RetrogeneDB ID:

retro_pabe_3656

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:X:71560962..71562487(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UHRF2
Ensembl ID:ENSPPYG00000019227
Aliases:None
Description:ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12557]


Retrocopy-Parental alignment summary:






>retro_pabe_3656
GGGGGTTCTGAAGGGGCATTAAATGAGTGCAAGATAATATCTGTAGATGAAATCTTCAAGACTGAGAAACGTGGAGCCTA
TCCTCTTCCGTTTGCAGATGTAAAGTTTTTAAGGAGAAATAACCCTGAATGTGACCTGTGTGGTGGAGACCCAGATAAGA
AATGCCATTCTTGCTTCTTTCATGTATATGGTGGGAAACATGAACCCAACATGCAGCTTCTATGTGATGAATGTAATGTG
GCTTATCATATTTACTGCTTGAATACACCTTTGGATAAAGTCCCAGAAGAGGAATACTGGTATTGTTCTTCCTGTAAAAC
TGATTCCAGTTAGGTTGTAAAGGCTGGTGAAAGACTCGAGATAAGCGAAAAGAAAGCAAAGATGCCATCCGCTAGTACTG
AAAGCCAGAGAGACTGATGCAGGAGAATGGCTTGTGTTGGTCATATGACAGAATGCACTATTGTCTCTTCTAATCATTAT
GGACCTATTCCTGTTGGATCAACTTGGAGATTTAGAGTTCAGGTGAGTGAAGTATGTGTTCACAGACCTCATGTTGGTGG
ACTTCATGGTCGAAGTAATGATGGAGTTTATTCTCTTGTCTTGGCTGGTGGATTTGTGGATAAAGTTGACCGAGGTGATG
AGTTCTTGTACACTGGAAGTGGCAGTAAAAAGCTTGCTGGTAATAAAAGAATTGGCACACCTTCAGCTGATCAAACATTA
ACAAACACGAACAGGGCATTGGCCCTAAACTGTGATGCTACATTGGGTGATAAAATTGGAGAAGAGTCTCGGAATTGGAG
AGCTGGTAAGCCAGTCAGAGTGATATGCAGTTTTAAAGGGAGGAAGATCAGCAAATATGCTCCTGAAGAAGGCAACAGAT
ATGATGGCATTTATAAGGTAGTGAAATACTGGCCAGAGATTTCATCAAGCCATGGATTCTTGATTTGGCGCTATCTTTTA
AGAAGAGATGATGTTAAACCTGCTCCTTGGACCTCTGAAGGAATAGAATGGTCAAGGAGATTATGTCTACATTTACAGCA
TCCAGCAGGTTACCCTTCAGATAAAGAAAGGAAGAAGACTAAAGGACAGTCAAAGAAGCAGGCCAGTGGAACCACAAAAA
GGCCGATTTCAGATGTCTAAGTGCCTCCAAAGTATACAAAGCATCAGATTCAGCAGGAGCAATTGAGGCTTTTCAACTTA
CTCCTCAACAGCAACATCTCATCAGAGAAGACTGTCAAAATCAGAAGCTGTGGGATGAAGTGCTTGCATATCTTGTGGAA
GGACCAAATTTTCTGAAAAAATTGGAACAATCTTTTATGTGTGTTTGCTGCCAGAAGCTAGTTTACCAGCCTGTGACAAC
TGAGTGCTTCCACAATGTCTGTAAAGATTGCCTACAGTGCTCCTTTAAGGCACAGGTTTTCTCCTGCCCTGCTTGCTGGC
ATGATCTTGGCCAGAATTACATCATAATTCCCCATGAGATTCTGCAGACTCTACTAGACATTTCTTCCCTGGCTACAGCA
AAGGA

ORF - retro_pabe_3656 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.69 %
Parental protein coverage: 64.09 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGGSEGTLNDCKIISVDEIFKIERPGAHPLSFADGKFLRRNDPECDLCGGDPEKKCHSCSCRVCGGKHEPN
GGSEG.LN.CKIISVDEIFK.E..GA.PL.FAD.KFLRRN.PECDLCGGDP.KKCHSC...V.GGKHEPN
RetrocopyGGSEGALNECKIISVDEIFKTEKRGAYPLPFADVKFLRRNNPECDLCGGDPDKKCHSCFFHVYGGKHEPN
ParentalMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKTDSSEVVKAGERLKMSKKKAKMPSASTESRRDWG
MQLLCDECNVAYHIYCLN.PLDKVPEEEYWYC.SCKTDSS.VVKAGERL..S.KKAKMPSASTES.RD..
RetrocopyMQLLCDECNVAYHIYCLNTPLDKVPEEEYWYCSSCKTDSS*VVKAGERLEISEKKAKMPSASTESQRD*C
ParentalRGMACVGRTRECTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFAD
R.MACVG...ECTIV.SNHYGP...IPVGSTWRFRVQVSE..VHRPHVGG.HGRSNDG.YSLVLAGGF.D
RetrocopyRRMACVGHMTECTIVSSNHYGP---IPVGSTWRFRVQVSEVCVHRPHVGGLHGRSNDGVYSLVLAGGFVD
ParentalEVDRGDEFTYTGSGGKNLAGNKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRS
.VDRGDEF.YTGSG.K.LAGNKRIG.PSADQTLTN.NRALALNCDA.L.DKIG.ESRNWRAGKPVRVI.S
RetrocopyKVDRGDEFLYTGSGSKKLAGNKRIGTPSADQTLTNTNRALALNCDATLGDKIGEESRNWRAGKPVRVICS
ParentalFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQY
FKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFL.WRYLLRRDDV.PAPWTSEGIE.SRRLCL.LQ.
RetrocopyFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLIWRYLLRRDDVKPAPWTSEGIEWSRRLCLHLQH
ParentalPAGYPSDKEGKKTKGQSKKQPSGTTKRPISDDGCPSASKVYKASDSAEAIEAF-QLTPQQQHLIREDCQN
PAGYPSDKE.KKTKGQSKKQ.SGTTKRPISD...P...K..K.....E....F.QLTPQQQHLIREDCQN
RetrocopyPAGYPSDKERKKTKGQSKKQASGTTKRPISDV*VP--PKYTKHQIQQEQLRLF<QLTPQQQHLIREDCQN
ParentalQKLWDEVLAHLVEGPNFLKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG
QKLWDEVLA.LVEGPNFLKKLEQSFMCVCCQ.LVYQPVTTECFHNVCKDCLQ.SFKAQVFSCPAC.HDLG
RetrocopyQKLWDEVLAYLVEGPNFLKKLEQSFMCVCCQKLVYQPVTTECFHNVCKDCLQCSFKAQVFSCPACWHDLG
ParentalQNYIMIPNEILQTLLDL-FFPGYSKG
QNYI.IP.EILQTLLD..FFPGYSKG
RetrocopyQNYIIIPHEILQTLLDI<FFPGYSKG

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 .11 RPM 20 .51 RPM
SRP007412_cerebellum 0 .00 RPM 47 .55 RPM
SRP007412_heart 0 .00 RPM 15 .05 RPM
SRP007412_kidney 0 .03 RPM 19 .36 RPM
SRP007412_liver 0 .09 RPM 16 .52 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_3656 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_3656 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_3656 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000001478541 retrocopy
retro_hsap_4708,
Gorilla gorilla ENSGGOG000000088531 retrocopy
retro_ggor_2925,
Nomascus leucogenys ENSNLEG000000091351 retrocopy
retro_nleu_1985,
Pongo abelii ENSPPYG00000019227 1 retrocopy
retro_pabe_3656 ,


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