RetrogeneDB ID:

retro_mmul_895

Retrocopy
location
Organism:Rhesus macaque (Macaca mulatta)
Coordinates:11:110291978..110293700(-)
Located in intron of:ENSMMUG00000031568
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MMU.3044
Ensembl ID:ENSMMUG00000017786
Aliases:None
Description:polyadenylate-binding protein 1 [Source:RefSeq peptide;Acc:NP_001244826]


Retrocopy-Parental alignment summary:






>retro_mmul_895
GCGGACGCGGAGCGTGCTTTGGACACCATGAATTTTGATGTTATAAAGGGCAAACCAGTACGCATCATGTGGTCTCAGCG
TGATCCATCACTTCGCAAAAGTGGAGTAGGCAACATATTCATTAAAAATCTGGACAAATCCATTGATAATAAAGCACTGT
ATGATACATTTTCTGCTTTTGGTAACATCCTTTCATGTAAGGTGGTTTGTGATGAAAATGGTTCCAAGGGCTATGGATTT
GTACACTTTGAGACGCAGGAAGCAGCTGAACGAGCTATTGAAAAAATGAATGGAATGCTCCTGAATGATCGCAAAGTATT
TGTTGGACGATTTAAGTCTCGTAAAGAACGAGAAGCTGAACTTGGAGCTAGGGCAAAAGAATTCACCAATGTTTACATCA
AGAATTTTGGAGAAGACATGGATGATGAGCGCCTTAAGGATCTCTTTGGCAAGTTTGGGCCTGCCTTAAGTGTGAAAGTA
GTGACTGATGAAAGTGGAAAATCCAAAGGATTTGGATTTGTAAGCTTTGAAAGGCATGAAGATGCACGGAAAGCTGTGGA
TGAGATGAATGGAAAGGAGCTCAATGGAAAACAAATTTATGTTGGTCGAGCTCAGAAAAAGGTGGAACGGCAGACGGAAC
TTAAGCGCAAATTTGAACAGATGAAGCAAGATAGGATCACCAGATACCAGGGTGTTAATCTTTATGTGAAAAATCTTGAT
GATGGTATTGATGATGAACGTCTCCGGAAAGAGTTTTCTCCATTTGGTACAATCACTAGTGCAAAGGTTATGATGGAGGG
TGGTCGCAGCAAAGGGTTTGGTTTTGTATGTTTCTCCTCCCCAGAAGAAGCCACTAAAGCAGTTACAGAAATGAACGGTA
GAATTGTGGCCACAAAGCCATTGTATGTAGCTTTAGCTCAGCGCAAAGAAGAGCGCCAGGCTCACCTCACTAACCAGTAT
ATGCAGAGAATGGCAAGTGTACGAGCTGTGCCCAACCCTGTAATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTT
CATGGCAGCTATCCCACAGACTCAGAACCGTGCTGCATACTATCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTC
GCTGGACTGCTCAGGGTGCCAGACCTCATCCATTCCAAAATATGCCCGGTGCTATCTGCCCAGCTGCTCCTAGACCACCA
TTTAGTACTATGAGACCAGCTTCTTCACAGGTTCCACGAGTCATGTCAACACAGCGTGTTGCTAACACATCAACACAGAC
AATGGGTCCACGTCCTGCAGCTGCAGCTGCTGCAGCTACTCCTGCTGTCCGCACCGTTCCACAGTATAAATATGCTGCAG
GAGTTCGCAATCCTCAGCAACATCTTAATGCACAGCCACAAGTTACAATGCAACAGCCTGCTGTTCATGTACAAGGTCAG
GAACCTTTGACTGCTTCCATGTTGGCATCTGCCCCTCCTCAAGAGCAAAAGCAAATGTTGGGTGAACGGCTGTTTCCTCT
TATTCAAGCCATGCACCCTACTCTTGCTGGTAAAATCACTGGCATGTTGTTGGAGATTGATAATTCAGAACTTCTTCATA
TGCTCGAGTCTCCTGAGTCACTCCGTTCTAAGGTTGATGAAGCTGTAGCTGTACTACAAGCCCACCAAGCTAAAGAGGCT
GCCCAGAAAGCAGTTCACAATGCCACCGGTGTTCCAACTGTT

ORF - retro_mmul_895 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.13 %
Parental protein coverage: 90.25 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC
ADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC
RetrocopyADAERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFIKNLDKSIDNKALYDTFSAFGNILSCKVVC
ParentalDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDM
DENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDM
RetrocopyDENGSKGYGFVHFETQEAAERAIEKMNGMLLNDRKVFVGRFKSRKEREAELGARAKEFTNVYIKNFGEDM
ParentalDDERLKDLFGKFGPALSVKVMTDESGKSKGFGFVSFERHEDAQKAVDEMNGKELNGKQIYVGRAQKKVER
DDERLKDLFGKFGPALSVKV.TDESGKSKGFGFVSFERHEDA.KAVDEMNGKELNGKQIYVGRAQKKVER
RetrocopyDDERLKDLFGKFGPALSVKVVTDESGKSKGFGFVSFERHEDARKAVDEMNGKELNGKQIYVGRAQKKVER
ParentalQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSS
QTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSS
RetrocopyQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAKVMMEGGRSKGFGFVCFSS
ParentalPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAA
PEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAA
RetrocopyPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPNPVINPYQPAPPSGYFMAA
ParentalIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFSTMRPASSQVPRVMSTQRV
IPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAI.PAAPRPPFSTMRPASSQVPRVMSTQRV
RetrocopyIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAICPAAPRPPFSTMRPASSQVPRVMSTQRV
ParentalANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS
ANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS
RetrocopyANTSTQTMGPRPAAAAAAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQPAVHVQGQEPLTASMLAS
ParentalAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA
APPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA
RetrocopyAPPQEQKQMLGERLFPLIQAMHPTLAGKITGMLLEIDNSELLHMLESPESLRSKVDEAVAVLQAHQAKEA
ParentalAQKAVNSATGVPTV
AQKAV..ATGVPTV
RetrocopyAQKAVHNATGVPTV

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 2 .58 RPM 44 .82 RPM
SRP007412_brain_prefrontal_cortex 2 .62 RPM 93 .45 RPM
SRP007412_cerebellum 4 .91 RPM 49 .34 RPM
SRP007412_heart 4 .24 RPM 52 .23 RPM
SRP007412_kidney 8 .45 RPM 91 .31 RPM
SRP007412_liver 6 .41 RPM 157 .39 RPM
SRP007412_testis 17 .23 RPM 975 .73 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_895 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_895 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmul_895 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 24 parental genes, and 48 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 ENSMMUG000000074971 retrocopy
retro_mmul_178,
Macaca mulatta ENSMMUG00000017786 2 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 ENSPPYG000000187903 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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