RetrogeneDB ID:

retro_hsap_2551

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:22:26044125..26045196(+)
Located in intron of:ENSG00000100077
Retrocopy
information
Ensembl ID:ENSG00000224003
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YES1
Ensembl ID:ENSG00000176105
Aliases:YES1, HsT441, P61-YES, Yes, c-yes
Description:v-yes-1 Yamaguchi sarcoma viral oncogene homolog 1 [Source:HGNC Symbol;Acc:12841]


Retrocopy-Parental alignment summary:






>retro_hsap_2551
GAGAGCGAAACTACTAAAGGTGCTTATTCCCTCTCTATTCGTGATTGGGATGAGGTAAGGGGTGACAATGTGAAACACCA
CAAAATTAGGAAACTTGACAATGGTAGATACTATATCACAACCAGAGAACAACTTGATACTCTGCAGAAATTGGCAAAAC
ACTACACAGAACATGCTGATGGTTTATGCCACAAGTTAACAACTGTGTGTCCAACTGTGAAACCTCAGATTCAAGGTCTA
GCAAAAGATGCTTGGGAAATCCCTTGATAATCTTTGCGACTAGAGGTTAAACTAGGACAAGGATGTTTTGGCAAAGTGTG
GATGGGAATATGGAATGGAACCACAAAAGTAGCAATCAAAACACTAAAACCAGGTACAATGATGCCAGAAGCTTTTCTTC
AAGAAGCTCAGGTAATGAAAAAAATAAGACATGGTAAACTTGTTCCACTATATGCTGTTGTTTCTGAAGAGCCAATTTAC
ATTGTCACTGAATTGATGTCAAAAGGAAGCTTATTCAATTTCCTTAAGGAAGGAGATGGAAAGTATTTGAAGCTTCCACA
AATGGTTGATATGCCTGCTCAGATTGCTGATGGTATGGCATATATTAAAAGAATGAACTATATTCACCGAGATCTCTGGG
CTGCTAATATTCTTGTAGGAGAAAATCTTCTGTGCAAAATAGCAGATTTTGGTTTAGCAAGGTTAATTGAAGACAATGAA
TACACATCAAGACAAGGTGCAGAATTTCCAATCAAATGGACAGCTCCTGAAGTTGCACTGTATGGTGGGTTTACAATAAA
GTCTGGTGTCTGCTCATTTGGAATTCTACAGACAGAACTGGTAACAAAGGGCAGAGTGCCATATCCAGGTATGGTGAACC
ATGAAATACTGGAACAGGTGGAGCGAGGATACAGGATGCCTTGCCCTCAGGGCTGTCCAGAATCCCTCCATGAATTGATG
AATCTGTGTTGGAAGAAGGACCCTGATGAAAGACCAACATTTGAATATGTTCAGTCCTTCTTGGGAGACTACTTCACTGC
TACAGAGCCATAGTACCAGCCAGGAGAAAAC

ORF - retro_hsap_2551 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.76 %
Parental protein coverage: 65.75 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalESETTKGAYSLSIRDWDEIRGDNVKHYKIRKLDNGGYYITTRAQFDTLQKLVKHYTEHADGLCHKLTTVC
ESETTKGAYSLSIRDWDE.RGDNVKH.KIRKLDNG.YYITTR.Q.DTLQKL.KHYTEHADGLCHKLTTVC
RetrocopyESETTKGAYSLSIRDWDEVRGDNVKHHKIRKLDNGRYYITTREQLDTLQKLAKHYTEHADGLCHKLTTVC
ParentalPTVKPQTQGLAKDAWEIPRESLRLEVKLGQGCFGEVWMGTWNGTTKVAIKTLKPGTMMPEAFLQEAQIMK
PTVKPQ.QGLAKDAWEIP..SLRLEVKLGQGCFG.VWMG.WNGTTKVAIKTLKPGTMMPEAFLQEAQ.MK
RetrocopyPTVKPQIQGLAKDAWEIP**SLRLEVKLGQGCFGKVWMGIWNGTTKVAIKTLKPGTMMPEAFLQEAQVMK
ParentalKLRHDKLVPLYAVVSEEPIYIVTEFMSKGSLLDFLKEGDGKYLKLPQLVDMAAQIADGMAYIERMNYIHR
K.RH.KLVPLYAVVSEEPIYIVTE.MSKGSL..FLKEGDGKYLKLPQ.VDM.AQIADGMAYI.RMNYIHR
RetrocopyKIRHGKLVPLYAVVSEEPIYIVTELMSKGSLFNFLKEGDGKYLKLPQMVDMPAQIADGMAYIKRMNYIHR
ParentalDLRAANILVGENLVCKIADFGLARLIEDNEYTARQGAKFPIKWTAPEAALYGRFTIKSDVWSFGILQTEL
DL.AANILVGENL.CKIADFGLARLIEDNEYT.RQGA.FPIKWTAPE.ALYG.FTIKS.V.SFGILQTEL
RetrocopyDLWAANILVGENLLCKIADFGLARLIEDNEYTSRQGAEFPIKWTAPEVALYGGFTIKSGVCSFGILQTEL
ParentalVTKGRVPYPGMVNREVLEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYIQSFLEDYFTATEP
VTKGRVPYPGMVN.E.LEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEY.QSFL.DYFTATEP
RetrocopyVTKGRVPYPGMVNHEILEQVERGYRMPCPQGCPESLHELMNLCWKKDPDERPTFEYVQSFLGDYFTATEP
ParentalQYQPGEN
.YQPGEN
Retrocopy*YQPGEN

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 .70 RPM 205 .98 RPM
bodymap2_adrenal 1 .56 RPM 89 .66 RPM
bodymap2_brain 0 .49 RPM 48 .31 RPM
bodymap2_breast 1 .50 RPM 103 .50 RPM
bodymap2_colon 0 .46 RPM 148 .07 RPM
bodymap2_heart 0 .15 RPM 40 .49 RPM
bodymap2_kidney 0 .00 RPM 92 .59 RPM
bodymap2_liver 0 .04 RPM 66 .29 RPM
bodymap2_lung 0 .25 RPM 171 .52 RPM
bodymap2_lymph_node 0 .20 RPM 64 .25 RPM
bodymap2_ovary 0 .60 RPM 90 .74 RPM
bodymap2_prostate 0 .19 RPM 64 .71 RPM
bodymap2_skeletal_muscle 0 .00 RPM 27 .34 RPM
bodymap2_testis 0 .49 RPM 95 .92 RPM
bodymap2_thyroid 0 .73 RPM 114 .42 RPM
bodymap2_white_blood_cells 0 .22 RPM 7 .38 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_2551 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_2551 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_2551 retrocopy 5' end.

Lab - click to see more details

retro_hsap_2551 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_2551 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_1487
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000176105 1 retrocopy
retro_hsap_2551 ,
Monodelphis domestica ENSMODG000000214771 retrocopy
retro_mdom_1121,
Oryctolagus cuniculus ENSOCUG000000058741 retrocopy
retro_ocun_894,
Otolemur garnettii ENSOGAG000000033751 retrocopy
retro_ogar_1684,
Pan troglodytes ENSPTRG000000098241 retrocopy
retro_ptro_1487,

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 = 0.52 RPM Legend:


Library Retrogene expression
CEU_NA11831 0 .06 RPM
CEU_NA11843 0 .17 RPM
CEU_NA11930 0 .42 RPM
CEU_NA12004 0 .08 RPM
CEU_NA12400 0 .11 RPM
CEU_NA12751 0 .15 RPM
CEU_NA12760 0 .04 RPM
CEU_NA12827 0 .28 RPM
CEU_NA12872 0 .11 RPM
CEU_NA12873 0 .32 RPM
FIN_HG00183 0 .52 RPM
FIN_HG00277 0 .37 RPM
FIN_HG00315 0 .19 RPM
FIN_HG00321 0 .18 RPM
FIN_HG00328 0 .12 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .07 RPM
FIN_HG00377 0 .13 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .17 RPM
GBR_HG00111 0 .04 RPM
GBR_HG00114 0 .21 RPM
GBR_HG00119 0 .24 RPM
GBR_HG00131 0 .23 RPM
GBR_HG00133 0 .19 RPM
GBR_HG00134 0 .22 RPM
GBR_HG00137 0 .36 RPM
GBR_HG00142 0 .08 RPM
GBR_HG00143 0 .19 RPM
TSI_NA20512 0 .14 RPM
TSI_NA20513 0 .22 RPM
TSI_NA20518 0 .17 RPM
TSI_NA20532 0 .27 RPM
TSI_NA20538 0 .28 RPM
TSI_NA20756 0 .12 RPM
TSI_NA20765 0 .44 RPM
TSI_NA20771 0 .11 RPM
TSI_NA20786 0 .13 RPM
TSI_NA20798 0 .06 RPM
YRI_NA18870 0 .14 RPM
YRI_NA18907 0 .10 RPM
YRI_NA18916 0 .32 RPM
YRI_NA19093 0 .18 RPM
YRI_NA19099 0 .19 RPM
YRI_NA19114 0 .03 RPM
YRI_NA19118 0 .12 RPM
YRI_NA19213 0 .07 RPM
YRI_NA19214 0 .10 RPM
YRI_NA19223 0 .34 RPM

Indel association:

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



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