RetrogeneDB ID:

retro_rnor_175

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:2:150259444..150260557(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000029749
Aliases:Pabpc4l, RGD1559517
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Pabpc4
Ensembl ID:ENSRNOG00000015642
Aliases:None
Description:polyadenylate-binding protein 4 [Source:RefSeq peptide;Acc:NP_001094008]


Retrocopy-Parental alignment summary:






>retro_rnor_175
ATGAGTGTGGAAACTAAGTACCGTGCGGCTTCCCTGTATGTGGGTGACCTCCACGAAGATGTCACGGAGGACCTTCTGTT
CAGGAAGTTCAACACAGTAGGACCTGTGTTGTCCATCCGAATCTGCAGGGACCTGATTTCCCATCGTTCACTAGGCTACG
GCTATGTCAATTTTCTCCAGGTGGGTGATGCCCAGAAGGCCCTAGAAACTATGAACTTTGACTTGATCAAAGGTAAATCC
ATCCGTCTCATGTGGTCTCAACGGGATGCTTGCCTAAGGAAGTCGGGAATCGGGAATGTGTTTATCAAGAATCTGGACAA
ATCCATTGACAACAAAACCTTGTATGAACACTTCTCACCTTTCGGAAAGATCATGTCCTCCAAGGTGATGACTGATGAAG
AAGGCTCCAAGGGTTACGGCTTCGTGCACTACCAGGACCAGAGAGCAGCTGACAGGGCCATTGAGGAGATGAATGGGAAG
CTGCTGAGGGACAGCACTTTGTTCGTGGCCAGATTCAAAAGCCGTAAGGATCGGGAGGCTGAGCTCAGAGAGAAACCCGC
CGAATTCACTAATGTGTATATCAAAAATTTTGGGGATGACATGGACGATGAGAGCCTCAGGTCAGTTTTCAGCAAATACG
GCCAAACTTTGAGCGTTAAGGTGATGAAAGATGCCTCTGGCAAGTCCAAACGCTTTGGATTTGTGAGCTTTGATAGCCAC
AAGGCTGCGAAAAACGCAGTTGAGGACATGAATGGGCGGGACATAAACGGGCAGACAATTTTTGTAGGCAGAGCCCAGAA
GAAGGTGGAAAGACAGGCGGAGTTAAAGGAAATGTTTGAGCAAATGAAAAAGGAAAGAATCCGTGCCCGCCAGGCAGCTA
AGCTCTACATTAAGAACCTGGATGACACCATCGATGATGAAACACTGCGCAAGGAATTTTCTGTCTTTGGGTCCATTTGC
AGAGTTAAAGTGATGCAGGAAGCAGGGCAGAGCAAAGGGTTTGGCTTGATCTGCTTCTTCTCCCCGGAGGCAGCTGCTAA
AGCAATGGCTGAGATGAATGGCCGCATCCTGGGCTCCAAACCCCTCAACATTGCACTGGGTCAGAAGCACTGA

ORF - retro_rnor_175 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 68.77 %
Parental protein coverage: 56.68 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSSYPMASLYVGDLHSDVTEAMLYEKFSPAGPVLSIRVCRDMITRRSLGYAYVNFQQPADAERALDTMNFD
..Y..ASLYVGDLH.DVTE..L..KF...GPVLSIR.CRD.I..RSLGY.YVNF.Q..DA..AL.TMNFD
RetrocopyTKYRAASLYVGDLHEDVTEDLLFRKFNTVGPVLSIRICRDLISHRSLGYGYVNFLQVGDAQKALETMNFD
ParentalVIKGKPIRIMWSQRDPSLRKSGVGNVFIKNLDKSIDNKALYDTFSAFGNILSCKVVCDENGSKGYAFVHF
.IKGK.IR.MWSQRD..LRKSG.GNVFIKNLDKSIDNK.LY..FS.FG.I.S.KV..DE.GSKGY.FVH.
RetrocopyLIKGKSIRLMWSQRDACLRKSGIGNVFIKNLDKSIDNKTLYEHFSPFGKIMSSKVMTDEEGSKGYGFVHY
ParentalETQEAANKAIEKMNGMLLNDRKVFVGRFKSRKEREAELGAKAKEFTNVYIKNFGEEVDDENLRELFSQFG
..Q.AA..AIE.MNG.LL.D...FV.RFKSRK.REAEL..K..EFTNVYIKNFG...DDE.LR..FS..G
RetrocopyQDQRAADRAIEEMNGKLLRDSTLFVARFKSRKDREAELREKPAEFTNVYIKNFGDDMDDESLRSVFSKYG
ParentalKTLSVKVMRDCSGKSKGFGFVSYEKHEDANKAVEEMNGKEMSGKSIFVGRAQKKVERQAELKRKFEQLKQ
.TLSVKVM.D.SGKSK.FGFVS...H..A..AVE.MNG....G..IFVGRAQKKVERQAELK..FEQ.K.
RetrocopyQTLSVKVMKDASGKSKRFGFVSFDSHKAAKNAVEDMNGRDINGQTIFVGRAQKKVERQAELKEMFEQMKK
ParentalERISRYQGVNLYIKNLDDTIDDEKLRKEFSPFGSITSAKVMLEDGRSKGFGFVCFSSPEEATKAVTEMNG
ERI...Q...LYIKNLDDTIDDE.LRKEFS.FGSI...KVM.E.G.SKGFG..CF.SPE.A.KA..EMNG
RetrocopyERIRARQAAKLYIKNLDDTIDDETLRKEFSVFGSICRVKVMQEAGQSKGFGLICFFSPEAAAKAMAEMNG
ParentalRIVGSKPLYVALAQR
RI.GSKPL..AL.Q.
RetrocopyRILGSKPLNIALGQK

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 .22 RPM 34 .01 RPM
SRP017611_kidney 0 .00 RPM 70 .62 RPM
SRP017611_liver 0 .00 RPM 44 .98 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_175 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_175 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_175 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_109
Pan troglodytes retro_ptro_2093
Gorilla gorilla retro_ggor_2127
Pongo abelii retro_pabe_2563
Callithrix jacchus retro_cjac_214
Canis familiaris retro_cfam_837
Parental genes homology:
Parental genes homology involve 29 parental genes, and 65 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000115352 retrocopies
retro_amel_107, retro_amel_676,
Bos taurus ENSBTAG000000171253 retrocopies
retro_btau_1492, retro_btau_28, retro_btau_656,
Canis familiaris ENSCAFG000000030812 retrocopies
retro_cfam_45, retro_cfam_837,
Choloepus hoffmanni ENSCHOG000000053273 retrocopies
retro_chof_1150, retro_chof_1182, retro_chof_1274,
Callithrix jacchus ENSCJAG000000025123 retrocopies
retro_cjac_214, retro_cjac_2722, retro_cjac_284,
Cavia porcellus ENSCPOG000000095522 retrocopies
retro_cpor_1330, retro_cpor_77,
Equus caballus ENSECAG000000093962 retrocopies
retro_ecab_2, retro_ecab_502,
Felis catus ENSFCAG000000152542 retrocopies
retro_fcat_116, retro_fcat_545,
Homo sapiens ENSG000000906212 retrocopies
retro_hsap_109, retro_hsap_74,
Gorilla gorilla ENSGGOG000000040023 retrocopies
retro_ggor_2127, retro_ggor_87, retro_ggor_916,
Loxodonta africana ENSLAFG000000001513 retrocopies
retro_lafr_1144, retro_lafr_390, retro_lafr_597,
Microcebus murinus ENSMICG000000166331 retrocopy
retro_mmur_675,
Myotis lucifugus ENSMLUG000000120682 retrocopies
retro_mluc_228, retro_mluc_397,
Macaca mulatta ENSMMUG000000074971 retrocopy
retro_mmul_178,
Monodelphis domestica ENSMODG000000176572 retrocopies
retro_mdom_1090, retro_mdom_1805,
Mustela putorius furoENSMPUG000000144142 retrocopies
retro_mputfur_152, retro_mputfur_546,
Mus musculus ENSMUSG000000112577 retrocopies
retro_mmus_2006, retro_mmus_2326, retro_mmus_2327, retro_mmus_798, retro_mmus_801, retro_mmus_803, retro_mmus_805,
Nomascus leucogenys ENSNLEG000000119282 retrocopies
retro_nleu_1517, retro_nleu_62,
Oryctolagus cuniculus ENSOCUG000000005622 retrocopies
retro_ocun_153, retro_ocun_792,
Otolemur garnettii ENSOGAG000000040671 retrocopy
retro_ogar_71,
Ochotona princeps ENSOPRG000000119841 retrocopy
retro_opri_1133,
Pongo abelii ENSPPYG000000015062 retrocopies
retro_pabe_190, retro_pabe_2563,
Pan troglodytes ENSPTRG000000005733 retrocopies
retro_ptro_101, retro_ptro_2093, retro_ptro_8,
Rattus norvegicus ENSRNOG000000030761 retrocopy
retro_rnor_1374,
Rattus norvegicus ENSRNOG000000086393 retrocopies
retro_rnor_1228, retro_rnor_2321, retro_rnor_265,
Rattus norvegicus ENSRNOG00000015642 2 retrocopies
retro_rnor_175 , retro_rnor_92,
Sarcophilus harrisii ENSSHAG000000181391 retrocopy
retro_shar_823,
Sus scrofa ENSSSCG000000036603 retrocopies
retro_sscr_1210, retro_sscr_974, retro_sscr_975,
Tursiops truncatus ENSTTRG000000143402 retrocopies
retro_ttru_1117, retro_ttru_246,


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