RetrogeneDB ID:

retro_hsap_798

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:11:79698555..79699865(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000254471
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ORC3
Ensembl ID:ENSG00000135336
Aliases:ORC3, LAT, LATHEO, ORC3L
Description:origin recognition complex, subunit 3 [Source:HGNC Symbol;Acc:8489]


Retrocopy-Parental alignment summary:






>retro_hsap_798
ATGGCCACCTCCTCAGTGTCTAAGGGCTGCTTTGTTTTTAAGCCAAACTCCAAAAAGAGAAAGATCTCTGTGCCAATGGA
GGACTATTTTAACAAAGGGAAAAATGAGCCTAAGGACAGTAAGCTTCAATTTGGAACTTAGTTGATATGGCAGCAAATGA
AATCTGAAAATGAGCCACTACAAGAGGAATTAAATAAAAACTTGTTTGACAATCTAACTGAATTTCTGCAAAAATCTCAT
TCTGGATTCCAGAAGAATTCAAGAGACTTGGGCTGTCAAACAAAACTCAGAGAAATTCCAACTGCTGCTCTTGTTCTTGG
TGTGAAAGTCACAGATCATGATTTAACATTCAGAAGTCTAACAGAGGCCCTTCAGAATAAAGTCACACCATATGTAGTCT
CATCGCAAGCTAAAGACTGTCCAGATATGAAACATTTTTTGCAAAATTTGGTCTCATAATTAATGAACTGCTGTGTACAT
CTAAAATCCAAAGAGGGGGAAAGCGTTCAGGTCACCCAGAGAAATACACATTATTTAATGGATTCACTTTCCAGTTGGTA
CATGACTGTCACACAGAAGACAGACCCAAAAATGCCAAGCAAAAAGAGGACTACTTCTAGCCAATGGCAGTCTCCTCCTG
TTTTGGCTACCTTAAAGGATATGGAAAGCTTTGCCACAAAAGTACTGCAAGATTTCATAATTATCAGCAGTCAACATCTG
CATGAATTTCCACTAATACTCATTGTGGGAATCGCCACATCTATTATCAACCACCGATTGTTTCCTCATGCAGTATCATC
TCTGTTGTGTATAGAACTGTTCCAATTTTTGTCTTGCAAGGAGCATCAGACTATGGTACTCAATAAGCTACTTCTTACAA
CTCAGTTTCCCTTTAAAATAAATGAAAAAGTATTGCAGGTTCTGACCAACATCTTTTTGTATCATGATTTCTCGATTCAA
AACTTTATAAAAGTCTTCAACTTTCTTTATTAGAGCATTTCTGTTCCCAGCCCTTAAGTGTCCTGTGCTGTAATCTTCCA
TAAGTCAAAAGAAGAATAAATTTTTTATCAAATAATCAATGTGAAAACATCTGACGTCTTCCATCTTTTAGGAGATATGT
GGAAAAGCAAGCTTCAGAAAAGCAAGTTGCGCTCTTGACCAGTGAGAGATGTTTGAAGAAGGAAACGCAATTATTACTAG
AAAACCTGCATGTTTATCATATGAATTACTTTCTGGTTTTGAGATGTGTTCATAAGTTCACCTCTTCTCTTCCCAAGTAT
CCACTAGGTCGACAGATCAGAGAGTTGTAC

ORF - retro_hsap_798 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.86 %
Parental protein coverage: 61.74 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMATSSMSKGCFVFKPNSKKRKISLPIEDYFNKGKNEPEDSKLRFETYQLIWQQMKSENERLQEELNKNLF
MATSS.SKGCFVFKPNSKKRKIS.P.EDYFNKGKNEP.DSKL.F.T..LIWQQMKSENE.LQEELNKNLF
RetrocopyMATSSVSKGCFVFKPNSKKRKISVPMEDYFNKGKNEPKDSKLQFGT*-LIWQQMKSENEPLQEELNKNLF
ParentalDNLIEFLQKSHSGFQKNSRDLGGQIKLREIPTAALVLGVNVTDHDLTFGSLTEALQNNVTPYVVSLQAKD
DNL.EFLQKSHSGFQKNSRDLG.Q.KLREIPTAALVLGV.VTDHDLTF.SLTEALQN.VTPYVVS.QAKD
RetrocopyDNLTEFLQKSHSGFQKNSRDLGCQTKLREIPTAALVLGVKVTDHDLTFRSLTEALQNKVTPYVVSSQAKD
ParentalCPDMKHFLQKLISQLMDCCVDIKSKEEESVHVTQRKTHYSMDSLSSWYMTVTQKTDPKMLSKKRTTSSQW
CPDMKHFLQ.L.S.LM.CCV..KSKE.ESV.VTQR.THY.MDSLSSWYMTVTQKTDPKM.SKKRTTSSQW
RetrocopyCPDMKHFLQNLVS*LMNCCVHLKSKEGESVQVTQRNTHYLMDSLSSWYMTVTQKTDPKMPSKKRTTSSQW
ParentalQSPPVVVILKDMESFATKVLQDFIIISSQHLHEFPLILIFGIATSPIIIHRLLPHAVSSLLCIELFQSLS
QSPPV...LKDMESFATKVLQDFIIISSQHLHEFPLILI.GIATS.II.HRL.PHAVSSLLCIELFQ.LS
RetrocopyQSPPVLATLKDMESFATKVLQDFIIISSQHLHEFPLILIVGIATS-IINHRLFPHAVSSLLCIELFQFLS
ParentalCKEHLTTVLDKLLLTTQFPFKINEKVLQVLTNIFLYHDFSVQNFI-KGLQLSLLEHFYSQPLSVLCCNLP
CKEH.T.VL.KLLLTTQFPFKINEKVLQVLTNIFLYHDFS.QNFI.K.LQLSLLEHF.SQPLSVLCCNLP
RetrocopyCKEHQTMVLNKLLLTTQFPFKINEKVLQVLTNIFLYHDFSIQNFI<KSLQLSLLEHFCSQPLSVLCCNLP
ParentalEAKRRINFLSNNQCENIRRLPSFRRYVEKQASEKQVALLTNERYLKEETQLLLENLHVYHMNYFLVLRCL
..KRRINFLSNNQCENI.RLPSFRRYVEKQASEKQVALLT.ER.LK.ETQLLLENLHVYHMNYFLVLRC.
Retrocopy*VKRRINFLSNNQCENI*RLPSFRRYVEKQASEKQVALLTSERCLKKETQLLLENLHVYHMNYFLVLRCV
ParentalHKFTSSLPKYPLGRQIRELY
HKFTSSLPKYPLGRQIRELY
RetrocopyHKFTSSLPKYPLGRQIRELY

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
bodymap2_adipose 0 .00 RPM 17 .83 RPM
bodymap2_adrenal 0 .00 RPM 21 .96 RPM
bodymap2_brain 0 .00 RPM 29 .28 RPM
bodymap2_breast 0 .00 RPM 24 .32 RPM
bodymap2_colon 0 .00 RPM 15 .66 RPM
bodymap2_heart 0 .00 RPM 20 .90 RPM
bodymap2_kidney 0 .00 RPM 20 .95 RPM
bodymap2_liver 0 .00 RPM 9 .00 RPM
bodymap2_lung 0 .00 RPM 12 .34 RPM
bodymap2_lymph_node 0 .00 RPM 17 .41 RPM
bodymap2_ovary 0 .04 RPM 42 .62 RPM
bodymap2_prostate 0 .00 RPM 27 .56 RPM
bodymap2_skeletal_muscle 0 .00 RPM 27 .43 RPM
bodymap2_testis 0 .11 RPM 60 .05 RPM
bodymap2_thyroid 0 .00 RPM 33 .82 RPM
bodymap2_white_blood_cells 0 .00 RPM 16 .48 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_798 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_798 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_798 retrocopy 5' end.

Lab - click to see more details

retro_hsap_798 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_798 has 2 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_555
Pongo abelii retro_pabe_712
Parental genes homology:
Parental genes homology involve 6 parental genes, and 6 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000007301 retrocopy
retro_cjac_913,
Homo sapiens ENSG00000135336 1 retrocopy
retro_hsap_798 ,
Macaca mulatta ENSMMUG000000028211 retrocopy
retro_mmul_1075,
Nomascus leucogenys ENSNLEG000000129901 retrocopy
retro_nleu_413,
Pongo abelii ENSPPYG000000168301 retrocopy
retro_pabe_712,
Pan troglodytes ENSPTRG000000184081 retrocopy
retro_ptro_555,

Expression level across human populations :
image/svg+xml GBR_HG00142 GBR_HG00099 GBR_HG00114 GBR_HG00143 GBR_HG00131 GBR_HG00137 GBR_HG00133 GBR_HG00119 GBR_HG00111 GBR_HG00134 FIN_HG00378 FIN_HG00338 FIN_HG00349 FIN_HG00375 FIN_HG00315 FIN_HG00277 FIN_HG00328 FIN_HG00321 FIN_HG00377 FIN_HG00183 TSI_NA20756 TSI_NA20538 TSI_NA20798 TSI_NA20532 TSI_NA20765 TSI_NA20518 TSI_NA20513 TSI_NA20512 TSI_NA20771 TSI_NA20786 YRI_NA19114 YRI_NA19099 YRI_NA18870 YRI_NA18907 YRI_NA19223 YRI_NA19214 YRI_NA18916 YRI_NA19093 YRI_NA19118 YRI_NA19213 Toscaniin Italia: Finnish inFinland: British in England and Scotland: Utah Residents (CEPH) with Northernand Western European Ancestry: Yoruba in Ibadan, Nigeria: CEU_NA12760 CEU_NA12827 CEU_NA12872 CEU_NA12751 CEU_NA12873 CEU_NA12400 CEU_NA11930 CEU_NA12004 CEU_NA11831 CEU_NA11843 No expression ( = 0 RPM ) > 0 RPM = 0.05 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .05 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .00 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .00 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .00 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .00 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .00 RPM
GBR_HG00131 0 .00 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .00 RPM
GBR_HG00143 0 .03 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .00 RPM
TSI_NA20532 0 .00 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .02 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .00 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .00 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .00 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .00 RPM

Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).





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