RetrogeneDB - Retrocopy retro_ptro

                        
>retro_ptro_3208
ATGGACATGGGCAAACTTCTGAGCTACCAGCCCAACAGGGGCATAAAACGTCCCCGAGATGGCAAAGAGGAGGAGCAGAA

GATGCATCGGAAACAAACTAGTACTCAAGATTGGGAAGAGGAAATGATTGTGGTGGAAGAAGCAAAGGATGACAAAAATT

TGCTGCTTCAGATTATTGACACAGAGGGTGAGGAGGAAGAGAAAGAGGAGGAGCCATTGGATGAAAGCTCAGTGAAGAAA

ATGATCCTTGCATTTGAATAGTGAGCATATAAAAACCAAGAATTGCAGATTAAGTTTCCAGACAATCCAGAGAAGTTCAT

GGAATCCCAACTGGACCTACATGACATCATTCAGAAGATGCACTTGGTGGCCACCATGCCAGACCTGTACCTTTTGCTGG

AGCTGAATGCTGTGCAGTCACTTCTTGGTTTGCTTGGACACAATAATACAGACGTGTCCATAGCTGGGGTTGATTTGAGT

CAGGAATTAACAGATATAGACATCTTCTATGAGAGCAGAGAGGGAGCAGAAGTACTCATTGATGCTCTGGTGGATGGGCA

GGTGATAGCGCTGCTGGTGCAGAACGTGGAGCGCCTGGATGAGTCTGTGAAGGAGCAGGTCAATGGTGCCCATAACACTC

TTGTTATTGTGGAAAACATGGCTGAGTTCTAGCTGGAGATGTGTACAAAAGATGCCCAGCAGGGTCTTCCTCAGTGGCTG

TTGAAGAGGCTGAAGGCAAAGAAGCCTTTTGATGCCAACAAACTGTATTGCAGTGAAATGCAGGCCATATTGCTCCAGGA

CAATGATGAAAACAGGAAATTGCTTGGGGAGCTGGATAGAATTGATGCACTTCTTCACAGTTATCTGTGTTTAAAAGACA

CAATCCCAGCACAGCAAAGGAGCAGGAGATGATGGAGAATCTGTTTGATTCACTCTGCTTCTAACTAATGCTCACTTCCA

ATCGTGAGCACTTCCTGAAGGGCGAGGGTCTTCAGGTGATGAATCTCATGCTCAGGGAAAAGAAGATCTCACGGAGCAGG

GTCCTGAAAGTGCTGATTGCACCCGAGGGCATCTACAACTGCGGTAAATTTGTTGACATTCTTGGCTTATGAACCATCTT

TCCCCTCTTTATGGAATTTCCCAGGAAGATCAAGAAAGTGGGTACCACTGACAAGGAACACAAACAGCATGTCTGTTCCA

TTCTGGCTTCCCTTTTGTGGAACCTGAGAGGGCATCAGTGAACCCGGCTTCTGAATAAATTCACTGAAAATGACAGTGAG

TAGGCTGACAGACTAATGGAGTTGCATTTTCAATATCTGGGTGCAATGCAGGTGGCAGACAAGAGGAATGAAGGGGAAAA

ACATGACATGGTCCAGCGTGGAGAGATCATAGACAGTGACATGGGGGATGAGTTCTACCTCCAGTGCTTGGATGCAGAGC

TGTTTGTTCTCCAGTGCATCTGCTGCATTATGTCCAAGATCTGCAATGCCAATGTCCCCCAGATTTGCCAGAGGGTTCAC

CAGATCCTAAACATGTGAGGACGCTCCATCAAAATTGTCAGGCATATTATCAAGGGGTATGCGGAG

ORF - retro_ptro_3208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	80.33 %
Parental protein coverage:	95.56 %
Number of stop codons detected:	8
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalMDVGELLSYQPNRGTKRPRDDEEEEQKMRRKQTGTRERGRYREEEMTVVEEADDDKKRLLQIIDRDGEEE
MD.G.LLSYQPNRG.KRPRD..EEEQKM.RKQT.T.......EE.M.VVEEA.DDK..LLQIID..GEEE
RetrocopyMDMGKLLSYQPNRGIKRPRDGKEEEQKMHRKQTSTQD---WEEE-MIVVEEAKDDKNLLLQIIDTEGEEE
ParentalEEEEEPLDESSVKKMILTFEKRSYKNQELRIKFPDNPEKFMESELDLNDIIQEMHVVATMPDLYHLLVEL
E.EEEPLDESSVKKMIL.FE...YKNQEL.IKFPDNPEKFMES.LDL.DIIQ.MH.VATMPDLY.LL.EL
RetrocopyEKEEEPLDESSVKKMILAFE**AYKNQELQIKFPDNPEKFMESQLDLHDIIQKMHLVATMPDLY-LLLEL
ParentalNAVQSLLGLLGHDNTDVSIAVVDLLQELTDIDTLHESEEGAEVLIDALVDGQVVALLVQNLERLDESVKE
NAVQSLLGLLGH.NTDVSIA.VDL.QELTDID...ES.EGAEVLIDALVDGQV.ALLVQN.ERLDESVKE
RetrocopyNAVQSLLGLLGHNNTDVSIAGVDLSQELTDIDIFYESREGAEVLIDALVDGQVIALLVQNVERLDESVKE
ParentalEADGVHNTLAIVENMAEFRPEMCTEGAQQGLLQWLLKRLKAKMPFDANKLYCSEVLAILLQDNDENRELL
...G.HNTL.IVENMAEF..EMCT..AQQGL.QWLLKRLKAK.PFDANKLYCSE..AILLQDNDENR.LL
RetrocopyQVNGAHNTLVIVENMAEF*LEMCTKDAQQGLPQWLLKRLKAKKPFDANKLYCSEMQAILLQDNDENRKLL
ParentalGELDGIDVLL-QQLSVFKRHNPSTAEEQEMMENLFDSLCSCLMLSSNRERFLKGEGLQLMNLMLREKKIS
GELD.ID.LL..QLSVFKRHNPSTA.EQEMMENLFDSLC..LML.SNRE.FLKGEGLQ.MNLMLREKKIS
RetrocopyGELDRIDALL<SQLSVFKRHNPSTAKEQEMMENLFDSLCF*LMLTSNREHFLKGEGLQVMNLMLREKKIS
ParentalRSSALKVLDHAMIGPEGTDNCHKFVDILGLRTIFPLFMKSPRKIKKVGTTEKEHEEHVCSILASLLRNLR
RS..LKVL....I.PEG..NC.KFVDILGL.TIFPLFM..PRKIKKVGTT.KEH..HVCSILASLL.NLR
RetrocopyRSRVLKVL----IAPEGIYNCGKFVDILGL*TIFPLFMEFPRKIKKVGTTDKEHKQHVCSILASLLWNLR
ParentalGQQRTRLLNKFTENDSEKVDRLMELHFKYLGAMQVADKKIEGEKHDMVRRGEIIDNDTEEEFYLRRLDAG
G.Q.TRLLNKFTENDSE..DRLMELHF.YLGAMQVADK..EGEKHDMV.RGEIID.D...EFYL..LDA.
RetrocopyGHQ*TRLLNKFTENDSE*ADRLMELHFQYLGAMQVADKRNEGEKHDMVQRGEIIDSDMGDEFYLQCLDAE
ParentalLFVLQHICYIMAEICNANVPQIRQRVHQILNMRGSSIKIVRHIIKEYAE
LFVLQ.IC.IM..ICNANVPQI.QRVHQILNM.G.SIKIVRHIIK.YAE
RetrocopyLFVLQCICCIMSKICNANVPQICQRVHQILNM*GRSIKIVRHIIKGYAE

                            

                            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	28 .74 RPM
SRP007412_cerebellum	0 .00 RPM	36 .78 RPM
SRP007412_heart	0 .00 RPM	27 .37 RPM
SRP007412_kidney	0 .00 RPM	26 .18 RPM
SRP007412_liver	0 .00 RPM	30 .54 RPM
SRP007412_testis	0 .00 RPM	59 .23 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_3208 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3208 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_3208 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4819
Gorilla gorilla	retro_ggor_3003
Pongo abelii	retro_pabe_3747
Macaca mulatta	retro_mmul_2571

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132792	1 retrocopy	retro_hsap_4819,
Gorilla gorilla	ENSGGOG00000000614	1 retrocopy	retro_ggor_3003,
Macropus eugenii	ENSMEUG00000013001	1 retrocopy	retro_meug_910,
Myotis lucifugus	ENSMLUG00000015803	1 retrocopy	retro_mluc_177,
Macaca mulatta	ENSMMUG00000017224	1 retrocopy	retro_mmul_2571,
Nomascus leucogenys	ENSNLEG00000006291	1 retrocopy	retro_nleu_2194,
Pongo abelii	ENSPPYG00000010989	1 retrocopy	retro_pabe_3747,
Pan troglodytes	ENSPTRG00000023688	1 retrocopy	retro_ptro_3208 ,

	RetrogeneDB ID:	retro_ptro_3208
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	X:46914741..46916327(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	CTNNBL1
	Ensembl ID:	ENSPTRG00000023688
	Aliases:	CTNNBL1, PDGFRA
	Description:	Pan troglodytes catenin, beta like 1 (CTNNBL1), mRNA. [Source:RefSeq mRNA;Acc:NM_001246652]

Parental	MDVGELLSYQPNRGTKRPRDDEEEEQKMRRKQTGTRERGRYREEEMTVVEEADDDKKRLLQIIDRDGEEE
	MD.G.LLSYQPNRG.KRPRD..EEEQKM.RKQT.T.......EE.M.VVEEA.DDK..LLQIID..GEEE
Retrocopy	MDMGKLLSYQPNRGIKRPRDGKEEEQKMHRKQTSTQD---WEEE-MIVVEEAKDDKNLLLQIIDTEGEEE

Parental	EEEEEPLDESSVKKMILTFEKRSYKNQELRIKFPDNPEKFMESELDLNDIIQEMHVVATMPDLYHLLVEL
	E.EEEPLDESSVKKMIL.FE...YKNQEL.IKFPDNPEKFMES.LDL.DIIQ.MH.VATMPDLY.LL.EL
Retrocopy	EKEEEPLDESSVKKMILAFE**AYKNQELQIKFPDNPEKFMESQLDLHDIIQKMHLVATMPDLY-LLLEL

Parental	NAVQSLLGLLGHDNTDVSIAVVDLLQELTDIDTLHESEEGAEVLIDALVDGQVVALLVQNLERLDESVKE
	NAVQSLLGLLGH.NTDVSIA.VDL.QELTDID...ES.EGAEVLIDALVDGQV.ALLVQN.ERLDESVKE
Retrocopy	NAVQSLLGLLGHNNTDVSIAGVDLSQELTDIDIFYESREGAEVLIDALVDGQVIALLVQNVERLDESVKE

Parental	EADGVHNTLAIVENMAEFRPEMCTEGAQQGLLQWLLKRLKAKMPFDANKLYCSEVLAILLQDNDENRELL
	...G.HNTL.IVENMAEF..EMCT..AQQGL.QWLLKRLKAK.PFDANKLYCSE..AILLQDNDENR.LL
Retrocopy	QVNGAHNTLVIVENMAEF*LEMCTKDAQQGLPQWLLKRLKAKKPFDANKLYCSEMQAILLQDNDENRKLL

Parental	GELDGIDVLL-QQLSVFKRHNPSTAEEQEMMENLFDSLCSCLMLSSNRERFLKGEGLQLMNLMLREKKIS
	GELD.ID.LL..QLSVFKRHNPSTA.EQEMMENLFDSLC..LML.SNRE.FLKGEGLQ.MNLMLREKKIS
Retrocopy	GELDRIDALL<SQLSVFKRHNPSTAKEQEMMENLFDSLCF*LMLTSNREHFLKGEGLQVMNLMLREKKIS

Parental	RSSALKVLDHAMIGPEGTDNCHKFVDILGLRTIFPLFMKSPRKIKKVGTTEKEHEEHVCSILASLLRNLR
	RS..LKVL....I.PEG..NC.KFVDILGL.TIFPLFM..PRKIKKVGTT.KEH..HVCSILASLL.NLR
Retrocopy	RSRVLKVL----IAPEGIYNCGKFVDILGL*TIFPLFMEFPRKIKKVGTTDKEHKQHVCSILASLLWNLR

Parental	GQQRTRLLNKFTENDSEKVDRLMELHFKYLGAMQVADKKIEGEKHDMVRRGEIIDNDTEEEFYLRRLDAG
	G.Q.TRLLNKFTENDSE..DRLMELHF.YLGAMQVADK..EGEKHDMV.RGEIID.D...EFYL..LDA.
Retrocopy	GHQTRLLNKFTENDSEADRLMELHFQYLGAMQVADKRNEGEKHDMVQRGEIIDSDMGDEFYLQCLDAE

Parental	LFVLQHICYIMAEICNANVPQIRQRVHQILNMRGSSIKIVRHIIKEYAE
	LFVLQ.IC.IM..ICNANVPQI.QRVHQILNM.G.SIKIVRHIIK.YAE
Retrocopy	LFVLQCICCIMSKICNANVPQICQRVHQILNM*GRSIKIVRHIIKGYAE

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

RetrogeneDB ID:

retro_ptro_3208