RetrogeneDB ID:

retro_pabe_2373

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:3:158440853..158442554(-)
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_2373
GCTTTGGGCACCATGAATTCTGATTTTATAAAGGGCAAACCAGTATGCACCATGTGGTCTCAGCGTGAACCATCACTTCG
CAAAAGTCGAATAGGCAACATATTCATTAAAAATCTGAACAAATCTATTGATAATAAAACACTGTATGATACATTTTCTG
CTTTTTGTAACATCGTTTCATGTAAAGTGGTTGGTGATGAAAATGGTTCCAAGGGCTATGGATTTGTACACTTTGAGATG
CAGGAAGCAGCTGAAAGAGGTATTGAAAAAAATGAATGGAATGCTCCTAAATGGTCGCAAAGTATTTGTTGGACGATTTA
AGTCTCATAAAAAACGGGAAACTGAACTTGGAGCTAGGGCAAAAGAGTTCACCAATGTTTACATCAAGAATTTTGGAGAA
GACATGGATGATGAGCACCTTAAGGATCCCTTTGGCAAGTTTGGCCCTGCCGTAAGTGTGAAAGTAATGACTGATGAAAG
TGGAAAATCCGAAGGATTTGGATTTATAAGCTTTGAAAGGCATGAGGATGCACAGAAAGCTGTGGATGAGATTAATGGAA
ATGGAGCTCAATGGAAAACAAATTTATGTTGGTCGAGCTCAGAAAAAGGTGGAACAGCAGACGGAACTTAAGCGCAAATT
TGAACAGATGAAGCAAGATAGGATTACCAGGTACTAGGGTGTTAATCTTTATGTGAAAAATCTTGATGATGGTATTGATG
ATGAACGTCTCCGGAGATGTTTTCTTCATTTGGTATAATCACTAGTGCAAAGGTTGGAGGGTGGTCGCAGCAGGGGTTTG
GTTTTGTATGTTTCTCCTCCCCAGAAAAAGCCACTAAAGCAGTTACAGAAATGAATCGTAGAATTGTGGCCACAAAGCCA
TTGTATTTAGCTTTAGCTCAGCGCAAAGGAGAGTGCCAGGCTCACCTCACTAACCAGTATATGCAGAGAATGCAAGTGTA
CGAGCTGTGCCCAACCCTGTAATCAACCCCTACCAGCTAGCACCTCCTTCAGGTTTCTTAATGGCAGCTATCTCACAGTC
TCAGAACTGTGCTGCATACCCTCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTCGCTGGACTGCTCAGGGTGCCA
GACCTCATCCATTCCAAAATATGCCCGGTGCTACCTGCTCAGCTGCTCCTAGACCACCATTTAGTACTATGAGACCAGCT
TCTTCACAGGTTCCACGAGTCGTGTCAACACAGTATGTTTCTAACACATCAACACAGACAATGGGTCCACGTCCTGCAGC
TGCAGCTGCTGCAACTACTCCTGCTGTCTGCACCGTTCCACAGTATAAATATGCTGCAGGAGTTCGCAATCCTCAGCAAC
ATCTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTGTTCATGTACAAGGTCAGGAACCTTTGACTGCTTCCATG
TTGGCATCTGCCCCTCCTCAAGAGGAAAAGCAAATGTTGGGTGAATGGCTGTTTCCTTTTATTCAAGCCTTGCGCCCTAC
TCTTGCTAGTAAAATCACTGGCATATTGTTGGAGATTGATAATTGAGAACTTCTTCATATGCTCGAGTCTCCAGAGTCAC
TCCGTTATAAGGTTGATGAAGCTGTAGCTATACTACAAGCCCATCAAGCTAAAGAGGCTTCCCAGAAAGCAGTTAACAGC
GCCACTGGTGTTCCAACTGTT

ORF - retro_pabe_2373 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.09 %
Parental protein coverage: 89.47 %
Number of stop codons detected: 2
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGS
AL.TMN.D.IKGKPV..MWSQR.PSLRKS..GNIFIKNL.KSIDNK.LYDTFSAF.NI.SCKVV.DENGS
RetrocopyALGTMNSDFIKGKPVCTMWSQREPSLRKSRIGNIFIKNLNKSIDNKTLYDTFSAFCNIVSCKVVGDENGS
ParentalKGYGFVHFETQEAAERAIEK-MNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDMDDER
KGYGFVHFE.QEAAER.IEK.MNGMLLN.RKVFVGRFKS.K.RE.ELGARAKEFTNVYIKNFGEDMDDE.
RetrocopyKGYGFVHFEMQEAAERGIEK>MNGMLLNGRKVFVGRFKSHKKRETELGARAKEFTNVYIKNFGEDMDDEH
ParentalLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGK-ELNGKQIYVGRAQKKVERQTE
LKD.FGKFGPA.SVKVMTDESGKS.GFGF.SFERHEDAQKAVDE.NG..ELNGKQIYVGRAQKKVE.QTE
RetrocopyLKDPFGKFGPAVSVKVMTDESGKSEGFGFISFERHEDAQKAVDEINGN>ELNGKQIYVGRAQKKVEQQTE
ParentalLKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRK-EFSPFGTITSAKVMMEGGRSKGFGFVCFSSPE
LKRKFEQMKQDRITRY.GVNLYVKNLDDGIDDERLR...FS.FG.ITSAKV...G....GFGFVCFSSPE
RetrocopyLKRKFEQMKQDRITRY*GVNLYVKNLDDGIDDERLRR<MFSSFGIITSAKV--GGWSQQGFGFVCFSSPE
ParentalEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRM-ASVRAVPNPVINPYQPAPPSGYFMAAI
.ATKAVTEMN.RIVATKPLY.ALAQRK.E.QAHLTNQYMQRM.ASVRAVPNPVINPYQ.APPSG..MAAI
RetrocopyKATKAVTEMNRRIVATKPLYLALAQRKGECQAHLTNQYMQRM<ASVRAVPNPVINPYQLAPPSGFLMAAI
ParentalPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRVA
.Q.QN.AAY.PPSQIAQLRPSPRWTAQGARPHPFQNMPGA...AAPRPPFSTMRPASSQVPRV.STQ.V.
RetrocopySQSQNCAAYPPPSQIAQLRPSPRWTAQGARPHPFQNMPGATCSAAPRPPFSTMRPASSQVPRVVSTQYVS
ParentalNTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA
NTSTQTMGPRPAAAAAA.TPAV.TVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA
RetrocopyNTSTQTMGPRPAAAAAATTPAVCTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLASA
ParentalPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEAA
PPQE.KQMLGE.LFP.IQA..PTLA.KITG.LLEIDN.ELLHMLESPESLR.KVDEAVA.LQAHQAKEA.
RetrocopyPPQEEKQMLGEWLFPFIQALRPTLASKITGILLEIDN*ELLHMLESPESLRYKVDEAVAILQAHQAKEAS
ParentalQKAVNSATGVPTV
QKAVNSATGVPTV
RetrocopyQKAVNSATGVPTV

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 66 .46 RPM
SRP007412_cerebellum 0 .24 RPM 77 .34 RPM
SRP007412_heart 0 .06 RPM 75 .41 RPM
SRP007412_kidney 0 .10 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_2373 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_2373 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_2373 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Gorilla gorilla retro_ggor_1986
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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