RetrogeneDB ID:

retro_pabe_2720

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:5:15652042..15653314(-)
Located in intron of:ENSPPYG00000015353
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RBBP4
Ensembl ID:ENSPPYG00000001588
Aliases:RBBP4, RBBP-4
Description:histone-binding protein RBBP4 [Source:RefSeq peptide;Acc:NP_001124686]


Retrocopy-Parental alignment summary:






>retro_pabe_2720
ATGGCCGACAAGGATCCTTCCTTCGACGACTCGGAGGGAGAATGAGTGATCCTCGAGGAATACATAATATGGAAAAAGAA
CACCCCTTTTCTTTATGATTTGGTGATGACCTATGCTCTGGAGTGGCCCAGCCTAACTGCCCAGTGGCTTCCAGATGTAA
CCAGACCAGAAGGGAAAGATTTCAGCATTCATCGACTTGTCCTGGGGACACACACATCGGATGAACAAAACCATCTTGTT
ATAGCCAGCGTGCAGCTCCCTAATGATGATGCTCAGTTTGATGCATCACATTACGACAGTGAGAAAGGAGAATTTGGAGG
TTTTGGTTCAGTTAGTGGAAAAATTGAAATAGAAATCAAGATCAACCATGAAGGAAAAGTAAACAGGGCCCCGTTATATG
CCCCAGAACCCTTGTATCATCGCAACAAAGACTCCTTCCAGTGATGTTCTTGTCTTTGACTATACAAAACATCCTTCTAA
CCAGATCCTTTTGGAGAGTGCAACCCGAACTTGCGTCTCCGTGGACATCAGAAGGAAGGCTATGGGCTTTCTTGGAACCT
AAATCTCAGTGGGCACTTACTTAGTGCTTCAGATGACCACACCATCCGCCTGTGGGACATCAGTGTCGTTCCAAAGGAGG
GAAAAGTGGTAGGTGTGAAGACCATCTTTACAGGGCATACAGCAGTAGTAGAAGATGTTCCCTGGCATCTACTCCGTGAG
TGTCTGTTTGGGTCAGTGGCTGATGATCAGAAACTTATGATTTGGGATACTCATTCAAACAATACTTCCAAACCAAGCCA
CTCAGTTGACACTCACACTGCTGAAGTGAACTGCCTTTCTTTCAGTCCTTATAGTGAGTTCATTCTTGCCACAGGATCAG
CTGACAAGACTGTTGCCTTGTGGGATCTGAGAAATCTGAAACTTAAGTTGCATTCCTTTGAGTCACCTAAGGATGAAATA
TTCCAGGTTCAGTGGTCACCTCACAATGAGACTATTTTAGCTTCTAGTGGTACTGATTGCAGACTGAATGTCTGATATTT
AAGTAAAAATGGAGAGGAACAATCCCCAGAAGATGCAAAAGACTGGCCACCAGAGTTGTTTATTCATGGTGGTCACACTG
CCAAGATACCTGATTTCTCCTGGAATCCCAATGAACCTTGAGTGATTTGTTCTGTATCGGAAGACAATATCATGCAAGTG
TGGCAAATGGCAGAGAACATTTATAATGATGAAGACCCTGAAGGAAGCATGGATCCAGAAGGACAAGGGTCC

ORF - retro_pabe_2720 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.1 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMADKEAAFDDAVEERVINEEYKIWKKNTPFLYDLVMTHALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
MADK...FDD...E.VI.EEY.IWKKNTPFLYDLVMT.ALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
RetrocopyMADKDPSFDDSEGE*VILEEYIIWKKNTPFLYDLVMTYALEWPSLTAQWLPDVTRPEGKDFSIHRLVLGT
ParentalHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGEVNRA-RYMPQNPCI
HTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEG.VNRA.RYMPQNPCI
RetrocopyHTSDEQNHLVIASVQLPNDDAQFDASHYDSEKGEFGGFGSVSGKIEIEIKINHEGKVNRA>RYMPQNPCI
ParentalIATKTPSSDVLVFDYTKHPSK-PDPSGECNPDLRLRGHQKEGYGLSWNPNLSGHLLSASDDHTICLWDIS
IATKTPSSDVLVFDYTKHPS..PDP.GECNP.LRLRGHQKEGYGLSWN.NLSGHLLSASDDHTI.LWDIS
RetrocopyIATKTPSSDVLVFDYTKHPSN<PDPFGECNPNLRLRGHQKEGYGLSWNLNLSGHLLSASDDHTIRLWDIS
ParentalAVPKEGKVVDAKTIFTGHTAVVEDVSWHLLHESLFGSVADDQKLMIWDTRSNNTSKPSHSVDAHTAEVNC
.VPKEGKVV..KTIFTGHTAVVEDV.WHLL.E.LFGSVADDQKLMIWDT.SNNTSKPSHSVD.HTAEVNC
RetrocopyVVPKEGKVVGVKTIFTGHTAVVEDVPWHLLRECLFGSVADDQKLMIWDTHSNNTSKPSHSVDTHTAEVNC
ParentalLSFNPYSEFILATGSADKTVALWDLRNLKLKLHSFESHKDEIFQVQWSPHNETILASSGTDRRLNVWDLS
LSF.PYSEFILATGSADKTVALWDLRNLKLKLHSFES.KDEIFQVQWSPHNETILASSGTD.RLNV..LS
RetrocopyLSFSPYSEFILATGSADKTVALWDLRNLKLKLHSFESPKDEIFQVQWSPHNETILASSGTDCRLNV*YLS
ParentalKIGEEQSPEDAEDGPPELLFIHGGHTAKISDFSWNPNEPWVICSVSEDNIMQVWQMAENIYNDEDPEGSV
K.GEEQSPEDA.D.PPE.LFIHGGHTAKI.DFSWNPNEP.VICSVSEDNIMQVWQMAENIYNDEDPEGS.
RetrocopyKNGEEQSPEDAKDWPPE-LFIHGGHTAKIPDFSWNPNEP*VICSVSEDNIMQVWQMAENIYNDEDPEGSM
ParentalDPEGQGS
DPEGQGS
RetrocopyDPEGQGS

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 .28 RPM 32 .18 RPM
SRP007412_cerebellum 0 .12 RPM 38 .18 RPM
SRP007412_heart 0 .18 RPM 15 .80 RPM
SRP007412_kidney 0 .27 RPM 25 .66 RPM
SRP007412_liver 0 .28 RPM 25 .34 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_2720 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2720 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2720 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_3292
Pan troglodytes retro_ptro_2226
Gorilla gorilla retro_ggor_1314
Parental genes homology:
Parental genes homology involve 21 parental genes, and 55 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000059042 retrocopies
retro_btau_1610, retro_btau_630,
Canis familiaris ENSCAFG000000105271 retrocopy
retro_cfam_1550,
Choloepus hoffmanni ENSCHOG000000040666 retrocopies
retro_chof_1382, retro_chof_1649, retro_chof_1867, retro_chof_2116, retro_chof_2327, retro_chof_908,
Callithrix jacchus ENSCJAG000000010217 retrocopies
retro_cjac_1157, retro_cjac_1787, retro_cjac_1873, retro_cjac_244, retro_cjac_2557, retro_cjac_2719, retro_cjac_2939,
Cavia porcellus ENSCPOG000000153523 retrocopies
retro_cpor_154, retro_cpor_27, retro_cpor_899,
Equus caballus ENSECAG000000227841 retrocopy
retro_ecab_767,
Echinops telfairi ENSETEG000000200084 retrocopies
retro_etel_1088, retro_etel_1462, retro_etel_1877, retro_etel_676,
Felis catus ENSFCAG000000270171 retrocopy
retro_fcat_1507,
Homo sapiens ENSG000001625216 retrocopies
retro_hsap_1305, retro_hsap_2675, retro_hsap_2814, retro_hsap_3292, retro_hsap_3600, retro_hsap_3601,
Macropus eugenii ENSMEUG000000143791 retrocopy
retro_meug_1032,
Myotis lucifugus ENSMLUG000000007492 retrocopies
retro_mluc_2275, retro_mluc_892,
Macaca mulatta ENSMMUG000000099401 retrocopy
retro_mmul_75,
Mustela putorius furoENSMPUG000000152141 retrocopy
retro_mputfur_104,
Mus musculus ENSMUSG000000572361 retrocopy
retro_mmus_356,
Nomascus leucogenys ENSNLEG000000028056 retrocopies
retro_nleu_1061, retro_nleu_1179, retro_nleu_1194, retro_nleu_1356, retro_nleu_1379, retro_nleu_2982,
Petromyzon marinus ENSPMAG000000071891 retrocopy
retro_pmar_26,
Pongo abelii ENSPPYG00000001588 6 retrocopies
retro_pabe_1093, retro_pabe_2210, retro_pabe_2720 , retro_pabe_2958, retro_pabe_3529, retro_pabe_3611,
Pteropus vampyrus ENSPVAG000000109812 retrocopies
retro_pvam_1094, retro_pvam_902,
Rattus norvegicus ENSRNOG000000214921 retrocopy
retro_rnor_1270,
Sarcophilus harrisii ENSSHAG000000109231 retrocopy
retro_shar_399,
Ictidomys tridecemlineatus ENSSTOG000000120111 retrocopy
retro_itri_1168,


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