DWQDILTYFRESELQNYFTKILEENLKAIIKSQYVDQIPKPAKGTVGSILD*KDETKTQAIVCQQLELTH

Parental	LKERNVEDLSGGELQRFACAVVCIQKADIFMFDEPSSYLDVKQRLKAAITIRSLINPDRYIIVVEHDLSV
	L.ERNVEDLSGGELQRFACAV.CIQKADIFMF.E.SSYLDVKQ.LK.AITI.SLINPDRYIIVVE.DL.V
Retrocopy	LTERNVEDLSGGELQRFACAVICIQKADIFMFGETSSYLDVKQHLKPAITIQSLINPDRYIIVVEYDLGV

Parental	LDYLSDFICCLYGVPSAYGVVTMPFSVREGINIFLDGYVPTENLRFRDASLVFKVAETANEEEVKKMCMY
	LDYLSDF.CCLYGVPS.YGVVT.PFSVR.GINIFLDGYVPTENLRF.DASLVFKVAETANEEEVK.MCMY
Retrocopy	LDYLSDFNCCLYGVPSTYGVVTVPFSVRKGINIFLDGYVPTENLRFQDASLVFKVAETANEEEVKMMCMY

Parental	KYPGM-KKKMGEFELAIVAGEFTDSEIMV-MLGENGTGKTTFIRMLAGRLKPDEGGEVPVLNVSYKPQKI
	KY.GM...KMGEFELAIVAGEFTDSEIMV.MLGENG.GKTTFIRMLAGRLKPDE..EVPVLNVSYK.QKI
Retrocopy	KYSGM<ELKMGEFELAIVAGEFTDSEIMVMMLGENGMGKTTFIRMLAGRLKPDE-EEVPVLNVSYKLQKI

Parental	SPKSTGSVRQLLHEKIRDAYTHPQFVTDVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
	SPK.TGSVRQLLHEKIRDAYTHPQFVT.VMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID
Retrocopy	SPKLTGSVRQLLHEKIRDAYTHPQFVTNVMKPLQIENIIDQEVQTLSGGELQRVALALCLGKPADVYLID

Parental	EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADRVIVFDGVPS-KNTVANSPQTLLAGM
	EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLAD.VI.F.G.PS.KNTVANSPQTLLAGM
Retrocopy	EPSAYLDSEQRLMAARVVKRFILHAKKTAFVVEHDFIMATYLADHVIIFYGLPSTKNTVANSPQTLLAGM

Parental	NKFLSQLEITFRRDPNNYRPRINKLNSIKDVEQKKSGNYFFL
	N.F.SQLE.TFRRDPN.YRPRINK.N.IKDVEQKKSGNYFFL
Retrocopy	NTF*SQLETTFRRDPNHYRPRINKFNLIKDVEQKKSGNYFFL

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

RetrogeneDB ID:

retro_ptro_2603