RetrogeneDB ID:

retro_pabe_183

Retrocopy
location
Organism:Orangutan (Pongo abelii)
Coordinates:14:65444093..65446013(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSPPYG00000005902
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:DKFZP459D1928
Ensembl ID:ENSPPYG00000003987
Aliases:HSPA8, HSC70
Description:heat shock cognate 71 kDa protein [Source:RefSeq peptide;Acc:NP_001125783]


Retrocopy-Parental alignment summary:






>retro_pabe_183
ATGTCTGCCCGTGGCCCGGCTATCGGCATCGACCTGGGCACCACCTACTCGTGCGTGGGTGTCTTCCAACATGGCAAGGT
GGAGATCATCGCCAACGACCAGGGCAACCGCACCACCCCCAGCTACGTGGCCTTCACGGACACCGAGCGCCTCATCGGCG
ACGCCGCCAAGAACCAGGTGGCCATGAACCCCACCAACACCATCTTCGACGCCAAGAGGCTGATTGGACGGAAGTTCGAG
GATGCCACAGTGCAGTCGGATATGAAACACTGGCCGTTCCGGGTGGTGAGCGAGGGAGGCAAGCCCAAAGTGCAAGTGGA
GTACAAGGGGGAGACCAAGACCTTCTTCCCAGAGGAGATATCCTCCATGGTCCTCACGAAGATGAAGGAGATTGCGGAAG
CCTACCTGGGGGGCAAGGTGCACAGCGCGGTCATAACGGTCCCGGCCTATTTCAACGACTCGCAGCGCCAGGCCACCAAG
GACGCGGGCACCATCACGGGGCTCAATGTGCTGCGCATCATCAACGAGCCCACGGCGGCGGCCATCGCCTACGGCCTGGA
CAAGAAGGGCTGCGCGGGCGGCGAGAAGAACGTGCTCATCTTTGACCTGGGCGGTGGCACTTTCGACGTGTCCATCCTGA
CCATCGAGGATGGCATCTTCGAGGTGAAGTCCACGGCCGGCGACACCCACCTGGGCGGTGAGGACTTCGACAACCGCATG
GTGAGCCACCTGGCGGAGGAGTTCAAGCGCAAGCACAAGAAGGACATTGGGCCCAACAAGCGCGCCGTGAGGCGGCTGCG
CACCGCCTGCGAGCGCGCCAAGCGCACCCTGAGCTCATCCACGCAGGCGAGCATCGAGATCGACTCGCTCTACGAGGGCG
TTGACTTCTATACGTCCATCACGCGCGCCCGCTTCGAGGAGCTCAATGCCGACCTCTTTCGCGGGACCCTGGAGCCAGTG
GAGAAGGCGCTGCGCGACGCCAAGCTGGACAAGGGCCAGATCCAGGAGATCGTGCTGGTGGGCGGCTCCACTCGTATCCC
CAAGATCCAGAAGCTGCTGCAGGATTTCTTCAACGGCAAGGAGCTGAACAAGAGCATCAACCCCGACGAGGCGGTGGCCT
ATGGCGCCGCGGTGCAGGCGGCCATCCTCATCGGCGACAAATCAGAGAATGTGCAGGACCTGCTGCTACTCGACGTGACC
CCGTTGTCGCTGGGCATCGAGACAGCTGGCGGTGTCATGACCCCACTCATCAAGAGGAACACCACGATCCCCACCAAGCA
GACGCAGACCTTCACCACCTACTCGGACAACCAGAGCAGCGTGCTGGTGCAGGTATACGAGGGCGAACGGGCCATGACCA
AGGACAATAACCTGCTGGGCAAGTTCGACCTGACCGGGATTCCCCCTGCGCCTCGCGGGGTCCCCCAGATCGAGGTTACC
TTCGACATTGACGCCAATGGCATCCTTAACGTTACCGCCGCCGACAAGAGCACCGGTAAGGAAAACAAAATCACCATCAC
CAATGACAAAGGTCGTCTGAGCAAGGACGACATTGACCGGATGGTGCAGGAGGCGGAGCGGTACAAATCGGAAGATGAGG
CGAATCGCGACCGAGTCGCGGCCAAAAACGCCCTGGAGTCCTATACCTACAACATCAAGCAGACAGTGGAAGACGAGAAA
CTGAGGGGCAAGATTAGCGAGCAGGACAAAAACAAGATCCTCGACAAGTGTCAGGAGGTGATCAACTGGCTCGACCGAAA
CCAGATGGCAGAGAAAGATGAGTATGAACACAAGCAGAAAGAGCTCGAAAGAGTTTGCAACCCCATCATCAGCAAACTTT
ACCAAGGTGGTTCTGGCGGCGGCAGCGGCGGCGGCGGTTCAGGAGCCTCCGGGGGACCCACCATCGAAGAAGTGGACTAA

ORF - retro_pabe_183 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.44 %
Parental protein coverage: 97.83 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSKGPAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAK
..GPA.GIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNT.FDAK
RetrocopyARGPAIGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTIFDAK
ParentalRLIGRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLGKTVTN
RLIGR.F.DA.VQSDMKHWPF.VV...G.PKVQVEYKGETK.F.PEE.SSMVLTKMKEIAEAYLG..V..
RetrocopyRLIGRKFEDATVQSDMKHWPFRVVSEGGKPKVQVEYKGETKTFFPEEISSMVLTKMKEIAEAYLGGKVHS
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..RD.V..KN.LESY..N.K.TVEDEKL.
RetrocopyAADKSTGKENKITITNDKGRLSKDDIDRMVQEAERYKSEDEANRDRVAAKNALESYTYNIKQTVEDEKLR
ParentalGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNPIITKLYQSAGGMPGGMPGGFPGGG
GKI...DK.KILDKC.E.INWLD.NQ.AEK.E.EH.QKELE.VCNPII.KLYQ..GG..GG..GG..G..
RetrocopyGKISEQDKNKILDKCQEVINWLDRNQMAEKDEYEHKQKELERVCNPIISKLYQ--GGSGGGSGGGGSGAS
ParentalAPPS
..P.
RetrocopyGGPT

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
SRP007412_brain_prefrontal_cortex 34 .50 RPM 425 .19 RPM
SRP007412_cerebellum 17 .02 RPM 531 .03 RPM
SRP007412_heart 9 .15 RPM 192 .27 RPM
SRP007412_kidney 16 .94 RPM 310 .15 RPM
SRP007412_liver 2 .82 RPM 196 .49 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

1 EST(s) were mapped to retro_pabe_183 retrocopy
EST ID Start End Identity Match Mis-match Score
CR854145 65443984 65444719 99.6 704 1 697

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_183 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_pabe_183 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_68
Gorilla gorilla retro_ggor_1053
Bos taurus retro_btau_354
Canis familiaris retro_cfam_140
Parental genes homology:
Parental genes homology involve 29 parental genes, and 88 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 ENSOCUG000000155334 retrocopies
retro_ocun_1308, retro_ocun_53, retro_ocun_584, retro_ocun_753,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pongo abelii ENSPPYG00000003987 9 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,
Pongo abelii ENSPPYG000000196091 retrocopy
retro_pabe_2491,
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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