RetrogeneDB ID:

retro_ptro_1743

Retrocopy
location
Organism:Chimpanzee (Pan troglodytes)
Coordinates:2B:213973924..213975302(-)
Located in intron of:None
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_1743
ACTATTTCCAATGTTATGGTCATAGGGCCTAATGACTCTAATGTCAGGCTACCAAAGATCCTGGAACCATTGCTGGTCTC
AATGTACTTAGAATTATCAATGAGCCAACTGCTGCTTCTATTGCTTATGGCACAGACAAAAAGTTTGGAGCTGAAAGACA
TGTGCTCATCTATGACTTAAGAGATGAAATTTTTGATGTGTCTGTCCTTACTCTTGAGGATGAAATCTTTGAGATCAAAT
CTACAGCTGGAGACACCCACTTAGGTGAAGAAGATTTTGACAACCAAATGATCAACCATTTTATTGCTGAGTTCAAATAC
AAGCATAAGGACAGTAGTGAGAACAACAGGGCTGTCTGACGCTTCTGTACTGCTTGTGATGGGCTAATTGCACTCTCCCT
TCCAGCACCCAGGCCAGTAGTGAGATTAATTCTCTCCATGAAGGAACAGATATTTATACCTCCATTACCCACGCCCAATT
TGAAGAACTGAATGCTGTCCTGTTCCGTGGCACCCAGGACCCCATAGATATAGCCCTTCAGGACACCAAACTAGACAAGT
TGCAGATCCATGTTATTGTCCTGGTAGGTGGTTCTATCTCTATCTCCTAGATCCAAAAGCTCCCTCAATAATTATTTAGT
GGAAAATAACTGAGCAAGAGCATTGACCCTGATAAAGCTGTTGCTTATGGTGCAGCAGTCCAGGCAGCCATCCTATCTTA
AGACAAATCTTAAACTGTTCAAGATTTGCTACTTTTGGATTCACTTCTCTTCTCTTTGGTAATGATGCTGCTGTGGAGTC
ATGACTGTTCCCATGAAATGCAGTACACTTTTCTTACCAAGCAGACCCAGACCTTCACTACCTACCCTGACAACCAACCT
GATGTCCTCATTCAAATTTATGAAGGTGAGAGTGCCATAACCAAGGATAACAATTTGCTTGTTATCCAGGGCAAGTTTGA
GCTCACAGGCATACTTCCTGCTCCCTTTGCTGTTCCTCAAATTAAAGTCACTTGTGATATTGATGTCAATAACAGCCTCA
ATATCTCTGCTGTAGGTAAGAGTACAGAAAAAGAGAACAAAATTATCATCACTAATGACCAGGGGCATTTGAGCAAGGAA
GACATTGAGAATATGGTCCAGGAAGCTGAGTACAAAGCTGAAGATGAGAAGCAGAAGAACAAGGTGGCATCAAAGAATTC
ACTTGACTCTTATGCATTCAACATGAAAGCAACTGAGAAACTTCAAGGCAAGATCAACAATAAGGATAAACAGAAGATAC
ATGACAAGTGTAATAAAATCATCAACTGACTTGATAAGAATCAGACTATAATGAAGGAAGAATTTGAACATCAGCAGAAA
GAGCTAGTTTGCAGTCCA

ORF - retro_ptro_1743 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.06 %
Parental protein coverage: 73.35 %
Number of stop codons detected: 7
Number of frameshifts detected: 5


Retrocopy - Parental Gene Alignment:

ParentalTVTNAVVTVPAYFNDSQR-QATKDAGTIAGLNVLRIINEPTAAAIAYGLDWQVGAERNVLIFDLGGGTFD
T..N..V..P...NDS...QATKD.GTIAGLNVLRIINEPTAA.IAYG.D...GAER.VLI.DL....FD
RetrocopyTISNVMVIGP---NDSNV<QATKDPGTIAGLNVLRIINEPTAASIAYGTDKKFGAERHVLIYDLRDEIFD
ParentalVSILTIEDGIFEVKSTAGDTHLGGEDFDNRMVNHFIAEFKRKHKKDISENKRAVRRLRTACER-AKRTLS
VS.LT.ED.IFE.KSTAGDTHLG.EDFDN.M.NHFIAEFK.KHK.D.SEN.RAV.R..TAC...A..TL.
RetrocopyVSVLTLEDEIFEIKSTAGDTHLGEEDFDNQMINHFIAEFKYKHK-DSSENNRAV*RFCTACDG<ANCTLP
ParentalSSTQASIEIDSLYEGIDFYTSITRARFEELNADLFRGTLDPVEKALRDAKLDKSQIHDIVLVGGSTRIPK
SSTQAS.EI.SL.EG.D.YTSIT.A.FEELNA.LFRGT.DP...AL.D.KLDK.QIH.IVLVGGS..I..
RetrocopySSTQASSEINSLHEGTDIYTSITHAQFEELNAVLFRGTQDPIDIALQDTKLDKLQIHVIVLVGGSISIS*
ParentalIQKLLQDFFNGKELNKSINPDEAVAYGAAVQAAILSGDKSENVQDLLLLD-VTPLSLGIETAG-GVMTVL
IQKL.Q..F.GK.L.KSI.PD.AVAYGAAVQAAILS.DKS..VQDLLLLD..T.L..G...A..GVMTV.
RetrocopyIQKLPQ*LFSGK*LSKSIDPDKAVAYGAAVQAAILS*DKS*TVQDLLLLD<FTSLLFGNDAAV<GVMTVP
ParentalIKRNT-TIPTKQTQTFTTYSDNQPGVLIQVYEGERAMTKDNNLL---GKFELTGIPPAPRGVPQIEVTFD
.K..T.T..TKQTQTFTTY.DNQP.VLIQ.YEGE.A.TKDNNLL...GKFELTGI.PAP..VPQI.VT.D
RetrocopyMKCST<TFLTKQTQTFTTYPDNQPDVLIQIYEGESAITKDNNLLVIQGKFELTGILPAPFAVPQIKVTCD
ParentalIDANGILNVSAVDKSTGKENKITITNDKGRLSKEDIERMVQEAEKYKAEDEKQRDKVSSKNSLESYAFNM
ID.N..LN.SAV.KST.KENKI.ITND.G.LSKEDIE.MVQEAE.YKAEDEKQ..KV.SKNSL.SYAFNM
RetrocopyIDVNNSLNISAVGKSTEKENKIIITNDQGHLSKEDIENMVQEAE-YKAEDEKQKNKVASKNSLDSYAFNM
ParentalKATVEDEKLQGKINDEDKQKILDKCNEIINWLDKNQTAEKEEFEHQQKELEKVCNP
KAT...EKLQGKIN..DKQKI.DKCN.IIN.LDKNQT..KEEFEHQQKEL..VC.P
RetrocopyKAT---EKLQGKINNKDKQKIHDKCNKIIN*LDKNQTIMKEEFEHQQKEL--VCSP

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 .02 RPM 845 .51 RPM
SRP007412_cerebellum 0 .00 RPM 738 .30 RPM
SRP007412_heart 0 .03 RPM 709 .86 RPM
SRP007412_kidney 0 .00 RPM 971 .90 RPM
SRP007412_liver 0 .00 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_1743 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1743 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ptro_1743 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_2384
Gorilla gorilla retro_ggor_1810
Macaca mulatta retro_mmul_963
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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