RetrogeneDB ID:

retro_cfam_257

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:1:36457993..36459220(+)
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:ENSCAFG00000029331
Aliases:None
Description:aurora kinase A [Source:HGNC Symbol;Acc:11393]


Retrocopy-Parental alignment summary:






>retro_cfam_257
ACGGGCATCATGGACAAATCTAAAGAAAACTGCATTGCAGGGCCTGTTAAGACTACAATTGCACTTGGTGATGGTCCAAA
ACGTGTTCTGGTGACTCAGCAAGTTCCTTCACAGAATCCGTCATCTACAAATAGTGGCCAGGCCCAGTGGGCCTTTTGTC
CTTCAAATTCTTCCCAGAGAGTTCCTCCACAAACCCAAAAGCTCATCTCCAGCCATAAACCGGCTCAGAATCTGAAGCAG
AAGCAATTGCAGGCAACTGGTGTCCCTCGTCCTGTCTCTAGGTCACTGACTAATACCCAAAAGAATGAGCAACCCTCGTC
ATCAGCTCCTGGAAATAATTCTGAAAAGGAACTGGCAACAAAACAGAAAAAATGAAGAATCAATAAAAAGGCAATGGGCT
TTGGAAGATTTTGAAATTGGTCGTCCACTGGGTAAAGGAAAGTTTGGTAATGTTTACTTGGCAAGGGAAAAACAAAGCAA
GTTTATCTTGGCTATTAAAGTATTACTTAAAGCTCAACTGGAGAAAGCAGGAGTTGAGCATCAGCTGAGAAGAGAAGTAG
AAATACAGTCCCACCTTAGGCATCCAAATATTCTTTGGCTGTATGGTTATTTCCATGATGCTACCAGAGTTTACCTAATT
CTAGAATATGCATCTCTTGGAGCTGTCTACAGAGAACTTCAGAAACTGTCAAAGTTTGATGAGCAGAGAACTGCTATTAT
ATCACAGAGTTGGCAGATGCCCTGTCTTACTGTTGTCACTCAAAGAGAGTCATTCACAGAGACATTAAGCCAGAGAACCT
ATTCCTTGGATCAGCTGGAGAGCTTAAGATTGCAGATTTTGGGTGATCAGTACATGCTCCATCCTCCAGGAGAACCATCC
TGCATGGCACCCTGGATTATTGGCCCCCAGAGATGATTGAAGGCCAAATGCATGATGAGAAGGTGGATCTCTGGAGCCTT
GGGGTTCTTTGTTATGAATTTCTAGTTGGGAAGCCTCCTTTTGAGGCAAGCATATACCAAGAGACCTACAAATGAATATC
ACGGGTTGAATTCACATTCCCTGACTTCCTGCCAGAGGGAGCCAGGGATCTCATTTCAAGACTATTGAAACATAATCCCA
GCCAAAGGCCAACTCTCAGAGATGTACTTGAACACCCATGGATCATGGCTAACTCCTCAAAACCGTCAAGTAGCCAAAAA
AGCAAAGACTCAACTAGCAAACAGTCT

ORF - retro_cfam_257 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.7 %
Parental protein coverage: 100. %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalSGIMDKSKENCIAGPVKTAIALGDGPKRVLVTQQVPSQNPLSANSGQAQRVLCPSNSSQRVPPQTQKLVS
.GIMDKSKENCIAGPVKT.IALGDGPKRVLVTQQVPSQNP.S.NSGQAQ...CPSNSSQRVPPQTQKL.S
RetrocopyTGIMDKSKENCIAGPVKTTIALGDGPKRVLVTQQVPSQNPSSTNSGQAQWAFCPSNSSQRVPPQTQKLIS
ParentalSHKPAQNLKQKQLQATGVPRPASRSLNNTQKSEQPSSSAPGNNSEKELATKQK-NEESKKRQWALEDFEI
SHKPAQNLKQKQLQATGVPRP.SRSL.NTQK.EQPSSSAPGNNSEKELATKQK.NEES.KRQWALEDFEI
RetrocopySHKPAQNLKQKQLQATGVPRPVSRSLTNTQKNEQPSSSAPGNNSEKELATKQK>NEESIKRQWALEDFEI
ParentalGRPLGKGKFGNVYLAREKQSKFILAIKVLFKAQLEKAGVEHQLRREVEIQSHLRHPNILRLYGYFHDATR
GRPLGKGKFGNVYLAREKQSKFILAIKVL.KAQLEKAGVEHQLRREVEIQSHLRHPNIL.LYGYFHDATR
RetrocopyGRPLGKGKFGNVYLAREKQSKFILAIKVLLKAQLEKAGVEHQLRREVEIQSHLRHPNILWLYGYFHDATR
ParentalVYLILEYAPLGAVYRELQKLSKFDEQRTAT-YITELADALSYC-HSKRVIHRDIKPENLLLGSAGELKIA
VYLILEYA.LGAVYRELQKLSKFDEQRTA..YITELADALSYC.HSKRVIHRDIKPENL.LGSAGELKIA
RetrocopyVYLILEYASLGAVYRELQKLSKFDEQRTAI<YITELADALSYCCHSKRVIHRDIKPENLFLGSAGELKIA
ParentalDFGWSVHAPSSRRTTLCGTLDYLPPEMIEGRMHDEKVDLWSLGVLCYEFLVGKPPFEASTYQETYKRISR
DFG.SVHAPSSRRT.L.GTLDY.PPEMIEG.MHDEKVDLWSLGVLCYEFLVGKPPFEAS.YQETYK.ISR
RetrocopyDFG*SVHAPSSRRTILHGTLDYWPPEMIEGQMHDEKVDLWSLGVLCYEFLVGKPPFEASIYQETYK*ISR
ParentalVEFTFPDFVPEGARDLISRLLKHNPSQRPTLKDVLEHPWIMANSSKPSSSQKNKDSTSKQS
VEFTFPDF.PEGARDLISRLLKHNPSQRPTL.DVLEHPWIMANSSKPSSSQK.KDSTSKQS
RetrocopyVEFTFPDFLPEGARDLISRLLKHNPSQRPTLRDVLEHPWIMANSSKPSSSQKSKDSTSKQS

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
SRP012049_cerebellum 0 .00 RPM 4 .79 RPM
SRP017611_brain 0 .00 RPM 1 .98 RPM
SRP017611_kidney 0 .00 RPM 1 .85 RPM
SRP017611_liver 0 .00 RPM 1 .09 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_257 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_257 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_257 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 19 parental genes, and 33 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000232971 retrocopy
retro_cfam_1177,
Canis familiaris ENSCAFG00000029331 3 retrocopies
retro_cfam_1027, retro_cfam_257 , retro_cfam_764,
Choloepus hoffmanni ENSCHOG000000059768 retrocopies
retro_chof_1302, retro_chof_1575, retro_chof_1709, retro_chof_2213, retro_chof_2389, retro_chof_259, retro_chof_565, retro_chof_764,
Cavia porcellus ENSCPOG000000066331 retrocopy
retro_cpor_106,
Felis catus ENSFCAG000000244931 retrocopy
retro_fcat_495,
Homo sapiens ENSG000000875861 retrocopy
retro_hsap_510,
Gorilla gorilla ENSGGOG000000071971 retrocopy
retro_ggor_470,
Myotis lucifugus ENSMLUG000000079251 retrocopy
retro_mluc_1931,
Macaca mulatta ENSMMUG000000000701 retrocopy
retro_mmul_431,
Mus musculus ENSMUSG000000274961 retrocopy
retro_mmus_2825,
Nomascus leucogenys ENSNLEG000000070291 retrocopy
retro_nleu_1553,
Otolemur garnettii ENSOGAG000000044413 retrocopies
retro_ogar_2805, retro_ogar_3440, retro_ogar_980,
Pongo abelii ENSPPYG000000111481 retrocopy
retro_pabe_231,
Pan troglodytes ENSPTRG000000136461 retrocopy
retro_ptro_381,
Rattus norvegicus ENSRNOG000000044792 retrocopies
retro_rnor_664, retro_rnor_670,
Sus scrofa ENSSSCG000000074931 retrocopy
retro_sscr_936,
Ictidomys tridecemlineatus ENSSTOG000000119582 retrocopies
retro_itri_366, retro_itri_772,
Tupaia belangeri ENSTBEG000000132842 retrocopies
retro_tbel_1137, retro_tbel_2604,
Tarsius syrichta ENSTSYG000000092211 retrocopy
retro_tsyr_378,


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