RetrogeneDB ID:

retro_rnor_1228

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:16:41375986..41377129(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Pabpc1
Ensembl ID:ENSRNOG00000008639
Aliases:Pabpc1, Pabp, Pabp1
Description:Polyadenylate-binding protein 1 [Source:UniProtKB/Swiss-Prot;Acc:Q9EPH8]


Retrocopy-Parental alignment summary:






>retro_rnor_1228
GAGCTCAGTGGAAAACAGATTTATGTTGGTAGAGCTCAGAAAAAAGTGGAATGGCAGACAGAACTTAAGCACAAATTTGA
GCAGATGAAGCAAGACAAGATCACCAGATATCAGGGTGTTAACCTTTATGTGAAAAATCTTGATGACAGTATTGATGAGC
GTCTCCGGAAACAGTTTTCTCCATTTGGTACAATCACTAGTGCAAAAGTAATGATGGAGGGTGGGCACAGCAAAAGATTC
GGTTTTATATGTTTCTCCTCCCATGAAGAAGCCTTTAAAGCAGTTATGGAGATGAATGGTAAAATTGTGGCCACCAAGCC
ACTCTATGTAGCTTTAGCTCAGCACAAAGAAGAGTGCCAGACTCACCTCACTAACCAGTATATGCACAGGATGGCAAGTG
TACGAACTGTGCCCAACCCTGTTATCAACCCCTACCAGCCAGCACCTCCTTCAGGTTACTTCATGGCAGCTATCCCACAG
ACTCAGAACCATGCTGCATACTACCCTCCTAGCCAAATTGCTCAACTAAGACCAAGTCCTTGCTGGATTGCTCAGGGTGC
CAGACCTCATCCATTCCAGAATATGCCCGGTGCTATCTGCCCAGCTGCTCCTAGACCACCATTTAGTATGATGAGACCAG
CTTCCTCATAGGTTCCACGAGTCATGCCAACACAGCATGTTGCTAACACATCAACACAGACAATGGGTCCACGTTCTGCA
GCTGTTGTTACTGCAGCCACTCCTGCTGTCCACACTGTTCCCCAGTATAAATATGCTGCGGGAGTCTGCAATCCCCAGCA
ATATCTTAATGCACAGCCACAAGTTACCATGCAACAGCCTGCGGTTCATGTGCAAGGTCAAGAACATTTAACTGCTTCCA
TGTTGGCATCTGCACCCCCGCAGGAGCAAAAGCAAATGTTGGGTGAATGGCTGTTTCCTCTTATTCAAGTCCTGCACCCT
TCTCCTGCTGGCAAAATTACTGGCATGCTGTTGGAGATTGATAACTCAGAATTGCTTCACATGCTTGCATCTCCAGAGTC
TCTCCACTCAAAAGTAGATGAAGCTGTAGCTCTACTACAAGCCCACCAAGTGAAAGAGGCTGCTCAGAAAATAGTGAACA
GTGCTACTGGTGTTCCAACTGTC

ORF - retro_rnor_1228 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.74 %
Parental protein coverage: 60.06 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalELNGKQIYVGRAQKKVERQTELKRKFEQMKQDRITRYQGVNLYVKNLDDGIDDERLRKEFSPFGTITSAK
EL.GKQIYVGRAQKKVE.QTELK.KFEQMKQD.ITRYQGVNLYVKNLDD.ID.ERLRK.FSPFGTITSAK
RetrocopyELSGKQIYVGRAQKKVEWQTELKHKFEQMKQDKITRYQGVNLYVKNLDDSID-ERLRKQFSPFGTITSAK
ParentalVMMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEERQAHLTNQYMQRMASVRAVPN
VMMEGG.SK.FGF.CFSS.EEA.KAV.EMNG.IVATKPLYVALAQ.KEE.Q.HLTNQYM.RMASVR.VPN
RetrocopyVMMEGGHSKRFGFICFSSHEEAFKAVMEMNGKIVATKPLYVALAQHKEECQTHLTNQYMHRMASVRTVPN
ParentalPVINPYQPAPPSGYFMAAIPQTQNRAAYYPPSQIAQLRPSPRWTAQGARPHPFQNMPGAIRPAAPRPPFS
PVINPYQPAPPSGYFMAAIPQTQN.AAYYPPSQIAQLRPSP.W.AQGARPHPFQNMPGAI.PAAPRPPFS
RetrocopyPVINPYQPAPPSGYFMAAIPQTQNHAAYYPPSQIAQLRPSPCWIAQGARPHPFQNMPGAICPAAPRPPFS
ParentalTMRPASSQVPRVMSTQRVANTSTQTMGPRPAAAATAATPAVRTVPQYKYAAGVRNPQQHLNAQPQVTMQQ
.MRPASS.VPRVM.TQ.VANTSTQTMGPR.AA..TAATPAV.TVPQYKYAAGV.NPQQ.LNAQPQVTMQQ
RetrocopyMMRPASS*VPRVMPTQHVANTSTQTMGPRSAAVVTAATPAVHTVPQYKYAAGVCNPQQYLNAQPQVTMQQ
ParentalPAVHVQGQEPLTASMLASAPPQEQKQMLGERLFPLIQAMHPSLAGKITGMLLEIDNSELLHMLESPESLR
PAVHVQGQE.LTASMLASAPPQEQKQMLGE.LFPLIQ..HPS.AGKITGMLLEIDNSELLHML.SPESL.
RetrocopyPAVHVQGQEHLTASMLASAPPQEQKQMLGEWLFPLIQVLHPSPAGKITGMLLEIDNSELLHMLASPESLH
ParentalSKVDEAVAVLQAHQAKEAAQKAVNSATGVPTV
SKVDEAVA.LQAHQ.KEAAQK.VNSATGVPTV
RetrocopySKVDEAVALLQAHQVKEAAQKIVNSATGVPTV

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
SRP017611_brain 0 .00 RPM 141 .49 RPM
SRP017611_kidney 0 .00 RPM 275 .36 RPM
SRP017611_liver 0 .00 RPM 207 .09 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_1228 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_1228 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_1228 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 50 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 ENSPPYG000000187903 retrocopies
retro_pabe_2373, retro_pabe_68, retro_pabe_854,
Pteropus vampyrus ENSPVAG000000166402 retrocopies
retro_pvam_10, retro_pvam_855,
Rattus norvegicus ENSRNOG000000030761 retrocopy
retro_rnor_1374,
Rattus norvegicus ENSRNOG00000008639 3 retrocopies
retro_rnor_1228 , retro_rnor_2321, retro_rnor_265,
Rattus norvegicus ENSRNOG000000156422 retrocopies
retro_rnor_175, retro_rnor_92,
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,




Copyright © RetrogeneDB 2014-2017