RetrogeneDB ID:

retro_pabe_68

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:13:24259582..24261487(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000005219
Aliases:None
Status:KNOWN_PROTEIN_CODING
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_68
ATGAACCCCAGCACCCCCAGCTACCCAACGGCCTCGCTCTACGTGGGGGACCTCCACCCCGACGTGACTGAGGCGATGCT
CTACGAGAAGTTCAGTCCGGCTGGGCCCATCCTTTCCATCCGGGTCTGCAGGGACTTGATCACCCGCCGCTCCTCCAACT
ACGCGTATGTGAACTTCCAGCACCCGAAGGACGCGGAGCATGCTCTGGACACCATGAATTTTGATGTTATAAAGGGCAAA
CCAGTACGCATCATGTGGTCTCAGCATGATCCATCACTTCGCAAAAGTGGAGTGGGCAACATATTCGTTAAAAATTTGGA
TAAATCCATTAATAATAAAGCACTGTATGATACAGTTTCTGCTTTTGGTAACATCCTTTCATGTAAGGTGGTTTGTGATG
AAAATGGTTCCAAGGGCTATGGATTTGTACACTTTGAGACACACGAAGCAGCTGAAAGAGCTATTGAAAAAATGAATGGA
ATGCTCCTAAATGATCGCAAAGTATTTGTTGGACGATTTAAGTCTCGTAAAGAACGAGAGGCTGAACTTGGAGCTAAGGC
AAAAGAGTTCCCCAATGTTTACATCAAGAATTTTGGAGAAGACATGGACGATGAGCGCCTTAAGGATCTCTTTGGCAAGT
TCGGGCCCGCCTTAAGTGTAAAAGTAATGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAAG
CATGAAGATGCGCAGAAAGCTGTAGATGAGATGAATGGAAAGGAGCTCAGTGGAAAACAAATTTACGTTGGTCGAGCTCA
GAAAAAAGTGGAACGGCAGACGGAACTTAAGCGCAAATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGTTG
TTAATCTTTATGTGAAAAATCTTGATGATGATATTGATGATGAACGTCTCCGGAAAGCGTTTTCTCCATTTGGTACAATC
ACTAGTGCAAAGGTTATGATGGAAGGTGGTCGCAGCAAAGGGTTTGGTTTCGTATGTTTCTCTTCCCCAGAAGAAGCCAC
TAAAGCAGTTACAGAAATGAACGGTAGAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGC
GCCAGGCTTACCTCACTAACGAGTATATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCCTGTAATCAACCCCTAC
CAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTGTCCCACAGACTCAGAACCATGCTGCATACTATCCTCCTAGCCA
AATTGCTCAACTAAGACCAAGTCCTTGTTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATAAGCCCAGTGCTA
TCTGCCCAGCTGCTCCTAGAGTACCGTTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACGCAG
CGTGTTGCTAACACATCAACACAGACAGTGGGTCCACGTCCTGCAGCTGCTGCTGCTGCAGCTACCCCTGCTGTGCGCAC
GGTTCCACGGTATAAATATGCTGCGGGAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCGGAAGTTACAATGCAAC
AGCCTGCTGTTCATGTACAAGGTCAGGAAACTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAAAGCAAAAGCAA
ATGTTGGGTGAACGGCTCTTTCCTCTTATTGAAGCCATGCGCCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGA
GATTGATAATTCAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCACTCGGTTCTAAGGTTGATGAAGCTGTAGCTGTAC
TACAAGCCCACCAAGCTAAAGAGGCTACCCAGAAAGCAGTTAACAGTGCTACCGGTGTTCCAACT

ORF - retro_pabe_68 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.02 %
Parental protein coverage: 99.84 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMNPSAPSYPMASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDMITRRSLGYAYVNFQQPADAERALD
MNPS.PSYP.ASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRD.ITRRS..YAYVNFQ.P.DAE.ALD
RetrocopyMNPSTPSYPTASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVCRDLITRRSSNYAYVNFQHPKDAEHALD
ParentalTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGY
TMNFDVIKGKPVRIMWSQ.DPSLRKSGVGNIF.KNLDKSI.NKALYDT.SAFGNILSCKVVCDENGSKGY
RetrocopyTMNFDVIKGKPVRIMWSQHDPSLRKSGVGNIFVKNLDKSINNKALYDTVSAFGNILSCKVVCDENGSKGY
ParentalGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDERLKDL
GFVHFET.EAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGA.AKEF.NVYIKNFGEDMDDERLKDL
RetrocopyGFVHFETHEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFPNVYIKNFGEDMDDERLKDL
ParentalFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVERQTELKRKF
FGKFGPALSVKVMTDESGKSKGFGFVSFE.HEDAQKAVDEMNGKEL.GKQIYVGRAQKKVERQTELKRKF
RetrocopyFGKFGPALSVKVMTDESGKSKGFGFVSFEKHEDAQKAVDEMNGKELSGKQIYVGRAQKKVERQTELKRKF
ParentalEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
EQMKQDRITRYQ.VNLYVKNLDD.IDDERLRK.FSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
RetrocopyEQMKQDRITRYQVVNLYVKNLDDDIDDERLRKAFSPFGTITSAKVMMEGGRSKGFGFVCFSSPEEATKAV
ParentalTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAAIPQTQNRA
TEMNGRIVATKPLYVALAQRKEERQA.LTN.YMQRMASVRAVPNPVINPYQPAPPSGYFMAA.PQTQN.A
RetrocopyTEMNGRIVATKPLYVALAQRKEERQAYLTNEYMQRMASVRAVPNPVINPYQPAPPSGYFMAAVPQTQNHA
ParentalAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVANTSTQTM
AYYPPSQIAQLRPSP.WTAQGARPHPFQN.P.AI.PAAPR.PFSTMRPASSQVPRVMSTQRVANTSTQT.
RetrocopyAYYPPSQIAQLRPSPCWTAQGARPHPFQNKPSAICPAAPRVPFSTMRPASSQVPRVMSTQRVANTSTQTV
ParentalGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASAPPQEQKQ
GPRPAAAAAAATPAVRTVP.YKYAAGVRNPQQHLNAQP.VTMQQPAVHVQGQE.LTASMLASAPPQ.QKQ
RetrocopyGPRPAAAAAAATPAVRTVPRYKYAAGVRNPQQHLNAQPEVTMQQPAVHVQGQETLTASMLASAPPQKQKQ
ParentalMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAAQKAVNSA
MLGERLFPLI.AM.PTLAGKITGMLLEIDNSELLHMLESPESL.SKVDEAVAVLQAHQAKEA.QKAVNSA
RetrocopyMLGERLFPLIEAMRPTLAGKITGMLLEIDNSELLHMLESPESLGSKVDEAVAVLQAHQAKEATQKAVNSA
ParentalTGVPT
TGVPT
RetrocopyTGVPT

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 .17 RPM 66 .46 RPM
SRP007412_cerebellum 0 .00 RPM 77 .34 RPM
SRP007412_heart 0 .09 RPM 75 .41 RPM
SRP007412_kidney 0 .03 RPM 161 .86 RPM
SRP007412_liver 0 .12 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_68 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_68 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_68 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_88
Pan troglodytes retro_ptro_8
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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