RetrogeneDB ID:

retro_hsap_637

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:10:125751263..125752188(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000213438
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:YBX2
Ensembl ID:ENSG00000006047
Aliases:YBX2, CONTRIN, CSDA3, DBPC, MSY2
Description:Y box binding protein 2 [Source:HGNC Symbol;Acc:17948]


Retrocopy-Parental alignment summary:






>retro_hsap_637
ATGAGCGAGGTGGAGGCGGCAGCGGTGGCGACAGCGGTCCCCGCGGCGACGGTGCCCGCGACGGTGGCAGGGGTGGTAGC
GGTGGTGGTACCGGTGCCCGCAGGGGAGCCGCAGAAAGCAGGCGGCGGGGCGGGCGGCTGCGGCGGGGACGCAGCCGCCT
TGGACCCCGCTGCTGGGACCCCCTCGGCGCCGGGCCCCCGCACCCCTGGCAACCCGGCGACGGCGGCCTCGGGAACCCCC
GCCCGGAGTCAGGCGGACAAGCCGGTGCTGGCAACCCGAGTCCTGCCTGGGCACTGCCAAACGGTTCAACGTCCGGAGTG
GTTACGGATTCACCAACAGGAATGACGCCAAGGAAGATGTCTTCGTTCACTGGACAGCTGTTAAAAGAAACAACCCCAGG
AAGTTTCTGCGCAGCGTTAGAGATGGGGAGACTGTGGAATTTGATGTCGTGGAAGGAGAGAAGGGCGCAGAAGCCACTAA
TGTAACTGGGCCCAGGGCGGCGGGGGTGCCCATGAAGGGCACCGTTATGCCCCCAACCGACGTAGGTTCCGCTGATTCAT
CCCCGGCCTCCCTCAGTTGCCCCACCACCCATGGTGGCAGAGATCCCCTCTCGGGGGACAGAACCTGGCGGCGAAGGGGA
GCGGGCCGAAGACTCTGGGCAGCGGCCCAGACGATGGCGCCCCCCACCCTTCTACCTACGGCGGTTTGTGCGAGGCCCCC
GGCCCCCCAACCAGCAGCAGCCTATAGAGGGCACTGATGGGGTAGAACCAAACAGACAGCCCCATTGGAGGGGCACCAAC
AGCAGGGAGATGAGTGGGTCCCCCCGCCCAGATTCCGGCCCAGGTACCTAAGGCCTTTACGCCCCAGGCCACCCCAGCAG
CCTACCATGGAAGGTGGGGACAGTGATACCAAGCCCAGCCAAGGA

ORF - retro_hsap_637 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.75 %
Parental protein coverage: 84.34 %
Number of stop codons detected: 1
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalMSEVEAAAGATAVPAATVPATAAGVVAVVVPV-PAGEPQKGGGAGGGGGAASGPAAGTPSAPGSRTPGNP
MSEVEAAA.ATAVPAATVPAT.AGVVAVVVPV.P.G...K...AG....A...P.......P..R....P
RetrocopyMSEVEAAAVATAVPAATVPATVAGVVAVVVPV>PQGSRRKQA-AGRAAAAGTQPPWTPLLGPPRRRAPAP
ParentalATAVSGTPA--PPARSQADKPVLAIQVLGTVKWFNVRNGYGFINRNDTKEDVFVHQTAIKRNNPRKFLRS
.......P...PP..............LGT.K.FNVR.GYGF.NRND.KEDVFVH.TA.KRNNPRKFLRS
RetrocopyLATRRRRPREPPPGVRRTSRCWQPESCLGTAKRFNVRSGYGFTNRNDAKEDVFVHWTAVKRNNPRKFLRS
ParentalVGDGETVEFDVVEGEKGAEATNVTGP--GGVPVKGS-RYAPNRRKSRRFI-PRPPSVAPPPMVAEIPSAG
V.DGETVEFDVVEGEKGAEATNVTGP...GVP.KG..RYAPNRR..R.FI.PRPPSVAPPPMVAEIPS.G
RetrocopyVRDGETVEFDVVEGEKGAEATNVTGPRAAGVPMKGT<RYAPNRRRFR*FI<PRPPSVAPPPMVAEIPSRG
ParentalTGPGSKGERAEDSGQRPRRWCPPPFFYRRRFVRGPRPPNQQQPIEGTDRVEP-KETAPLEGHQQQGDERV
T.PG..GERAEDSGQRPRRW.PPP.FY.RRFVRGPRPPNQQQPIEGTD.VEP.K.TAPLEGHQQQGDE.V
RetrocopyTEPGGEGERAEDSGQRPRRWRPPP-FYLRRFVRGPRPPNQQQPIEGTDGVEP<KQTAPLEGHQQQGDEWV
ParentalPPPRFRPRYRRPFRPRPRQQPTTEGGDGETKPSQG
PPPRFRPRY.RP.RPRP.QQPT.EGGD..TKPSQG
RetrocopyPPPRFRPRYLRPLRPRPPQQPTMEGGDSDTKPSQG

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 .02 RPM 1 .93 RPM
bodymap2_adrenal 0 .00 RPM 2 .33 RPM
bodymap2_brain 0 .02 RPM 0 .52 RPM
bodymap2_breast 0 .00 RPM 6 .07 RPM
bodymap2_colon 0 .00 RPM 2 .94 RPM
bodymap2_heart 0 .00 RPM 0 .72 RPM
bodymap2_kidney 0 .00 RPM 1 .57 RPM
bodymap2_liver 0 .00 RPM 0 .42 RPM
bodymap2_lung 0 .02 RPM 0 .32 RPM
bodymap2_lymph_node 0 .00 RPM 1 .11 RPM
bodymap2_ovary 0 .02 RPM 0 .25 RPM
bodymap2_prostate 0 .00 RPM 1 .89 RPM
bodymap2_skeletal_muscle 0 .00 RPM 3 .07 RPM
bodymap2_testis 0 .21 RPM 244 .41 RPM
bodymap2_thyroid 0 .00 RPM 1 .92 RPM
bodymap2_white_blood_cells 0 .04 RPM 0 .00 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_637 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_hsap_637 retrocopy
EST ID Start End Identity Match Mis-match Score
HY029655 125751208 125751670 99.8 460 1 459

TSS - click to see more details

No TSS is located nearby retro_hsap_637 retrocopy 5' end.

Lab - click to see more details

retro_hsap_637 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_637 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_464
Parental genes homology:
Parental genes homology involve 8 parental genes, and 13 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000165811 retrocopy
retro_cjac_1473,
Homo sapiens ENSG00000006047 1 retrocopy
retro_hsap_637 ,
Homo sapiens ENSG000000601381 retrocopy
retro_hsap_1674,
Homo sapiens ENSG000000659784 retrocopies
retro_hsap_1433, retro_hsap_3886, retro_hsap_4250, retro_hsap_4301,
Macaca mulatta ENSMMUG000000227121 retrocopy
retro_mmul_2237,
Nomascus leucogenys ENSNLEG000000080631 retrocopy
retro_nleu_1954,
Oryctolagus cuniculus ENSOCUG000000150641 retrocopy
retro_ocun_1762,
Pan troglodytes ENSPTRG000000086733 retrocopies
retro_ptro_1264, retro_ptro_464, retro_ptro_50,

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 ) 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 .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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