RetrogeneDB - Retrocopy retro_pabe

                        
>retro_pabe_3517
CTCACAAGAAGCCTAGTCCTGACGAATCAAGGATATCTTCAAGAAGCTGCTTGTGGACCAAACAAGTTCTGACCATCATG

GAGAAATCTCTGGTCTTGCTCAGGGAGATGATGGATGGCTCCCTCTATCAAAGAGTTGTTATGGAAGCTACACCACTAGA

TCACTCTTCCAATACATGTTTCTCATCCAGAGGCACTTCAACATCAACCACGTTGGCCATCCATGGCTTAAACAACACTT

TGCATTTATGTATTGAACCATCCTGCCAGGGTTTCAAAGGACTGTGGCTATTGCAGACTCAAATTACAACTGATTTTGTG

GTCCAGAAAGCCAATTAGTGTTCCTTGATAAATTTGTCATGCGTAACAGCAATGGTAACTGGCTAGCTGACCAAATCAGA

AGGAACCGTGTGGTGGAAGGTCCAGGAACACTGTCCAAAGGGCAGCGCTTGTGCACTCTGCACACAGAATTTCTCTGGTA

TGATGCCAGCTTGAAATCCGTTCCTCCTCCAGACTTTGGCACCCCTACACTGCATTATTTTGAAGACTGGGTGTCGTGAC

TTATGGAAGTGCACTACCTGCTGAAATCAATAAATCTTTCCTCTCTTTCAAGTCTGGAAAACTGGGGGGACATGCAATAT

GTGACATTGTCCACAGAAACAAATACAAAGATTAGATCAAAGGATGGAGAAATTTTAGGGCAGGGCATGAACATTATGAT

CAAAACTCATTTACTTTTGCTCTCAGTTGTGTGCCTTTCATTATTGAGGCTCTGTATGGGCCAAAGTACACCTTCTTCAA

CAATGTTTTGATGTTTTCTGCAGTTGTGTCAAAGAGCTGCTTTTCTCCCTGGAATGGTCAAGTCACAGAAGACTGTTCAT

CAAAATGGTCTAAATACCAGCATGACCTGGCAGCTAGCTGTCAAGGGACAGTGGTTGCAGCAGAGGAGAAAAATGGGGTG

GTTTTCATCTGAGGAGAAGGTGTGGGAGCTTATAACCCCCAGCTCAACCTGAAGAATGTTCAGAGGAATCTGATCCTCCT

ACGTCCACAGCTGCTTCTCCTTGTAGACCAAATACACCTGGGAGAGGAGAGTCCCTTGGAGATAGCAGCGAGCTTCTTCC

ACAATGTGGATGTTCCTTTTGAGGAGACTGTGGTAGATGGCATCCATGGGGCTTTCTTCAGGTAGTGAGATGGTCTCTAT

AAAAAGTACTGGATGGACAATACTGGCTACAGCAAGAAAGCAACATTTGCCTCAGTGACATATCCTGGGAGCTATCCCTA

CAATGGGACAAACTATGTGAATGTCACCATGCACCTCTGAAGTCCCATCACCAGGCCAGCTTACCTCTTCATACGGTCAT

CTATAGATGTTCAGAGCTTCACCATCCACAGAGACTCTCAGCAACTGGATGTGTTCATAGCCACCAGTGAACATGCCTAC

GTAACATACCTGTGGACAGGTGAGGCCACAGGACAGTCTGCTTTTGCACAGGTCATTGCTGATCATCACAAAATTCTGTT

TGACTGGAATTCAGCCATCAAGAGCAGCATTGTCCCTGAGGTGAAGAACTATGCTGCTATTGTGGAACAGAACCTGCAGC

ATTTTAAGCCAGTGTTTCAGCTGGAGAAGCAGATACTGTCCTGAGTCCAGAACCAGCTAGCTTTAGGAAGACTGCTGACC

ACCTGCTGAGATTTTCAGATAAGAGACAGGCTGAAGAGGCCATCGACAGGATTTTTGCCATAACACAGCAACAGCAGCAG

CAAAGCAAGTCAAAGAAAAACCAAAGGGCAGGTGAACGCTATAAATTTGTGGACGCTGTCCCTGATATTTTTACACAGAT

TGAGGTCAATGAGAAAAAGATTAGACAGAAAGCTCAGATTCAGGCACAGAAAGAACTACCCATAAATGAAGATGAAGAAA

TGAAAAACCTCTTAGATTTTGCAGATGTAACATATGAAAACATAAAAATGGGGCTTGATGAAAGGCCGGGTTGGACAGGC

ATGGATGGTGACAACCACTCGTAGCAGGGCCTCATCACTATCTGCTTCCTACACCAGATTGTTCCTCATCCTGAACATTG

CTATCTTCTTTGTCATGTTGGCAATACAACTGACTTATTTCCAGAGGGCCCAGAACCTACATGGCCAAAGACGTCTTTAT

GCAGTTCTTCTAATAGATAGCTGTATTTTATTGTGGTTGTACTCTTCTTGTTCCCAATCACAATGT

ORF - retro_pabe_3517 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	88.55 %
Parental protein coverage:	77.77 %
Number of stop codons detected:	8
Number of frameshifts detected:	6

Retrocopy - Parental Gene Alignment:

                                ParentalLTGSLVLMNQGYLQEAY-LWTKQVLTIMEKSLVLLREVTDGSLYEGVA-YGSYTTRSLFQYMFLVQRHFN
LT.SLVL.NQGYLQEA..LWTKQVLTIMEKSLVLLRE..DGSLY..V..YGSYTTRSLFQYMFL.QRHFN
RetrocopyLTRSLVLTNQGYLQEAA<LWTKQVLTIMEKSLVLLREMMDGSLYQRVV<YGSYTTRSLFQYMFLIQRHFN
ParentalINHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRNRV
INH.GHPWLKQHFAFMY.TILPGFQRTVAIADSNYN.F.GPESQLVFLDKFVMRN..GNWLADQIRRNRV
RetrocopyINHVGHPWLKQHFAFMY*TILPGFQRTVAIADSNYN*FCGPESQLVFLDKFVMRNSNGNWLADQIRRNRV
ParentalVEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSFKSG
VEGPGT.SKGQR.CTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW.GVVTYGSALPAEIN.SFLSFKSG
RetrocopyVEGPGTLSKGQRLCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GVVTYGSALPAEINKSFLSFKSG
ParentalKLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAV
KLGG.AI.DIVHRNKYKD.IKGWRNF.AGHEH.DQNSFTFA...VPFI.EALYGPKYTFFNNVLMFS..V
RetrocopyKLGGHAICDIVHRNKYKD*IKGWRNFRAGHEHYDQNSFTFALSCVPFIIEALYGPKYTFFNNVLMFSAVV
ParentalSKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLIL
SKSCFSPW.GQVTEDCSSKWSKY.HDLAASCQG.VVAAEEKNGVVFI.GEGVGAYNPQLNLKNVQRNLIL
RetrocopySKSCFSPWNGQVTEDCSSKWSKYQHDLAASCQGTVVAAEEKNGVVFI*GEGVGAYNPQLNLKNVQRNLIL
ParentalLHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATF
L.PQLLLLVDQIHLGEESPLE.AASFFHNVDVPFEETVVDG.HGAF.R..DGLYK.YWMD.TGYS.KATF
RetrocopyLRPQLLLLVDQIHLGEESPLEIAASFFHNVDVPFEETVVDGIHGAFFR**DGLYKKYWMDNTGYSKKATF
ParentalASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSIDVQSFTVHGDSQQLDVFVATSKHAYATYLWT
ASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFI..SIDVQSFT.H.DSQQLDVF.ATS.HAY.TYLWT
RetrocopyASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIRSSIDVQSFTIHRDSQQLDVFIATSEHAYVTYLWT
ParentalGEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVRN-TAS
GEATGQSAFAQVIAD.HKILFD.NSAIKSSIVPEVK.YAAIVEQNLQHFKPVFQ.LEKQILS.V.N..AS
RetrocopyGEATGQSAFAQVIADHHKILFDWNSAIKSSIVPEVKNYAAIVEQNLQHFKPVFQ-LEKQILS*VQN<PAS
ParentalFRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIRQK
FRKTA..LLRFSDKRQ.EEAIDRIFAI.QQQQQQSKSKKN.RAG.RYKFVDAVPDIF.QIEVNEKKIRQK
RetrocopyFRKTADHLLRFSDKRQAEEAIDRIFAITQQQQQQSKSKKNQRAGERYKFVDAVPDIFTQIEVNEKKIRQK
ParentalAQILAQKELPIDEDEEMKDLLDFADVTYE-KHKNG-GLIEGRFGQARMVTTTHSRAPSLSASYTRLFLIL
AQI.AQKELPI.EDEEMK.LLDFADVTYE.KHKNG.GL..GR.GQA.MVTTT.SRA.SLSASYTRLFLIL
RetrocopyAQIQAQKELPINEDEEMKNLLDFADVTYE<KHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLFLIL
ParentalNIAIFFVMLAMQLTYFQKAQSLHGQRCLYAVLLIDSCILLWLYSSCSQSQC
NIAIFFVMLA.QLTYFQ.AQ.LHGQR.LYAVLLIDSCILLWLYSSCSQSQC
RetrocopyNIAIFFVMLAIQLTYFQRAQNLHGQRRLYAVLLIDSCILLWLYSSCSQSQC

                            

                            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	4 .48 RPM
SRP007412_cerebellum	0 .00 RPM	3 .16 RPM
SRP007412_heart	0 .00 RPM	6 .92 RPM
SRP007412_kidney	0 .07 RPM	5 .77 RPM
SRP007412_liver	0 .00 RPM	15 .70 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_3517 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3517 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_3517 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013791	1 retrocopy	retro_acar_15,
Callithrix jacchus	ENSCJAG00000004530	1 retrocopy	retro_cjac_1174,
Homo sapiens	ENSG00000111817	1 retrocopy	retro_hsap_4178,
Gorilla gorilla	ENSGGOG00000026746	2 retrocopies	retro_ggor_1419, retro_ggor_2802,
Nomascus leucogenys	ENSNLEG00000013106	1 retrocopy	retro_nleu_2476,
Pongo abelii	ENSPPYG00000016948	2 retrocopies	retro_pabe_3418, retro_pabe_3517 ,
Pan troglodytes	ENSPTRG00000018529	1 retrocopy	retro_ptro_2833,
Sorex araneus	ENSSARG00000010799	1 retrocopy	retro_sara_560,
Takifugu rubripes	ENSTRUG00000006239	1 retrocopy	retro_trub_32,
Xenopus tropicalis	ENSXETG00000032776	1 retrocopy	retro_xtro_8,

	RetrogeneDB ID:	retro_pabe_3517
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	9_random:9243815..9246041(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	DSE
	Ensembl ID:	ENSPPYG00000016948
	Aliases:	None
	Description:	dermatan sulfate epimerase [Source:HGNC Symbol;Acc:21144]

Parental	LTGSLVLMNQGYLQEAY-LWTKQVLTIMEKSLVLLREVTDGSLYEGVA-YGSYTTRSLFQYMFLVQRHFN
	LT.SLVL.NQGYLQEA..LWTKQVLTIMEKSLVLLRE..DGSLY..V..YGSYTTRSLFQYMFL.QRHFN
Retrocopy	LTRSLVLTNQGYLQEAA<LWTKQVLTIMEKSLVLLREMMDGSLYQRVV<YGSYTTRSLFQYMFLIQRHFN

Parental	INHFGHPWLKQHFAFMYRTILPGFQRTVAIADSNYNWFYGPESQLVFLDKFVMRNGSGNWLADQIRRNRV
	INH.GHPWLKQHFAFMY.TILPGFQRTVAIADSNYN.F.GPESQLVFLDKFVMRN..GNWLADQIRRNRV
Retrocopy	INHVGHPWLKQHFAFMYTILPGFQRTVAIADSNYNFCGPESQLVFLDKFVMRNSNGNWLADQIRRNRV

Parental	VEGPGTPSKGQRWCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW-GVVTYGSALPAEINRSFLSFKSG
	VEGPGT.SKGQR.CTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW.GVVTYGSALPAEIN.SFLSFKSG
Retrocopy	VEGPGTLSKGQRLCTLHTEFLWYDASLKSVPPPDFGTPTLHYFEDW<GVVTYGSALPAEINKSFLSFKSG

Parental	KLGGRAIYDIVHRNKYKDWIKGWRNFNAGHEHPDQNSFTFAPNGVPFITEALYGPKYTFFNNVLMFSPAV
	KLGG.AI.DIVHRNKYKD.IKGWRNF.AGHEH.DQNSFTFA...VPFI.EALYGPKYTFFNNVLMFS..V
Retrocopy	KLGGHAICDIVHRNKYKD*IKGWRNFRAGHEHYDQNSFTFALSCVPFIIEALYGPKYTFFNNVLMFSAVV

Parental	SKSCFSPWEGQVTEDCSSKWSKYKHDLAASCQGRVVAAEEKNGVVFIRGEGVGAYNPQLNLKNVQRNLIL
	SKSCFSPW.GQVTEDCSSKWSKY.HDLAASCQG.VVAAEEKNGVVFI.GEGVGAYNPQLNLKNVQRNLIL
Retrocopy	SKSCFSPWNGQVTEDCSSKWSKYQHDLAASCQGTVVAAEEKNGVVFI*GEGVGAYNPQLNLKNVQRNLIL

Parental	LHPQLLLLVDQIHLGEESPLETAASFFHNVDVPFEETVVDGVHGAFIRQRDGLYKMYWMDDTGYSEKATF
	L.PQLLLLVDQIHLGEESPLE.AASFFHNVDVPFEETVVDG.HGAF.R..DGLYK.YWMD.TGYS.KATF
Retrocopy	LRPQLLLLVDQIHLGEESPLEIAASFFHNVDVPFEETVVDGIHGAFFR**DGLYKKYWMDNTGYSKKATF

Parental	ASVTYPRGYPYNGTNYVNVTMHLRSPITRAAYLFIGPSIDVQSFTVHGDSQQLDVFVATSKHAYATYLWT
	ASVTYP..YPYNGTNYVNVTMHL.SPITR.AYLFI..SIDVQSFT.H.DSQQLDVF.ATS.HAY.TYLWT
Retrocopy	ASVTYPGSYPYNGTNYVNVTMHL*SPITRPAYLFIRSSIDVQSFTIHRDSQQLDVFIATSEHAYVTYLWT

Parental	GEATGQSAFAQVIADRHKILFDRNSAIKSSIVPEVKDYAAIVEQNLQHFKPVFQLLEKQILSRVRN-TAS
	GEATGQSAFAQVIAD.HKILFD.NSAIKSSIVPEVK.YAAIVEQNLQHFKPVFQ.LEKQILS.V.N..AS
Retrocopy	GEATGQSAFAQVIADHHKILFDWNSAIKSSIVPEVKNYAAIVEQNLQHFKPVFQ-LEKQILS*VQN<PAS

Parental	FRKTAERLLRFSDKRQTEEAIDRIFAISQQQQQQSKSKKNRRAGKRYKFVDAVPDIFAQIEVNEKKIRQK
	FRKTA..LLRFSDKRQ.EEAIDRIFAI.QQQQQQSKSKKN.RAG.RYKFVDAVPDIF.QIEVNEKKIRQK
Retrocopy	FRKTADHLLRFSDKRQAEEAIDRIFAITQQQQQQSKSKKNQRAGERYKFVDAVPDIFTQIEVNEKKIRQK

Parental	AQILAQKELPIDEDEEMKDLLDFADVTYE-KHKNG-GLIEGRFGQARMVTTTHSRAPSLSASYTRLFLIL
	AQI.AQKELPI.EDEEMK.LLDFADVTYE.KHKNG.GL..GR.GQA.MVTTT.SRA.SLSASYTRLFLIL
Retrocopy	AQIQAQKELPINEDEEMKNLLDFADVTYE<KHKNG<GLMKGRVGQAWMVTTTRSRASSLSASYTRLFLIL

Parental	NIAIFFVMLAMQLTYFQKAQSLHGQRCLYAVLLIDSCILLWLYSSCSQSQC
	NIAIFFVMLA.QLTYFQ.AQ.LHGQR.LYAVLLIDSCILLWLYSSCSQSQC
Retrocopy	NIAIFFVMLAIQLTYFQRAQNLHGQRRLYAVLLIDSCILLWLYSSCSQSQC

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

RetrogeneDB ID:

retro_pabe_3517