RetrogeneDB ID:

retro_pabe_2172

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:2b_random:993812..995631(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CDC27
Ensembl ID:ENSPPYG00000008945
Aliases:None
Description:cell division cycle 27 [Source:HGNC Symbol;Acc:1728]


Retrocopy-Parental alignment summary:






>retro_pabe_2172
TACCAAGNNNNNNNNNNAGAAGAAGCCTTGTTTTTAATGGCGACCTGTTCTTACCTCCCAGGAAAGTCCTATAAAGCATA
TAGACTCTTGAAAAGACATAGTTGTCCTACACCGCAATGCAAATACCTGCTTGCAAAATGTTGTGTTGATCTCAGTAAGC
TTGCAGACTGGGAGCAAATCTTATCTGGTGGAGTGTTTAATAAGAAGAAAAGCCATGATGATATTGTTACTGAGTTTGGT
GATTCAGTTTGCTTTCCCCTTCCATTGTTGGGACGTGTATATTGCAAGACAGATCGGCTTGCTAAAGGATAAGAATGTTA
CCAAAAGAGACTTAGTTTAAATCCTTTCCTCTGGTATCCCTTTGAATCATTATGTGAAATAGGTGAAAAGCCAGATCCTG
GCCAAACATTTAAATTCACATCTTTACAGAACTTTAGCAACTGTCTGCCCAACTCTTGTACAACACAAGTACCTAATCAC
AGTTTATGTCACAGACAGCCTGAGACCATTCTTATGGAAACACCCCAGGACACAACTGAATTAAACAGAGTCAGTTTAGA
ATCTTCCAATTCAAAGTACTCCTTGAATACAGATTCCCCAGTGTCTTTTATTGATTCAGCTGTAATTTCACCTGAAACTG
TCCCACTGGGAACAGAAACTTCCATGTTATCTAAACAGGTTAAAAATAAACCAAAAACTGGTCGAAGTTTATTAACAGGA
CCAGCAGCTCTTAGTCCATTTACTCCAAGTTTTGGGATTTTGCCATTAGAAACCCCAAGTCCTGGAGATGGATCTTATTT
ACAAACTACACTAATACACCTTCTGTAATTGATGTGCCATCCACCGGAGCCCCTTCAATAAAGTCTGTTGCCAGAATTGG
CCAAACTGGAGCAAAGTCTGTCTTCTCGCAGAGTGGAAATAGCCGAGAGGTAACTCCAATTCTTTCACTAACATAAAGTT
CTGGTCCATAAATAACTACAACACCTCAGGTAATGAGCCCCACTATGACAACTCCCCCAAATGCACTGCATCGAAGAAGT
TCATGACTCTTTACTAGTGACAGTTCCACAACCAAGGAGAATAAGAAGAAATTAAAAATGAAGTTTCCACCTGAAATCCT
AAAGAGAAAAACAAAAAGTAAAACTAATAAAGGAGGAATAACCCAATCTAATATAAATGAAAACCTGGAAATTACAAAAT
TGGACTCTTCCATCAATTCAGAAGAGGAAATATCCACAATCACACCTCAGATTCAGGCTTTTAATCTACAAAAAGCAGCA
GCAGAAGGCTTGATGAGCCTTCTTCATGAAAGCAGGAAAGGTTATTTAGCTTTATGTTCATACCACTGCAAAGAAGCTAT
AAATATTTTGAGCCATCTACCTTCTCACCACTACAATATTGGTTGGGAACTGTGCCAAATTGGAAGGTCCTATTTTGAAC
TTTCAGAGTACATGCAAGCTGAAAGAATATTCTCAGAGGTTAGAAGGATTGAGAATTATAGATTCGAAGGCATGGAAATC
TACTCTACAACACTTTGGCATCTTCAAAAAGATGTCGCTCTTTCATTTCTGTCAAAAGACTTAACAGACATGGATAAAAA
TTCTCCAGAGGCCTGGTGTGCTGCAGGGAACTGTTTCAGTCTGCAACAGGACACGATATTGCAATTAAATTCTCCCAGAG
AGCTATCCAAGTGGATCCAAATTATGCTTATGCCTATACTTTATTAGGGCGAGAGTTTGTCTTAATTGAAGAATTGGACA
AAGCGTTAGCTTGTTTTTGAAATGCTATCAGAGTCAATCCTAGACATTACAATGCATGG

ORF - retro_pabe_2172 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.19 %
Parental protein coverage: 73.67 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalYAEXHSEEALFLLATCYYRSGKAYKAYRLLKGHSCTTPQCKYLLAKCCVDLSKLAEGEQILSGGVFNKQK
Y..X..EEALFL.ATC.Y..GK.YKAYRLLK.HSC.TPQCKYLLAKCCVDLSKLA..EQILSGGVFNK.K
RetrocopyYQXXXXEEALFLMATCSYLPGKSYKAYRLLKRHSCPTPQCKYLLAKCCVDLSKLADWEQILSGGVFNKKK
ParentalSHDDIVTEFGDSACFTLSLLGHVYCKTDRLAKGSECYQKSLSLNPFLWSPFESLCEIGEKPDPDQTFKFT
SHDDIVTEFGDS.CF.L.LLG.VYCKTDRLAKG.ECYQK.LSLNPFLW.PFESLCEIGEKPDP.QTFKFT
RetrocopySHDDIVTEFGDSVCFPLPLLGRVYCKTDRLAKG*ECYQKRLSLNPFLWYPFESLCEIGEKPDPGQTFKFT
ParentalSLQNFSNCLPNSCTTQVPNHSLSHRQPETVLTETPQDTIELNRLNLESSNSKYSLNTDSSVSYIDSAVIS
SLQNFSNCLPNSCTTQVPNHSL.HRQPET.L.ETPQDT.ELNR..LESSNSKYSLNTDS.VS.IDSAVIS
RetrocopySLQNFSNCLPNSCTTQVPNHSLCHRQPETILMETPQDTTELNRVSLESSNSKYSLNTDSPVSFIDSAVIS
ParentalPDTVPLGTGTSILSKQVQNKPKTGRSLLGGPAALSPLTPSFGILPLETPSPGDGSYLQ-NYTNTPSVIDV
P.TVPLGT.TS.LSKQV.NKPKTGRSLL.GPAALSP.TPSFGILPLETPSPGDGSYLQ.NYTNTPSVIDV
RetrocopyPETVPLGTETSMLSKQVKNKPKTGRSLLTGPAALSPFTPSFGILPLETPSPGDGSYLQ<NYTNTPSVIDV
ParentalPSTGAPSKKSVARIGQSGTKSVFSQSGNSREVTPILAQTQSSGPQTSTTPQVLSPTITSPTNALPRRSSR
PSTGAPS.KSVARIGQ.G.KSVFSQSGNSREVTPIL..T.SSGP...TTPQV.SPT.T.P.NAL.RRSS.
RetrocopyPSTGAPSIKSVARIGQTGAKSVFSQSGNSREVTPILSLT*SSGP*ITTTPQVMSPTMTTPPNALHRRSS*
ParentalLFTSDSSTTKENSKKLKMKFPPKIPNRKTKSKTNKGGITQPNINDSLEITKLDSSIISEGKISTITPQIQ
LFTSDSSTTKEN.KKLKMKFPP.I..RKTKSKTNKGGITQ.NIN..LEITKLDSSI.SE..ISTITPQIQ
RetrocopyLFTSDSSTTKENKKKLKMKFPPEILKRKTKSKTNKGGITQSNINENLEITKLDSSINSEEEISTITPQIQ
ParentalAFNLQKAAAEGLMSLLREMGKGYLALCSYNCKEAINILSHLPSHHYNTGWVLCQIGRAYFELSEYMQAER
AFNLQKAAAEGLMSLL.E..KGYLALCSY.CKEAINILSHLPSHHYN.GW.LCQIGR.YFELSEYMQAER
RetrocopyAFNLQKAAAEGLMSLLHESRKGYLALCSYHCKEAINILSHLPSHHYNIGWELCQIGRSYFELSEYMQAER
ParentalIFSEVRRIENYRVEGMEIYSTTLWHLQKDVALSVLSKDLTDMDKNSPEAWCAAGNCFSLQRE-HDIAIKF
IFSEVRRIENYR.EGMEIYSTTLWHLQKDVALS.LSKDLTDMDKNSPEAWCAAGNCFSLQ...HDIAIKF
RetrocopyIFSEVRRIENYRFEGMEIYSTTLWHLQKDVALSFLSKDLTDMDKNSPEAWCAAGNCFSLQQD<HDIAIKF
ParentalFQRAIQVDPNYAYAYTLLGHEFVLTEELDKALACFRNAIRVNPRHYNAW
.QRAIQVDPNYAYAYTLLG.EFVL.EELDKALACF.NAIRVNPRHYNAW
RetrocopySQRAIQVDPNYAYAYTLLGREFVLIEELDKALACF*NAIRVNPRHYNAW

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 43 .24 RPM
SRP007412_cerebellum 0 .00 RPM 52 .05 RPM
SRP007412_heart 0 .00 RPM 16 .95 RPM
SRP007412_kidney 0 .00 RPM 14 .25 RPM
SRP007412_liver 0 .00 RPM 15 .76 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_2172 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2172 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2172 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG000000048973 retrocopies
retro_hsap_2159, retro_hsap_4333, retro_hsap_4933,
Pongo abelii ENSPPYG00000008945 35 retrocopies
retro_pabe_2094, retro_pabe_2169, retro_pabe_2170, retro_pabe_2172 , retro_pabe_2178, retro_pabe_2182, retro_pabe_2183, retro_pabe_2184, retro_pabe_2185, retro_pabe_2186, retro_pabe_2190, retro_pabe_2192, retro_pabe_3526, retro_pabe_3545, retro_pabe_3547, retro_pabe_3550, retro_pabe_3551, retro_pabe_3553, retro_pabe_3556, retro_pabe_3582, retro_pabe_3583, retro_pabe_3589, retro_pabe_3592, retro_pabe_3598, retro_pabe_3599, retro_pabe_3603, retro_pabe_3605, retro_pabe_3606, retro_pabe_3607, retro_pabe_3609, retro_pabe_3610, retro_pabe_3827, retro_pabe_3828, retro_pabe_3833, retro_pabe_3834,
Pan troglodytes ENSPTRG000000093269 retrocopies
retro_ptro_1644, retro_ptro_2972, retro_ptro_3053, retro_ptro_3071, retro_ptro_3072, retro_ptro_3288, retro_ptro_3294, retro_ptro_3295, retro_ptro_3304,


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