RetrogeneDB ID:

retro_ocun_53

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:20:12231318..12233226(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000011745
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSOCUG00000015533
Aliases:None
Description:heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]


Retrocopy-Parental alignment summary:






>retro_ocun_53
ATGTCTGCCCGCGGCCCGGCCATCGGCATTGACCTGGGCACCACCTACTCGTGCGTGGGCGTGTTCCAGCACGGTAAAGT
GGAGATCATCGCCAACGACCAGGGCAACCGCACCACGCCCAGCTACGTGGCCTTCACGGACACGGAGCGCCTCATCGGCG
ACGCGGCCAAGAACCAGGTGGCCATGAACCCCGCCAACACCATCTTCGACGCCAAGCGGCTGATCGGCCGCAAGTTCGAG
GACGCCACGGTGCAGTCGGACATGAAGCACTGGCCGTTCCGCGTGGTGAGCGAGGGCGGCAAGCCCAAGGTGCAGGTGGA
GTACAAGGGCGAGGTGAAGACCTTCTTCCCGGAGGAGATCTCGTCCATGGTGCTGACGAAGATGAAGGAGATCGCCGAGG
CCTACCTGGGCGGCAAGGTGCAGAGCGCCGTCATCACGGTGCCGGCCTACTTCAACGACTCGCAGCGCCAGGCCACCAAG
GACGCGGGCACCATCACGGGCCTCAACGTGCTGCGCATCATCAACGAGCCCACGGCGGCCGCCATCGCCTACGGGCTGGA
CAAGAAGGGCTGCGCGGGCGGCGAGAAGAACGTGCTCATCTTCGACCTGGGCGGCGGCACCTTCGACGTGTCCATCCTGA
CCATCGAGGACGGCATCTTCGAGGTGAAGTCGACGGCCGGCGACACGCACCTGGGCGGCGAGGACTTCGACAACCGCATG
GTGAGCCACCTGGCCGAGGAGTTCAAGCGCAAGCACAAGAAGGACATCGGGCCCAACAAGCGCGCCGTGCGGCGGCTGCG
CACGGCCTGCGAGCGCGCCAAGCGCACGCTGAGCTCGTCCACGCAGGCCAGCATCGAGATCGACTCGCTCTACGAGGGCG
TGGACTTCTACACGTCCATCACGCGCGCCCGCTTCGAGGAGCTCAACGCCGACCTGTTCCGCGGCACGCTGGAGCCGGTG
GAGAAGGCGCTGCGCGACGCCAAGCTGGACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCCACGCGCATCCC
CAAGATCCAGAAGCTGCTGCAGGACTTCTTCAACGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCCGTGGCCT
ACGGCGCCGCGGTGCAGGCCGCCATCCTCATCGGCGACAAGTCCGAGAACGTGCAGGACCTGCTGCTGCTGGACGTGACG
CCCCTGTCGCTGGGCATCGAGACGGCGGGCGGGGTCATGACCCCGCTCATCAAGAGGAACACCACGATCCCCACCAAGCA
GACGCAGACCTTCACCACCTACTCGGACAACCAGAGCAGCGTGCTGGTGCAGGTGTACGAGGGCGAGCGCGCCATGACCA
AGGACAATAACCTGCTGGGCAAGTTCGACCTGACCGGGATCCCCCCGGCGCCCCGCGGGGTGCCCCAGATCGAGGTCACC
TTCGATATCGACGCCAACGGCATCCTCAACGTGACCGCCGCCGACAAGAGCACCGGCAAGGAGAACAAGATCACCATCAC
CAACGACAAGGGTCGCCTGAGCAAGGACGACATCGACCGCATGGTGCAGGAGGCGGAGCGCTACAAGTCGGAGGACGAGG
CGAACCGCGAGCGGGTGGCGGCCAAGAACGCCGTGGAGTCCTACACCTACAACATCAAGCAGACGGTGGAGGACGAGAAG
CTGCGGGGCAAGATCAGCGAGCAGGACAAAAGCAAGATCCTCGACAAGTGTCAGGAGGTGATCAGCTGGCTGGACCGGAA
CCAGATGGCCGAGAAAGACGAGTACGAGCACAAGCAGAAAGAGCTGGAAAGAGTGTGCAACCCCATCATCAGCAAACTTT
ACCAGGGCGGGCCTGGCGGCGGCGGCTCCGGCGGCTCCGGGGGACCGACCATCGAGGAAGTGGACTAA

ORF - retro_ocun_53 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.08 %
Parental protein coverage: 97.22 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNP.NT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPANTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGE.K.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGEVKTFFPEEISSMVLTKMKEIAEAYLGGKVQS
ParentalAVVTVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDKK--VGAERNVLIFDLGGGTFDVSI
AV.TVPAYFNDSQRQATKDAGTI.GLNVLRIINEPTAAAIAYGLDKK...G.E.NVLIFDLGGGTFDVSI
RetrocopyAVITVPAYFNDSQRQATKDAGTITGLNVLRIINEPTAAAIAYGLDKKGCAGGEKNVLIFDLGGGTFDVSI
ParentalLTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQ
LTIEDGIFEVKSTAGDTHLGGEDFDNRMV.H...EFKRKHKKDI..NKRAVRRLRTACERAKRTLSSSTQ
RetrocopyLTIEDGIFEVKSTAGDTHLGGEDFDNRMVSHLAEEFKRKHKKDIGPNKRAVRRLRTACERAKRTLSSSTQ
ParentalASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKL
ASIEIDSLYEG.DFYTSITRARFEELNADLFRGTL.PVEKALRDAKLDK.QI..IVLVGGSTRIPKIQKL
RetrocopyASIEIDSLYEGVDFYTSITRARFEELNADLFRGTLEPVEKALRDAKLDKGQIQEIVLVGGSTRIPKIQKL
ParentalLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTT
LQDFFNGKELNKSINPDEAVAYGAAVQAAIL.GDKSENVQDLLLLDVTPLSLGIETAGGVMT.LIKRNTT
RetrocopyLQDFFNGKELNKSINPDEAVAYGAAVQAAILIGDKSENVQDLLLLDVTPLSLGIETAGGVMTPLIKRNTT
ParentalIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLLGKFELTGIPPAPRGVPQIEVTFDIDANGILNVS
IPTKQTQTFTTYSDNQ..VL.QVYEGERAMTKDNNLLGKF.LTGIPPAPRGVPQIEVTFDIDANGILNV.
RetrocopyIPTKQTQTFTTYSDNQSSVLVQVYEGERAMTKDNNLLGKFDLTGIPPAPRGVPQIEVTFDIDANGILNVT
ParentalAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNMKATVEDEKLQ
A.DKSTGKENKITITNDKGRLSK.DI.RMVQEAE.YK.EDE..R..V..KN..ESY..N.K.TVEDEKL.
RetrocopyAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRERVAAKNAVESYTYNIKQTVEDEKLR
ParentalGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGG
GKI...DK.KILDKC.E.I.WLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ...G.PGG..GG..G.G
RetrocopyGKISEQDKSKILDKCQEVISWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQ---GGPGG--GGSGGSG
ParentalAP
.P
RetrocopyGP

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 134 .94 RPM 730 .91 RPM
SRP017611_kidney 23 .72 RPM 544 .39 RPM
SRP017611_liver 0 .85 RPM 185 .37 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_53 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_53 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_53 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Equus caballus retro_ecab_628
Parental genes homology:
Parental genes homology involve 28 parental genes, and 87 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000048842 retrocopies
retro_acar_21, retro_acar_6,
Ailuropoda melanoleuca ENSAMEG000000084251 retrocopy
retro_amel_126,
Anas platyrhynchos ENSAPLG000000106671 retrocopy
retro_apla_6,
Bos taurus ENSBTAG000000131621 retrocopy
retro_btau_354,
Canis familiaris ENSCAFG000000116663 retrocopies
retro_cfam_140, retro_cfam_191, retro_cfam_509,
Ciona intestinalis ENSCING000000096651 retrocopy
retro_cint_12,
Callithrix jacchus ENSCJAG000000076485 retrocopies
retro_cjac_2388, retro_cjac_3306, retro_cjac_3898, retro_cjac_4057, retro_cjac_721,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Echinops telfairi ENSETEG000000109961 retrocopy
retro_etel_43,
Ficedula albicollis ENSFALG000000058121 retrocopy
retro_falb_18,
Felis catus ENSFCAG000000011326 retrocopies
retro_fcat_132, retro_fcat_1331, retro_fcat_1571, retro_fcat_1775, retro_fcat_556, retro_fcat_79,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
Gorilla gorilla ENSGGOG000000083818 retrocopies
retro_ggor_1053, retro_ggor_1810, retro_ggor_1888, retro_ggor_1918, retro_ggor_2501, retro_ggor_3054, retro_ggor_3057, retro_ggor_360,
Loxodonta africana ENSLAFG000000303124 retrocopies
retro_lafr_1218, retro_lafr_391, retro_lafr_790, retro_lafr_797,
Meleagris gallopavo ENSMGAG000000019291 retrocopy
retro_mgal_9,
Myotis lucifugus ENSMLUG000000048343 retrocopies
retro_mluc_1800, retro_mluc_2300, retro_mluc_777,
Monodelphis domestica ENSMODG000000129582 retrocopies
retro_mdom_127, retro_mdom_99,
Mustela putorius furoENSMPUG000000058109 retrocopies
retro_mputfur_1048, retro_mputfur_1056, retro_mputfur_1144, retro_mputfur_131, retro_mputfur_188, retro_mputfur_309, retro_mputfur_627, retro_mputfur_694, retro_mputfur_958,
Mus musculus ENSMUSG000000156568 retrocopies
retro_mmus_2244, retro_mmus_2584, retro_mmus_26, retro_mmus_2621, retro_mmus_2840, retro_mmus_316, retro_mmus_351, retro_mmus_620,
Oryctolagus cuniculus ENSOCUG00000015533 4 retrocopies
retro_ocun_1308, retro_ocun_53 , retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG000000039879 retrocopies
retro_pabe_183, retro_pabe_2193, retro_pabe_2254, retro_pabe_2260, retro_pabe_2261, retro_pabe_3153, retro_pabe_355, retro_pabe_3804, retro_pabe_3808,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Taeniopygia guttata ENSTGUG000000004911 retrocopy
retro_tgut_7,
Takifugu rubripes ENSTRUG000000052651 retrocopy
retro_trub_30,
Tursiops truncatus ENSTTRG000000111396 retrocopies
retro_ttru_1507, retro_ttru_1650, retro_ttru_1696, retro_ttru_35, retro_ttru_741, retro_ttru_808,
Xiphophorus maculatus ENSXMAG000000016021 retrocopy
retro_xmac_20,




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