RetrogeneDB ID:

retro_rnor_670

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:10:11229637..11230558(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Aurka
Ensembl ID:ENSRNOG00000004479
Aliases:Aurka, ARK-1, Stk6
Description:aurora kinase A [Source:RefSeq peptide;Acc:NP_695208]


Retrocopy-Parental alignment summary:






>retro_rnor_670
GTCTCCAGGCCTGTTAAGACCACAGTTCCCTTCGGTCCGAAACGAGTCTTGGTGACTGAGCAGATTCCTTCTCAGCACCC
AGGATCAGCGAGCAGTGGCCAGGCCCAGTGGGTCCTGTGTCCTTCCAACTCCCAGCGTGTCCCTCCACAAGCACAGAAAC
CTGTCGCAGGTCAGAAGTCAGTGCTAAAGCAGTTGCCAGCTGCCAGCGTTCCTCGACCTGTGTCCCGGCTAAGTAACCCC
CCAGAAGAGTGAGCAGCCACAGCCTGCAGCCTCGGGAAATTCTGAAAAGGAACAGACATCCATCCAGAAAACTGAAGACT
CAAAAAGAAGGGAGTGGACTTTGGAAGATTTTGACATTGGCCGCCCACTAGGAAAAGGGAAGTTTGGAAATGTCTATTTG
GCGAGGGAGAAGCAAAGCAAGTTCATCCTGGCTCTGAAGATGCTGTTTAAAGTACAGCTGGAGAAGCAGGTGTGGAGCAC
CAGCTTCGGAGAGAAGTGGAGATCCAGTCCCACCTGCGGCACCCCAACATCCTCGGGTTGTATGGGTATTCCCATGACGC
CACCAGAGTTTATCTAATTCTAGAATATGCGCCCCTTGGAACAGTGTATAGAGAGCTTCAAAAACTCTCCAAGTTTGACG
AGCAGAGAATAGCTACCTACATCACGGAGTTGGCGAATGCTTTGTCCTAGTGCCATTCAAAGAGAGTCATCCACAGAGAC
ATCAAGCCAGAGAACCCGCTGCTTGGCTCAAATGGGGAGTTGAAGCTCGCAGACTTCGGGTGGTCTGCGCATGCTCCATC
TTCCAGGAGACCCACGCTGTACTGCACCGTGGACTACCTGCCCCCGGAGATGATTGAAGGGCAGATGCATGATGAGGAGG
TGGATCTCTGGAGCCTGGGTGTGCTCTGCTATGAATTCCTA

ORF - retro_rnor_670 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.26 %
Parental protein coverage: 77.58 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVSRPVKSTVPFGPKRVLVTEQIPSQHPGSASSGQAQRVLCPSNSQRVPPQAQKPVAGQKPVLKQLPAASG
VSRPVK.TVPFGPKRVLVTEQIPSQHPGSASSGQAQ.VLCPSNSQRVPPQAQKPVAGQK.VLKQLPAAS.
RetrocopyVSRPVKTTVPFGPKRVLVTEQIPSQHPGSASSGQAQWVLCPSNSQRVPPQAQKPVAGQKSVLKQLPAASV
ParentalPRPASRLSNP-QKSEQPQPAASGNNSEKEQTSIQKTEDSKKRQWTLEDFDIGRPLGKGKFGNVYLAREKQ
PRP.SRLSNP.QKSEQPQPAASGN.SEKEQTSIQKTEDSK.R.WTLEDFDIGRPLGKGKFGNVYLAREKQ
RetrocopyPRPVSRLSNP>QKSEQPQPAASGN-SEKEQTSIQKTEDSKRREWTLEDFDIGRPLGKGKFGNVYLAREKQ
ParentalSKFILALKVLFKVQLEK-AGVEHQLRREVEIQSHLRHPNILRLYGYFHDATRVYLILEYAPLGTVYRELQ
SKFILALK.LFKVQLEK.AGVEHQLRREVEIQSHLRHPNIL.LYGY.HDATRVYLILEYAPLGTVYRELQ
RetrocopySKFILALKMLFKVQLEK<AGVEHQLRREVEIQSHLRHPNILGLYGYSHDATRVYLILEYAPLGTVYRELQ
ParentalKLSKFDEQRTATYITELANALSYCHSKRVIHRDIKPENLLLGSNGELKIADFGWSVHAPSSRRTTLCGTL
KLSKFDEQR.ATYITELANALS.CHSKRVIHRDIKPEN.LLGSNGELK.ADFGWS.HAPSSRR.TL..T.
RetrocopyKLSKFDEQRIATYITELANALS*CHSKRVIHRDIKPENPLLGSNGELKLADFGWSAHAPSSRRPTLYCTV
ParentalDYLPPEMIEGRMHDEKVDLWSLGVLCYEFL
DYLPPEMIEG.MHDE.VDLWSLGVLCYEFL
RetrocopyDYLPPEMIEGQMHDEEVDLWSLGVLCYEFL

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 1 .15 RPM 4 .03 RPM
SRP017611_kidney 0 .91 RPM 3 .07 RPM
SRP017611_liver 0 .13 RPM 5 .24 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
1 EST(s) were mapped to retro_rnor_670 retrocopy
EST ID Start End Identity Match Mis-match Score
BF560471 11229919 11230058 100 139 0 139
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_670 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_670 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 32 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000293313 retrocopies
Choloepus hoffmanni ENSCHOG000000059768 retrocopies
Cavia porcellus ENSCPOG000000066331 retrocopy
Felis catus ENSFCAG000000244931 retrocopy
Homo sapiens ENSG000000875861 retrocopy
Gorilla gorilla ENSGGOG000000071971 retrocopy
Myotis lucifugus ENSMLUG000000079251 retrocopy
Macaca mulatta ENSMMUG000000000701 retrocopy
Mus musculus ENSMUSG000000274961 retrocopy
Nomascus leucogenys ENSNLEG000000070291 retrocopy
Otolemur garnettii ENSOGAG000000044413 retrocopies
Pongo abelii ENSPPYG000000111481 retrocopy
Pan troglodytes ENSPTRG000000136461 retrocopy
Rattus norvegicus ENSRNOG00000004479 2 retrocopies
retro_rnor_664, retro_rnor_670 ,
Sus scrofa ENSSSCG000000074931 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000119582 retrocopies
Tupaia belangeri ENSTBEG000000132842 retrocopies
Tarsius syrichta ENSTSYG000000092211 retrocopy



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