RetrogeneDB ID:

retro_rnor_42

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:6:20631349..20632939(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000030058
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Kpna2
Ensembl ID:ENSRNOG00000015329
Aliases:Kpna2, importin
Description:importin subunit alpha-2 [Source:RefSeq peptide;Acc:NP_445935]


Retrocopy-Parental alignment summary:






>retro_rnor_42
ATGTCCACCAACGAGAATGCTAACTCAACAGCTGCCCGGCTTAACAGATTCAAGAACAAGGGGAAAGACAGTACAGAAAT
GCGGCGCCGCCGAATAGAGGTTAATGTGGAACTTAGGAAAGCTAAAAAAGATGACCAGATGCTGAAAAGGAGGAACGTCA
GCTCATTCCCTGATGACGCTACTTCTCCACTACAGGAAAACCGAAACAACCAGGGTACTGTAAATTGGTCTGTTGAGGAC
ATTGTTAAAGGCATAAACAGTAACAATTTGGAAAGCCAGCTCCAAGCTACTCAAGCTGCTCGGAAACTGCTTTCAAGAGA
GAAGCAGCCTCCTATAGACAACATCATCCGGGCTGGTTTGATCCCAAAATTTGTGTCCTTCTTGGGCAAAACGGATTGTA
GTCCCATTCAGTTTGAATCTGCTTGGGCGCTCACCAACATTGCTTCTGGAACATCCGAACAGACCAAAGCTGTGGTGGAT
GGAGGTGCTATCCCAGCATTTATTTCTCTCTTGGCGTCGCCCCATGCTCACATCAGCGAGCAAGCTGTGTGGGCTCTTGG
AAACATTGCAGGTGATGGCTCAGTTTTCCGAGACTTGGTTATCAAACATGGTGCAATTGACCCACTGTTGGCACTTCTCG
CAGTTCCTGATCTGTCATCCTTGGCATGTGGTTACTTGCGGAATCTTACCTGGACACTTTCAAACCTCTGTCGGAACAAG
AATCCTGCACCCCCCTTAGATGCTGTTGAGCAGATCCTTCCTACTCTAGTTCGACTCCTACACCACAACGATCCAGAAGT
ATTAGCAGACTCCTGCTGGGCCATTTCCTATCTGACTGATGGGCCGAATGAGCGCATCGAGATGGTTGTGAAGAAGGGAG
TTGTTCCCCAACTTGTGAAGCTTCTAGGAGCTACTGAACTGCCCATTGTGACGCCGGCACTGAGAGCCATAGGGAATATT
GTCACCGGAACAGATGAACAGACTCAGAAAGTGATCGATGCAGGGGCACTTGCAGTCTTTCCCAGCCTGCTGACAAACCC
CAAAACTAATATTCAGAAGGAGGCCACATGGACAATGTCGAACATTACCGCCGGGCGCCAGGACCAGATACAGCAAGTGG
TGAATCACGGCCTCGTCCCATTTCTCATTGGTGTCCTCTCTAAGGCAGACTTTAAGACACAGAAGGAAGCCGCATGGGCT
ATAACCAACTACACCAGCGGCGGGACTGTTGAACAGATTGTGTATCTGGTTCATTGTGGAATAATAGAACCCTTGATGAA
CCTCTTGAGTGCAAAAGATACCAAAATTATTCAGGTTATTCTTGATGCTATTTCAAATATCTTTCAGGCTGCAGAGAAAC
TAGGTGAGACAGAAAAACTCAGTATAATGATTGAAGAGTGTGGAGGCTTGGATAAAATTGAAGCCCTACAGAGCCATGAG
AACGAGTCTGTGTACAAGGCCTCGTTGAACCTAATTGAGAAGTACTTCTCAGTGGAGGAAGAGGAAGATCAAAATGTGGT
GCCAGAAACTACCTCTGAAGGCTTCGCCTTCCAAGTTCAGGATGGAGCTCCCGGGACCTTTAACTTCTAA

ORF - retro_rnor_42 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.81 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSTNENANSTAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
MSTNENANSTAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
RetrocopyMSTNENANSTAARLNRFKNKGKDSTEMRRRRIEVNVELRKAKKDDQMLKRRNVSSFPDDATSPLQENRNN
ParentalQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFES
QGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFES
RetrocopyQGTVNWSVEDIVKGINSNNLESQLQATQAARKLLSREKQPPIDNIIRAGLIPKFVSFLGKTDCSPIQFES
ParentalAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKHGAIDPLL
AWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKHGAIDPLL
RetrocopyAWALTNIASGTSEQTKAVVDGGAIPAFISLLASPHAHISEQAVWALGNIAGDGSVFRDLVIKHGAIDPLL
ParentalALLAVPDLSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTD
ALLAVPDLSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTD
RetrocopyALLAVPDLSSLACGYLRNLTWTLSNLCRNKNPAPPLDAVEQILPTLVRLLHHNDPEVLADSCWAISYLTD
ParentalGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTN
GPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTN
RetrocopyGPNERIEMVVKKGVVPQLVKLLGATELPIVTPALRAIGNIVTGTDEQTQKVIDAGALAVFPSLLTNPKTN
ParentalIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLVGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCG
IQKEATWTMSNITAGRQDQIQQVVNHGLVPFL.GVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCG
RetrocopyIQKEATWTMSNITAGRQDQIQQVVNHGLVPFLIGVLSKADFKTQKEAAWAITNYTSGGTVEQIVYLVHCG
ParentalIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQSHENESVYKASLN
IIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQSHENESVYKASLN
RetrocopyIIEPLMNLLSAKDTKIIQVILDAISNIFQAAEKLGETEKLSIMIEECGGLDKIEALQSHENESVYKASLN
ParentalLIEKYFSVEEEEDQNVVPETTSEGFAFQVQDGAPGTFNF
LIEKYFSVEEEEDQNVVPETTSEGFAFQVQDGAPGTFNF
RetrocopyLIEKYFSVEEEEDQNVVPETTSEGFAFQVQDGAPGTFNF

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 .29 RPM 6 .83 RPM
SRP017611_kidney 1 .05 RPM 18 .42 RPM
SRP017611_liver 0 .67 RPM 19 .43 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

7 EST(s) were mapped to retro_rnor_42 retrocopy
EST ID Start End Identity Match Mis-match Score
BP498243 20631265 20631762 99.6 494 2 491
BP501952 20631247 20631832 99.7 557 1 552
CA339272 20631241 20631805 99.5 561 3 558
CB709559 20631543 20631856 99.7 312 0 310
DW298887 20631419 20631567 99.4 147 1 146
DW307852 20631419 20631563 100 143 0 143
DW322989 20631419 20631567 100 144 0 144

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_42 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_42 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 25 parental genes, and 72 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184113 retrocopies
retro_amel_1161, retro_amel_1318, retro_amel_440,
Bos taurus ENSBTAG000000122251 retrocopy
retro_btau_1830,
Canis familiaris ENSCAFG000000115982 retrocopies
retro_cfam_648, retro_cfam_90,
Cavia porcellus ENSCPOG000000263181 retrocopy
retro_cpor_46,
Dasypus novemcinctus ENSDNOG000000191516 retrocopies
retro_dnov_1184, retro_dnov_1811, retro_dnov_2161, retro_dnov_2279, retro_dnov_379, retro_dnov_693,
Equus caballus ENSECAG000000205732 retrocopies
retro_ecab_1017, retro_ecab_1123,
Echinops telfairi ENSETEG000000044452 retrocopies
retro_etel_346, retro_etel_347,
Felis catus ENSFCAG000000019362 retrocopies
retro_fcat_1176, retro_fcat_921,
Homo sapiens ENSG000001824811 retrocopy
retro_hsap_2950,
Gorilla gorilla ENSGGOG000000275352 retrocopies
retro_ggor_2044, retro_ggor_2609,
Myotis lucifugus ENSMLUG000000279467 retrocopies
retro_mluc_1034, retro_mluc_1258, retro_mluc_1414, retro_mluc_288, retro_mluc_50, retro_mluc_52, retro_mluc_993,
Macaca mulatta ENSMMUG000000182563 retrocopies
retro_mmul_1140, retro_mmul_1635, retro_mmul_1947,
Monodelphis domestica ENSMODG000000038971 retrocopy
retro_mdom_271,
Mus musculus ENSMUSG000000183621 retrocopy
retro_mmus_229,
Nomascus leucogenys ENSNLEG000000017493 retrocopies
retro_nleu_1052, retro_nleu_1634, retro_nleu_208,
Oryctolagus cuniculus ENSOCUG000000159134 retrocopies
retro_ocun_1765, retro_ocun_1916, retro_ocun_426, retro_ocun_690,
Otolemur garnettii ENSOGAG000000276727 retrocopies
retro_ogar_1044, retro_ogar_1142, retro_ogar_1757, retro_ogar_2008, retro_ogar_464, retro_ogar_477, retro_ogar_936,
Pongo abelii ENSPPYG000000085691 retrocopy
retro_pabe_3501,
Pteropus vampyrus ENSPVAG000000049762 retrocopies
retro_pvam_1321, retro_pvam_1333,
Rattus norvegicus ENSRNOG000000107681 retrocopy
retro_rnor_592,
Rattus norvegicus ENSRNOG000000149451 retrocopy
retro_rnor_987,
Rattus norvegicus ENSRNOG00000015329 1 retrocopy
retro_rnor_42 ,
Sarcophilus harrisii ENSSHAG000000113911 retrocopy
retro_shar_165,
Tupaia belangeri ENSTBEG0000000627414 retrocopies
retro_tbel_1635, retro_tbel_2077, retro_tbel_2672, retro_tbel_2792, retro_tbel_290, retro_tbel_3638, retro_tbel_4120, retro_tbel_4358, retro_tbel_4414, retro_tbel_4435, retro_tbel_4558, retro_tbel_810, retro_tbel_97, retro_tbel_976,
Vicugna pacos ENSVPAG000000018553 retrocopies
retro_vpac_124, retro_vpac_162, retro_vpac_163,




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