RetrogeneDB ID:

retro_ptro_3259

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:X:115357772..115359011(-)
Located in intron of:ENSPTRG00000022199
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HSPA8
Ensembl ID:ENSPTRG00000004404
Aliases:None
Description:heat shock 70kDa protein 8 [Source:HGNC Symbol;Acc:5241]


Retrocopy-Parental alignment summary:






>retro_ptro_3259
GCAGTTGGTATTGATCTTGACACTGCATACTCTTGTGTGGGTGTTTTCCAGCATGGAAAAGTAGAGATAATTACCAATGA
TCAGGGAAACTGAACCACTCCAAGCTATGTCACCTTTATGAACACTGAATGATTGATTGGTGATGCCGCAAAGAATCAAG
CTGCAATGAACCCCACCAACACGGTTTTTGATGCCAAACATCTGATTGGATGCAGATTTGATGATGCTGTTGTCTAGTCT
GATATGAAGCATTGGCCCTTCATGATGGTGAATGATACTGACAGGCCCAAGGTCCAAGTAGAATACAAGGGAGAGACCAA
AATCTTCTATCCAGAGGAGGTGTCCTCTATGGTCCTCACAAAGATGAAGGAAATTGCAGAAGCCTACCTTGGGAAGACTG
TTACCAATGCTGTGGTCACAGTGCCAGCTTACTTTAATAACTCTCAGCATCAGGCTACCAAAGATGCTGGAACTATTGCT
GGTCTCAATGTACTTAGAATTATCAATGAGCCAAGTGCTGCTGATATTGCTTACGGCTTAGACAAAAAGGTTGGAGCTGA
AAGAAATGTGTTTATCTTTGACCTGAGAGGTGGCACTTTTGATGTGTCAATCCTCATTATTCAGGATGGAATCTTTGAGG
TCAAATCTGGAGACATCCACTTGGGTGAAGAAGACTTTGACAACCGAATTGTCAGCCATTTTATTGCTGAGTTCAAGCAT
AAGTATAAGAAAGACATCAGTGAGAAGAAGAGAGCTATAAGACGCCTCCGTACTGCTTGTGAACACACTAAGCATACTCT
CTCTTCCAGGACCCAGGCCAGTATTGAGGTCGATTCTCTCTAAGAATGAATTGACTTCTGTACATCCATTGCCTGTGCCC
GATTTGAAGAACTGAATGCTGACCTGTTCCATGGCACCCTTGGCCCTGTATAAAAAGCCATTCGAGATGCCAAACTAGAC
AAGTCACAGATTCATGATATTGTCTCTATTGGTGGTTATACTCATATCCCCAAGATTCAGAAGCTTCTCCAAGATGTCTT
CAATAGAAAAGAACTGAATAAGAGCATCAATCTTGATGAAGCTGTTGCTTATGGTGCAGCTATCCAGGCAGCCATCCTAT
CTGGAGACAAATCTGAAAATGTTCAAGATTTGCTGCTCTTGGATGTCAATCCTCTTTCCTTTGGTATTGAACTTGCTGGT
GGAGTCATGACTGTCCTCCTGTCCTCATCAAGCATAGTA

ORF - retro_ptro_3259 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.37 %
Parental protein coverage: 64.89 %
Number of stop codons detected: 6
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalAVGIDLGTTYSCVGVFQHGKVEIIANDQGNRTTPSYVAFTDTERLIGDAAKNQVAMNPTNTVFDAKRLIG
AVGIDL.T.YSCVGVFQHGKVEII.NDQGN.TTPSYV.F..TE.LIGDAAKNQ.AMNPTNTVFDAK.LIG
RetrocopyAVGIDLDTAYSCVGVFQHGKVEIITNDQGN*TTPSYVTFMNTE*LIGDAAKNQAAMNPTNTVFDAKHLIG
ParentalRRFDDAVVQSDMKHWPFMVVNDAGRPKVQVEYKGETKSFYPEEVSSMVLTKMKEIAEAYLG-TVTNAVVT
.RFDDAVV.SDMKHWPFM.VND..RPKVQVEYKGETK.FYPEEVSSMVLTKMKEIAEAYLG.TVTNAVVT
RetrocopyCRFDDAVV*SDMKHWPFMMVNDTDRPKVQVEYKGETKIFYPEEVSSMVLTKMKEIAEAYLGKTVTNAVVT
ParentalVPAYFNDSQRQATKDAGTIAGLNVLRIINEPTAAAIAYGLDWQVGAERNVLIFDLGGGTFDVSILTIEDG
VPAYFN.SQ.QATKDAGTIAGLNVLRIINEP.AA.IAYGLD..VGAERNV.IFDL.GGTFDVSIL.I.DG
RetrocopyVPAYFNNSQHQATKDAGTIAGLNVLRIINEPSAADIAYGLDKKVGAERNVFIFDLRGGTFDVSILIIQDG
ParentalIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACERAKRTLSSSTQASIEID
IFEVKS..GD.HLG.EDFDNR.V.HFIAEFK.K.KKDISE.KRA.RRLRTACE..K.TLSS.TQASIE.D
RetrocopyIFEVKS--GDIHLGEEDFDNRIVSHFIAEFKHKYKKDISEKKRAIRRLRTACEHTKHTLSSRTQASIEVD
ParentalSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPKIQKLLQDFFN
SL.E.IDF.TSI..ARFEELNADLF.GTL.PV.KA.RDAKLDKSQIHDIV..GG.T.IPKIQKLLQD.FN
RetrocopySL*E*IDFCTSIACARFEELNADLFHGTLGPV*KAIRDAKLDKSQIHDIVSIGGYTHIPKIQKLLQDVFN
ParentalGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLDVTPLSLGIETAGGVMTVLIKRNTTI
.KELNKSIN.DEAVAYGAA.QAAILSGDKSENVQDLLLLDV.PLS.GIE.AGGVMTVL.......
RetrocopyRKELNKSINLDEAVAYGAAIQAAILSGDKSENVQDLLLLDVNPLSFGIELAGGVMTVLLSSSSIV

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 0 .91 RPM 845 .51 RPM
SRP007412_cerebellum 0 .22 RPM 738 .30 RPM
SRP007412_heart 0 .17 RPM 709 .86 RPM
SRP007412_kidney 0 .34 RPM 971 .90 RPM
SRP007412_liver 0 .29 RPM 502 .96 RPM
SRP007412_testis 0 .00 RPM 445 .77 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_3259 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_3259 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_3259 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_4892
Gorilla gorilla retro_ggor_3054
Pongo abelii retro_pabe_3804
Macaca mulatta retro_mmul_2628
Parental genes homology:
Parental genes homology involve 29 parental genes, and 76 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,
Cavia porcellus ENSCPOG000000041693 retrocopies
retro_cpor_1072, retro_cpor_619, retro_cpor_938,
Ciona savignyi ENSCSAVG000000085881 retrocopy
retro_csav_3,
Dipodomys ordii ENSDORG000000154671 retrocopy
retro_dord_16,
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,
Homo sapiens ENSG000001099718 retrocopies
retro_hsap_2384, retro_hsap_2710, retro_hsap_2758, retro_hsap_340, retro_hsap_3698, retro_hsap_4892, retro_hsap_4896, retro_hsap_68,
Gallus gallus ENSGALG000000065121 retrocopy
retro_ggal_8,
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,
Macaca mulatta ENSMMUG000000046967 retrocopies
retro_mmul_1536, retro_mmul_2188, retro_mmul_2628, retro_mmul_2632, retro_mmul_580, retro_mmul_778, retro_mmul_963,
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,
Oreochromis niloticus ENSONIG000000047591 retrocopy
retro_onil_2,
Pelodiscus sinensis ENSPSIG000000124502 retrocopies
retro_psin_17, retro_psin_5,
Pan troglodytes ENSPTRG000000005631 retrocopy
retro_ptro_2033,
Pan troglodytes ENSPTRG00000004404 5 retrocopies
retro_ptro_1743, retro_ptro_2507, retro_ptro_272, retro_ptro_3259 , retro_ptro_3264,
Pan troglodytes ENSPTRG000000172901 retrocopy
retro_ptro_1680,
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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