RetrogeneDB ID:

retro_hsap_3504

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:6:106114708..106115870(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000219088
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:CHAF1B
Ensembl ID:ENSG00000159259
Aliases:None
Description:chromatin assembly factor 1, subunit B (p60) [Source:HGNC Symbol;Acc:1911]


Retrocopy-Parental alignment summary:






>retro_hsap_3504
AAAAGTTATGTCCAAGGAATAAACTGGGACCCTTTAGGTCAATATGTTGCTACTCTGAGCTGTGACACGGTGCTGCAGGT
ATACAATATACAGAAGAAGCATGTGGTTTTTAATGTTTCAAAGATGCTATCTGGAATAGGGGCTGAAGGAGAGGCAAGAA
GCTACCGCATGTTTCATGATGACAGCATGAAGTTGTTCTTCCATAGACTGAGTTTCACTCCCAATGGATCTTTGCTCCTC
ACACCAGCCAGATGTGTGGAATCCGGTGAAAATGTAATGAACATCACTTACGTTTTCTCCGGGAAGGATCTTAAAAGGCC
CATCGCTCATCTTCCGTGTCCTGGAAAAGCCACTCTTGCTGTTGGCAGCTGTCTGGTCTATTTTGAACTGAGGCCAGTGG
TGGAAACAGGTGCGGAGCTAATGAGTCTGCCCTACCGCCTGGTATTTGCTGTGGCTTAGGAGGACTCTGTGCTTCTGGAC
ACCCAGGAGTCCTTCCCTTTCGGTTATGTGTCTAATATACATTACCACACCCTCAATGACATTTCATGGTCTAGCGATGG
CGCCTTCCTGGCCATTTCTTCCACAGACAGTTACTGCTCGTTTGTGACATTTGAGAAACGTGAACTTGGAATTCTTTTAA
AAGAGAAGTCAGTTTTGAGCATGAGAACTCCTGATACAGCAAAGAAAACCAAGAGTCAGACACACCAAGGGTCTTTGCCA
GGACCCAGACCCGTAGAGGGAACAACTGCCAGCAGAACCCAAGACCCCAGCAACCCCTGCTCAACCCCCACTCAGGCCAG
ACAGGCCCCAGCCCCAACAGCCACCAGGGACCCTCCCTCTATCATTCTGCTGTCAAAAGCTCCTTGCCGAGGCCTTCGGA
GGAGAAGACCCTGCCGCCCAGTAGTTAAAACACAAAAGCCCACCCATCCCGGAGGGTCACTCTGAACACACTGCAATCCT
GGAGCAAGACAACACCCTGGAGAATAAACTCAATACCCTTAAAGACAGACACTCCACCAAAGTCTGTACCAATCAATGTA
ATCTCCACCCCTTCTGCAGAAGAATTTAGTAAGAGACGCCTGGAAATGCTCAGGACAGTCCCGTAGAGCTAAAACAGCCC
AGACTCAGTGAAAACAAAGGGGGCACTGAAAGTCTGGAACCT

ORF - retro_hsap_3504 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.4 %
Parental protein coverage: 69.59 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKSYVQGVTWDPLGQYVATLSCDRVLRVYSIQKKRVAFNVSKMLSGIGAEGEARSYRMFHDDSMKSFFRRL
KSYVQG..WDPLGQYVATLSCD.VL.VY.IQKK.V.FNVSKMLSGIGAEGEARSYRMFHDDSMK.FF.RL
RetrocopyKSYVQGINWDPLGQYVATLSCDTVLQVYNIQKKHVVFNVSKMLSGIGAEGEARSYRMFHDDSMKLFFHRL
ParentalSFTPDGSLLLTPAGCVESGENVMNTTYVFSRKNLKRPIAHLPCPGKATLAVRCCPVYFELRPVVETGVEL
SFTP.GSLLLTPA.CVESGENVMN.TYVFS.K.LKRPIAHLPCPGKATLAV..C.VYFELRPVVETG.EL
RetrocopySFTPNGSLLLTPARCVESGENVMNITYVFSGKDLKRPIAHLPCPGKATLAVGSCLVYFELRPVVETGAEL
ParentalMSLPYRLVFAVASEDSVLLYDTQQSFPFGYVSNIHYHTLSDISWSSDGAFLAISSTDGYCSFVTFEKDEL
MSLPYRLVFAVA.EDSVLL.DTQ.SFPFGYVSNIHYHTL.DISWSSDGAFLAISSTD.YCSFVTFEK.EL
RetrocopyMSLPYRLVFAVA*EDSVLL-DTQESFPFGYVSNIHYHTLNDISWSSDGAFLAISSTDSYCSFVTFEKREL
ParentalGIPLKEKPVLNMRTPDTAKKTKSQTHRGSSPGPRPVEGTPASRTQDPSSPGTTPPQARQAPAPTVIRDPP
GI.LKEK.VL.MRTPDTAKKTKSQTH.GS.PGPRPVEGT.ASRTQDPS.P..TP.QARQAPAPT..RDPP
RetrocopyGILLKEKSVLSMRTPDTAKKTKSQTHQGSLPGPRPVEGTTASRTQDPSNPCSTPTQARQAPAPTATRDPP
ParentalSIT-PAVKSPLPGPSEEKTLQPSSQNTKAHPSRRVTLNTLQAWSKTTPRRINLTPLKTDTPPSSVPTSVI
SI...AVKS.LP.PSEEKTL.PSS.NTKAHPSRRVTLNTLQ.WSKTTP.RIN..PLKTDTPP.SVP..VI
RetrocopySII<SAVKSSLPRPSEEKTLPPSS*NTKAHPSRRVTLNTLQSWSKTTPWRINSIPLKTDTPPKSVPINVI
ParentalSTPSTEEIQS-ETPGDAQGSPPELKRPRLDENKGGTESLDP
STPS.EE....ETPG.AQ.SP.ELK.PRL.ENKGGTESL.P
RetrocopySTPSAEEFSK<ETPGNAQDSPVELKQPRLSENKGGTESLEP

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 4 .15 RPM
bodymap2_adrenal 0 .00 RPM 5 .22 RPM
bodymap2_brain 0 .00 RPM 7 .90 RPM
bodymap2_breast 0 .00 RPM 3 .77 RPM
bodymap2_colon 0 .00 RPM 1 .10 RPM
bodymap2_heart 0 .00 RPM 0 .89 RPM
bodymap2_kidney 0 .00 RPM 0 .95 RPM
bodymap2_liver 0 .00 RPM 0 .25 RPM
bodymap2_lung 0 .00 RPM 1 .97 RPM
bodymap2_lymph_node 0 .00 RPM 0 .75 RPM
bodymap2_ovary 0 .00 RPM 3 .66 RPM
bodymap2_prostate 0 .00 RPM 2 .39 RPM
bodymap2_skeletal_muscle 0 .00 RPM 16 .95 RPM
bodymap2_testis 0 .00 RPM 8 .69 RPM
bodymap2_thyroid 0 .00 RPM 6 .21 RPM
bodymap2_white_blood_cells 0 .00 RPM 2 .95 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_3504 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_3504 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_3504 retrocopy 5' end.

Lab - click to see more details

retro_hsap_3504 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_3504 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_2375
Gorilla gorilla retro_ggor_2369
Pongo abelii retro_pabe_2898
Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Homo sapiens ENSG00000159259 1 retrocopy
retro_hsap_3504 ,
Gorilla gorilla ENSGGOG000000157261 retrocopy
retro_ggor_2369,
Nomascus leucogenys ENSNLEG000000044291 retrocopy
retro_nleu_797,
Pongo abelii ENSPPYG000000114031 retrocopy
retro_pabe_2898,
Pan troglodytes ENSPTRG000000138911 retrocopy
retro_ptro_2375,

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 = 0.06 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 .04 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .00 RPM
FIN_HG00338 0 .00 RPM
FIN_HG00349 0 .06 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 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 .02 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 .05 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 .02 RPM
YRI_NA19093 0 .00 RPM
YRI_NA19099 0 .00 RPM
YRI_NA19114 0 .00 RPM
YRI_NA19118 0 .06 RPM
YRI_NA19213 0 .02 RPM
YRI_NA19214 0 .02 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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