RetrogeneDB ID:

retro_pabe_854

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:12:63817399..63819285(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP469O2326
Ensembl ID:ENSPPYG00000018790
Aliases:DKFZP469O2326, PABPC1
Description:polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001128842]


Retrocopy-Parental alignment summary:






>retro_pabe_854
ATGAACCCCAGTGCCCCCAGCTACCCCACGTCATCGCTGTACGTAGGGGACCTCCATCCCGACGTGACCGAGGCGATGCT
CTACGAGAAGTTCAGCCCGGCCGGGCCCCTCGTCTCCATCCGGGTCTGCAGGGACATGATCACCCGCGGCTCCTTGGGGT
ACGCGTATGTGAACTTCCAGCAGCCGGCGGACGCGGAGCATGCTGTGAACACTATGAATTTTGATGTTATAAAGGGCAAG
CCAGTACGTATCGTGTAGTCTCAGCGTGATCCATCACTTCGCAAAAGTGGAGTGGGCTACATATTCATTAAAAATCTGGA
CAAATCCATTGATAATAAAGCACTGTATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAGGTGGGCTGTGATG
AAAATGATTCCAAGGGCTATGGATCTGTACACTTTGAGACACAGGAAGCAGCTGAAAGAGCCATGGAAAAAATGAATGGA
ATGCTCCTAAATGATCGCAAAGTATTTGTTGGACGATTTACGTCTCATAAAGAACGAGAAGCTGAACTTGGAGCTACGCG
AAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGTTCTCTTTGGCAAGTT
TGGTCCTGCCTTAAATGTGAAGGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGC
TTGAAGATGCACAGAAAGCTGTGGATGAAATGAATGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTAGAGCTCAG
AAAAAAGTGGAACGGCAGACAGAACTTAAGCGCAAATTTGAACAGATGAGGCAAGATAGGATCACCAGATACCACAGTGT
TAATCTTTATGTGAAAAATCTTGATGATGGCATTGATGATTAACGTCTCCGGAAAGAGTTTTCTCCATTTGGTACAATCA
CTAGTGCAAAGGTTATGATGGAGGGTGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTTCTCACCAGAAGAAGCCACT
AAAGCAGTTACAGAAATGAATGGTAGAGTTGTGGCCACAAAGCCATTGTATGTTGCTTTAGCTCAGCGTAAAGAAGAGGG
CCAGGCTCACCTCACTAACCAGTATATGCAAAGAATGGCAAGTGTACGAGCTGTGCCCAACCTTGTAATCAACCCCTACC
AGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTAACCCACAGACTCAGAACGGTGCTGCCTACTATCCTCCTAGCCAA
ATTGCTCAACTAAGACCAAGTCCTCGCTGTACTGCTCAGGGTGCCAGACCCCATCCATTCCAAAATATGCCCAGTGCTAT
CTGCCCAGCTGCTCCTAGACCACCATTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCGTGTCAACACAGT
GTGTTGCTAACACATCAACACAGACAATGGGTCCACATCCTGCAGCTGCTGCTGCTGCTGCAACTCCACATTATAACTAT
GCTGCGGGAGTTCGCAGTCCTCAGAAACATCTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTGTTCATGTACA
ACAGGAACCTTTGACTGCTTCCATGTTGGTATCTGCCCCTCCTCAAGAGCAAAAGCAAATGTTGGGTGAACGGCTGTTTC
CTCTTATTCAAGCCATGCACCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGAGATTGGTAATTCAGAACTTCTT
CATATGCTGGAGTCTCCAGAGTCACTCCGTTCTAAGGTTGATGAAACTGTAGCTGTACTACAAGCCCACCAAGCTGAAGA
GGCTGCCCAGAAAGCAGTTAACAGTGCCACGGGTGTTCCAACTGTT

ORF - retro_pabe_854 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.21 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 2
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MNPSAPSYP..SLYVGDLHPDVTEAMLYEKFSPAGP..SIRVCRDMITR.SLGYAYVNFQQPADAE.A..
RetrocopyMNPSAPSYPTSSLYVGDLHPDVTEAMLYEKFSPAGPLVSIRVCRDMITRGSLGYAYVNFQQPADAEHAVN
ParentalTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDVIKGKPVRI..SQRDPSLRKSGVG.IFIKNLDKSIDNKALYDTFSAFGNILSCKV.CDEN.SKGY
RetrocopyTMNFDVIKGKPVRIV*SQRDPSLRKSGVGYIFIKNLDKSIDNKALYDTFSAFGNILSCKVGCDENDSKGY
ParentalGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAR-AKEFTNVYIKNFGEDMDDERLKD
G.VHFETQEAAERA.EKMNGMLLNDRKVFVGRF.S.KEREAELGA..AKEFTNVYIKNFGEDMDDERLK.
RetrocopyGSVHFETQEAAERAMEKMNGMLLNDRKVFVGRFTSHKEREAELGAT<AKEFTNVYIKNFGEDMDDERLKV
ParentalLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRK
LFGKFGPAL.VKVMTDESGKSKGFGFVSFER.EDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRK
RetrocopyLFGKFGPALNVKVMTDESGKSKGFGFVSFERLEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRK
ParentalFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKA
FEQM.QDRITRY..VNLYVKNLDDGIDD.RLRKEFSPFGTITSAKVMMEGGRSKGFGFVCF.SPEEATKA
RetrocopyFEQMRQDRITRYHSVNLYVKNLDDGIDD*RLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFFSPEEATKA
ParentalVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNR
VTEMNGR.VATKPLYVALAQRKEE.QAHLTNQYMQRMASVRAVPN.VINPYQPAPPSGYFMAA.PQTQN.
RetrocopyVTEMNGRVVATKPLYVALAQRKEEGQAHLTNQYMQRMASVRAVPNLVINPYQPAPPSGYFMAANPQTQNG
ParentalAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQT
AAYYPPSQIAQLRPSPR.TAQGARPHPFQNMP.AI.PAAPRPPFSTMRPASSQVPRV.STQ.VANTSTQT
RetrocopyAAYYPPSQIAQLRPSPRCTAQGARPHPFQNMPSAICPAAPRPPFSTMRPASSQVPRVVSTQCVANTSTQT
ParentalMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQK
MGP.P..AAAAA.......P.Y.YAAGVR.PQ.HLNAQPQVTMQQPAVHVQ.QEPLTASML.SAPPQEQK
RetrocopyMGPHP--AAAAAA----ATPHYNYAAGVRSPQKHLNAQPQVTMQQPAVHVQ-QEPLTASMLVSAPPQEQK
ParentalQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNS
QMLGERLFPLIQAMHPTLAGKITGMLLEI.NSELLHMLESPESLRSKVDE.VAVLQAHQA.EAAQKAVNS
RetrocopyQMLGERLFPLIQAMHPTLAGKITGMLLEIGNSELLHMLESPESLRSKVDETVAVLQAHQAEEAAQKAVNS
ParentalATGVPTV
ATGVPTV
RetrocopyATGVPTV

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 1 .94 RPM 66 .46 RPM
SRP007412_cerebellum 1 .95 RPM 77 .34 RPM
SRP007412_heart 0 .21 RPM 75 .41 RPM
SRP007412_kidney 0 .17 RPM 161 .86 RPM
SRP007412_liver 0 .46 RPM 196 .80 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_854 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_854 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_854 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 49 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000003481 retrocopy
retro_amel_1650,
Choloepus hoffmanni ENSCHOG000000081781 retrocopy
retro_chof_2531,
Callithrix jacchus ENSCJAG000000158335 retrocopies
retro_cjac_1586, retro_cjac_2571, retro_cjac_3218, retro_cjac_4039, retro_cjac_41,
Cavia porcellus ENSCPOG000000129171 retrocopy
retro_cpor_1324,
Dasypus novemcinctus ENSDNOG000000087182 retrocopies
retro_dnov_1530, retro_dnov_2259,
Felis catus ENSFCAG000000018741 retrocopy
retro_fcat_1927,
Homo sapiens ENSG000000707561 retrocopy
retro_hsap_88,
Gorilla gorilla ENSGGOG000000067851 retrocopy
retro_ggor_1986,
Myotis lucifugus ENSMLUG000000122451 retrocopy
retro_mluc_579,
Macaca mulatta ENSMMUG000000177862 retrocopies
retro_mmul_1462, retro_mmul_895,
Monodelphis domestica ENSMODG000000062224 retrocopies
retro_mdom_123, retro_mdom_1867, retro_mdom_216, retro_mdom_43,
Mus musculus ENSMUSG000000222832 retrocopies
retro_mmus_102, retro_mmus_2164,
Nomascus leucogenys ENSNLEG000000031423 retrocopies
retro_nleu_221, retro_nleu_2412, retro_nleu_611,
Oryctolagus cuniculus ENSOCUG000000043541 retrocopy
retro_ocun_13,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pongo abelii ENSPPYG00000018790 3 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854 ,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Sarcophilus harrisii ENSSHAG000000112671 retrocopy
retro_shar_24,
Sus scrofa ENSSSCG000000060632 retrocopies
retro_sscr_1153, retro_sscr_1205,
Ictidomys tridecemlineatus ENSSTOG000000163952 retrocopies
retro_itri_139, retro_itri_48,
Tarsius syrichta ENSTSYG000000042292 retrocopies
retro_tsyr_1743, retro_tsyr_273,
Tursiops truncatus ENSTTRG000000046892 retrocopies
retro_ttru_1050, retro_ttru_1812,
Vicugna pacos ENSVPAG000000038654 retrocopies
retro_vpac_14, retro_vpac_384, retro_vpac_620, retro_vpac_649,


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