RetrogeneDB ID:

retro_hsap_49

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:X:22291108..22292386(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000175809
Aliases:ZNF645, CT138, HAKAIL
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:CBLL1
Ensembl ID:ENSG00000105879
Aliases:CBLL1, HAKAI, RNF188
Description:Cbl proto-oncogene-like 1, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:21225]


Retrocopy-Parental alignment summary:






>retro_hsap_49
ATGAACAAGATGCCTGCTGGTGAACAAGAATGTGAATATAACAAAGAAGGGAAGTACTACTCTAAAGGAGTTAAACTGGT
GAGAAAAAAGAAAAAAATTCCTGGTTACCGTTGGGGGGACATTAAGATAAACATCATAGGTGAAAAGGATGATTTACCAA
TTCATTTCTGTGACAAATGTGATTTGCCTATTAAAATCTATGGGCGAATAATTCCGTGCAAGCATGCTTTTTGCTATCAC
TGTGCTAATTTATATGACAAAGTCGGATATAAAGTATGTCCGCGCTGTCGTTATCCTGTGCTGAGAATTGAGGCGCATAA
ACGAGGTTCTGTCTTCATGTGTAGTATTGTTCAGCAGTGCAAGAGAACATACTTGTCTCAGAAAAGCTTACAGGCTCATA
TCAAACGCCGCCATAAGAGAGCTCGAAAACAAGTTACCAGCGCTTCGCTTGAAAAAGTTCGTCCTCATATTGCTCCGCCA
CAAACTGAAATCTCTGACATCCCTAAAAGACTGCAAGACAGGGACCATCTAAGCTATATTCCACCAGAACAGCACACCAT
GGTGTCACTACCGTCTGTGCAACATATGCTACAAGAGCAACATAATCAGCCACATAAGGATATCCAGGCTCCTCCCCCAG
AACTATCTCTAAGTCTGCCTTTTCCCATCCAGTGGGAAACCGTTAGTATTTTTACGAGAAAACATGGCAATTTAACAGTT
GATCATATTCAGAATAACTCAGATTCTGGTGCTAAGAAGCCAACACCTCCCGACTATTATCCTGAGTGTCAAAGTCAACC
AGCGGTATCGTCCCCTCATCATATTATACCTCAGAAACAGCATTATGCGCCACCTCCATCTCCATCATCACCAGTAAACC
ATCAAATGCCATATCCTCCTCAGGATGTAGTTACTCCTAACTCGGTTCGTAGCCAAGTGCCAGCTCTAACCACGACCTAC
GATCCATCATCTGGATATATTATTGTAAAGGTGCCACCTGATATGAATTCTCCTCCACTACGTGCTCCCCAGTCTCAAAA
TGGTAATCCATCTGCAAGTGAATTTGCTTCTCACCATTATAACCTTAACATTTTACCTCAGTTCACCGAAAATCAAGAAA
CCTTGAGCCCTCAGTTTACACAAACAGATGCAATGGATCATAGAAGGTGGCCTGCATGGAAACGACTGTCACCTTGTCCA
CCAACGCGGAGTCCACCTCCTTCAACCCTACATGGTCGATCACATCATTCACACCAGAGAAGACATAGACGGTATTAA

ORF - retro_hsap_49 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.23 %
Parental protein coverage: 58.98 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKAPPGDEGFDYNEEERYDCKGGELFANQRRFPGHLFWDFQINILGEKDDTPVHFCDKCGLPIKIYGRMIP
K.P.G.....YN.E..Y..KG..L.......PG....D..INI.GEKDD.P.HFCDKC.LPIKIYGR.IP
RetrocopyKMPAGEQECEYNKEGKYYSKGVKLVRKKKKIPGYRWGDIKINIIGEKDDLPIHFCDKCDLPIKIYGRIIP
ParentalCKHVFCYDCAILHEKKGDKMCPGCSDPVQRIEQCTRGSLFMCSIVQGCKRTYLSQRDLQAHINHRHMRAG
CKH.FCY.CA.L..K.G.K.CP.C..PV.RIE...RGS.FMCSIVQ.CKRTYLSQ..LQAHI..RH.RA.
RetrocopyCKHAFCYHCANLYDKVGYKVCPRCRYPVLRIEAHKRGSVFMCSIVQQCKRTYLSQKSLQAHIKRRHKRAR
ParentalKPVTRASLENVHPPIAPPPTEIPERFIMPPDKHHMSHIPPKQHIMMPPPPLQHVPHEHYNQPHEDIRAPP
K.VT.ASLE.V.P.IAPP.TEI........D..H.S.IPP.QH.M...P..QH...E..NQPH.DI.APP
RetrocopyKQVTSASLEKVRPHIAPPQTEISDIPKRLQDRDHLSYIPPEQHTMVSLPSVQHMLQEQHNQPHKDIQAPP
ParentalAELSMAPPPPRSVSQETFRISTRKHSNLITVPIQDDSNSGAREPPPPAPAPAHHHPEYQGQP--VVSHPH
.ELS...P.P.....ET..I.TRKH.NL....IQ..S.SGA..P.PP...P..........P........
RetrocopyPELSLSLPFP--IQWETVSIFTRKHGNLTVDHIQNNSDSGAKKPTPPDYYPECQSQPAVSSPHHIIPQKQ
ParentalHIMPPQQHYAP
H..PP.....P
RetrocopyHYAPPPSPSSP

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 .75 RPM
bodymap2_adrenal 0 .00 RPM 18 .75 RPM
bodymap2_brain 0 .02 RPM 17 .32 RPM
bodymap2_breast 0 .00 RPM 15 .06 RPM
bodymap2_colon 0 .00 RPM 15 .84 RPM
bodymap2_heart 0 .00 RPM 18 .00 RPM
bodymap2_kidney 0 .00 RPM 13 .01 RPM
bodymap2_liver 0 .00 RPM 7 .61 RPM
bodymap2_lung 0 .00 RPM 11 .90 RPM
bodymap2_lymph_node 0 .00 RPM 16 .81 RPM
bodymap2_ovary 0 .00 RPM 28 .14 RPM
bodymap2_prostate 0 .09 RPM 19 .29 RPM
bodymap2_skeletal_muscle 0 .00 RPM 30 .19 RPM
bodymap2_testis 7 .32 RPM 29 .47 RPM
bodymap2_thyroid 0 .06 RPM 20 .92 RPM
bodymap2_white_blood_cells 0 .00 RPM 62 .67 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_49 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_49 retrocopy
EST ID Start End Identity Match Mis-match Score
BP370443 22291059 22291624 99.3 558 4 554

TSS - click to see more details

No TSS is located nearby retro_hsap_49 retrocopy 5' end.

Lab - click to see more details

retro_hsap_49 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_49 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_67
Gorilla gorilla retro_ggor_164
Pongo abelii retro_pabe_112
Canis familiaris retro_cfam_2047
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000163791 retrocopy
retro_cjac_4046,
Homo sapiens ENSG00000105879 1 retrocopy
retro_hsap_49 ,
Gorilla gorilla ENSGGOG000000049211 retrocopy
retro_ggor_164,
Microcebus murinus ENSMICG000000129361 retrocopy
retro_mmur_1635,
Nomascus leucogenys ENSNLEG000000086601 retrocopy
retro_nleu_19,
Pongo abelii ENSPPYG000000179041 retrocopy
retro_pabe_112,
Pan troglodytes ENSPTRG000000195831 retrocopy
retro_ptro_67,
Rattus norvegicus ENSRNOG000000072531 retrocopy
retro_rnor_1063,

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 = 0.02 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .02 RPM
CEU_NA11843 0 .00 RPM
CEU_NA11930 0 .00 RPM
CEU_NA12004 0 .00 RPM
CEU_NA12400 0 .00 RPM
CEU_NA12751 0 .00 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 .00 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 .00 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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