RetrogeneDB ID:

retro_hsap_4708

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:73326267..73327793(+)
Located in intron of:ENSG00000230590
Retrocopy
information
Ensembl ID:ENSG00000223650
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UHRF2
Ensembl ID:ENSG00000147854
Aliases:UHRF2, NIRF, RNF107, URF2
Description:ubiquitin-like with PHD and ring finger domains 2, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:12557]


Retrocopy-Parental alignment summary:






>retro_hsap_4708
GGGGGTTCTGAAGGGGCATTAAATGAGTGCAAAATAATATCTGTAGATGAAATCTTCAAGACTGAGAAACCTGGAGCCTA
TCCTCTTTCGTTTGCAGATGTAAAGTTTTTAAGGAGAAATAACTCTGAATATGACCTGTGTGGTGGAGACCCAGATAAGA
AATGCCATTCTTGCTTCTTTCATGTATATGGTGGGAAACATGAACCCAACATGCAGCTTCTATGTGATGAATGTAATGCG
GCTTATCATATTTACTGCTTGAATACACCTTTGGATAAAGTCCCAGAAGAGGAATACTGGTATTGTTCTTCCTGTAAAAC
TGATTCCAGTTAAGTTGTAAAGGCTGGTGAAAGACTCGAGATGAGTGAAAAGAAAGCAAAGATGCCATCCGCTAGTACTG
AAAGCCAGAGAGACTGGTGCAGGAGAATGGCTTGTGTTGGTCATATGACAGAATGCACTATTGTCTCTTCTAATCATTAT
GGACCTATTCCTGTTGGATCAACTTGGAGATTTAGAGTTCAGGTGAGTGAAGTAGGTGTTCACAGACCCCATGTTGGTGG
ACTTCATGGTCGAAGTAATGATGGAGTTTATTCTCTTGTCTTGGTTGGTGGATTTGTGGATAAAGTTGACCGAGGTGATG
AGTTCTTGTACACTGGAAGTGGTGGTAAAAAGCTTGCTGGTAATAAAAGAATTGGCACACCTTCAGCTGATCAAACATTA
ACAAACACAAACAGGGCATTGGCCCTAAACTGTGATGCTACATTGGGTGATAAAATTGGAGCAGAGTCTTGGAATTGGAG
AGCTGGTAAGCCAGTCAGAGTGATATGCAGTTTTAAAGGGAGGAAGATCAGCAAATATGCTCCTGAAGAAGGCAACAGAT
ATGATGGCATTTATAAGGTAGTGAAATACTGGCCAGAGATTTCATCAAGCCATGGACTCTTGATTTGGCGCTATCTTTTA
AGAAGAGATGATGTTGAACCTGCTCCTTGGACCTCTGAAGGAATAGAATGGTCAAGGAGATTATGTCTACATTTACAGTA
TCCAGCAGGTTACCCTTCAGATAAAGAAAGGAAGAAGACTAAAGGACAGTCAAAGAAGCAGGCCAGTGGAACCACAAAAA
GGCCGATTTCAAATGTCTAAGTGCCTCCAAAGTATACAAAGCATCAGATTCAGCAGGAGCAATTGAGGCTTTTCAACTAA
CTCCTCAACAGCAACATCTCATCAGAGAAGACTGTCAAAACCAGAAGCTGTGGGATGAAGTGCTTGCATATCTTGTGGAA
GGACCAAATTTTCTGAAAAAATTGGAACAATCTTTTATGTGTGTTTGCTGCCAGAAGCTAGTTTACCAGCCTGTGACAAC
TGAGTGCTTCCAGAATGTCTGTAAAAATTGCCAACAGTGCTCCTTTAAGGCATAGGTTTTCTCCTGCCCTGCTTGCTGGC
ATGATCTTGGCCAGAATTATGTCATAATTCCCCATGAGATTCTGCAGACTCTACTAGACCTTTTCTTCCCTGGCTACAGC
AAAGGA

ORF - retro_hsap_4708 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.08 %
Parental protein coverage: 64.09 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGGSEGTLNDCKIISVDEIFKIERPGAHPLSFADGKFLRRNDPECDLCGGDPEKKCHSCSCRVCGGKHEPN
GGSEG.LN.CKIISVDEIFK.E.PGA.PLSFAD.KFLRRN..E.DLCGGDP.KKCHSC...V.GGKHEPN
RetrocopyGGSEGALNECKIISVDEIFKTEKPGAYPLSFADVKFLRRNNSEYDLCGGDPDKKCHSCFFHVYGGKHEPN
ParentalMQLLCDECNVAYHIYCLNPPLDKVPEEEYWYCPSCKTDSSEVVKAGERLKMSKKKAKMPSASTESRRDWG
MQLLCDECN.AYHIYCLN.PLDKVPEEEYWYC.SCKTDSS.VVKAGERL.MS.KKAKMPSASTES.RDW.
RetrocopyMQLLCDECNAAYHIYCLNTPLDKVPEEEYWYCSSCKTDSS*VVKAGERLEMSEKKAKMPSASTESQRDWC
ParentalRGMACVGRTRECTIVPSNHYGPIPGIPVGSTWRFRVQVSEAGVHRPHVGGIHGRSNDGAYSLVLAGGFAD
R.MACVG...ECTIV.SNHYGP...IPVGSTWRFRVQVSE.GVHRPHVGG.HGRSNDG.YSLVL.GGF.D
RetrocopyRRMACVGHMTECTIVSSNHYGP---IPVGSTWRFRVQVSEVGVHRPHVGGLHGRSNDGVYSLVLVGGFVD
ParentalEVDRGDEFTYTGSGGKNLAGNKRIGAPSADQTLTNMNRALALNCDAPLDDKIGAESRNWRAGKPVRVIRS
.VDRGDEF.YTGSGGK.LAGNKRIG.PSADQTLTN.NRALALNCDA.L.DKIGAES.NWRAGKPVRVI.S
RetrocopyKVDRGDEFLYTGSGGKKLAGNKRIGTPSADQTLTNTNRALALNCDATLGDKIGAESWNWRAGKPVRVICS
ParentalFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGFLVWRYLLRRDDVEPAPWTSEGIERSRRLCLRLQY
FKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHG.L.WRYLLRRDDVEPAPWTSEGIE.SRRLCL.LQY
RetrocopyFKGRKISKYAPEEGNRYDGIYKVVKYWPEISSSHGLLIWRYLLRRDDVEPAPWTSEGIEWSRRLCLHLQY
ParentalPAGYPSDKEGKKPKGQSKKQPSGTTKRPISDDDCPSASKVYKASDSAEAIEAF-QLTPQQQHLIREDCQN
PAGYPSDKE.KK.KGQSKKQ.SGTTKRPIS....P...K..K.....E....F.QLTPQQQHLIREDCQN
RetrocopyPAGYPSDKERKKTKGQSKKQASGTTKRPISNV*VP--PKYTKHQIQQEQLRLF<QLTPQQQHLIREDCQN
ParentalQKLWDEVLSHLVEGPNFLKKLEQSFMCVCCQELVYQPVTTECFHNVCKDCLQRSFKAQVFSCPACRHDLG
QKLWDEVL..LVEGPNFLKKLEQSFMCVCCQ.LVYQPVTTECF.NVCK.C.Q.SFKA.VFSCPAC.HDLG
RetrocopyQKLWDEVLAYLVEGPNFLKKLEQSFMCVCCQKLVYQPVTTECFQNVCKNCQQCSFKA*VFSCPACWHDLG
ParentalQNYIMIPNEILQTLLDLFFPGYSKG
QNY..IP.EILQTLLDLFFPGYSKG
RetrocopyQNYVIIPHEILQTLLDLFFPGYSKG

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 .08 RPM 21 .93 RPM
bodymap2_adrenal 0 .00 RPM 60 .22 RPM
bodymap2_brain 0 .00 RPM 27 .96 RPM
bodymap2_breast 0 .12 RPM 31 .07 RPM
bodymap2_colon 0 .00 RPM 52 .26 RPM
bodymap2_heart 0 .07 RPM 15 .82 RPM
bodymap2_kidney 0 .00 RPM 38 .40 RPM
bodymap2_liver 0 .00 RPM 8 .51 RPM
bodymap2_lung 0 .00 RPM 41 .53 RPM
bodymap2_lymph_node 0 .00 RPM 81 .23 RPM
bodymap2_ovary 0 .12 RPM 50 .00 RPM
bodymap2_prostate 0 .00 RPM 73 .90 RPM
bodymap2_skeletal_muscle 0 .00 RPM 26 .08 RPM
bodymap2_testis 0 .00 RPM 60 .99 RPM
bodymap2_thyroid 0 .11 RPM 39 .66 RPM
bodymap2_white_blood_cells 0 .00 RPM 36 .25 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_4708 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_4708 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_4708 retrocopy 5' end.

Lab - click to see more details

retro_hsap_4708 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_4708 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000147854 1 retrocopy
retro_hsap_4708 ,
Gorilla gorilla ENSGGOG000000088531 retrocopy
retro_ggor_2925,
Nomascus leucogenys ENSNLEG000000091351 retrocopy
retro_nleu_1985,
Pongo abelii ENSPPYG000000192271 retrocopy
retro_pabe_3656,

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 = 0.11 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .00 RPM
CEU_NA11843 0 .06 RPM
CEU_NA11930 0 .03 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 RPM
CEU_NA12760 0 .00 RPM
CEU_NA12827 0 .05 RPM
CEU_NA12872 0 .00 RPM
CEU_NA12873 0 .00 RPM
FIN_HG00183 0 .00 RPM
FIN_HG00277 0 .11 RPM
FIN_HG00315 0 .00 RPM
FIN_HG00321 0 .09 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .03 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .00 RPM
GBR_HG00114 0 .00 RPM
GBR_HG00119 0 .02 RPM
GBR_HG00131 0 .06 RPM
GBR_HG00133 0 .00 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .00 RPM
TSI_NA20513 0 .00 RPM
TSI_NA20518 0 .03 RPM
TSI_NA20532 0 .10 RPM
TSI_NA20538 0 .00 RPM
TSI_NA20756 0 .00 RPM
TSI_NA20765 0 .04 RPM
TSI_NA20771 0 .00 RPM
TSI_NA20786 0 .00 RPM
TSI_NA20798 0 .03 RPM
YRI_NA18870 0 .00 RPM
YRI_NA18907 0 .00 RPM
YRI_NA18916 0 .02 RPM
YRI_NA19093 0 .05 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .00 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .00 RPM
YRI_NA19223 0 .02 RPM

Indel association:

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



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