RetrogeneDB ID:

retro_hsap_280

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:197191351..197192382(+)
Located in intron of:ENSG00000134376
Retrocopy
information
Ensembl ID:ENSG00000237861
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ATP6AP2
Ensembl ID:ENSG00000182220
Aliases:ATP6AP2, APT6M8-9, ATP6IP2, ATP6M8-9, ELDF10, M8-9, MRXE, MRXSH, MSTP009, XMRE, XPDS
Description:ATPase, H+ transporting, lysosomal accessory protein 2 [Source:HGNC Symbol;Acc:18305]


Retrocopy-Parental alignment summary:






>retro_hsap_280
ATGATTGTGTTTGCCGTGCTCCTGTCGTTGGTGGCGGGTGTTTGAGGGAACGAGTTTAGTTCTTGGTCTGTTATTTTCAG
AAATGGAAATTGGCCTATACCGGGAGAGTGAATCCCAGACGTGGCTGCATTGTCCATGGCCTTCTCTGTGAAGGAAAACC
TTTCTTGGCCAGGACTTGCAGTAGGTGACCTATTTCATCGTCCTCGGGCTACCGTCATGGTGATGGTGAAGGGAGTGGAC
AAACTGGCTCTACCACCAGGCAGTGTCATTTCATACCCTTTGGAGAATGCAGTTCCGTTTGGTCTTGGCAGTGTTGCAAA
TTCCATTCGCTCTTTATTTTCTGACGAAACTCCTGTTGTTTTGCAGTTGGCTCCTAGTGAGGAAAGAGTGTATTTGGTAG
GGAAGGCAAACTCAGTGTTTGAAGACCTTTCAGTCACCTTAGGACAGCTCCATAATTACTTGTTTCAGGAAAACTCCATT
CTCAGTTCATTTCCCCTGAATTCTCTGAGTAGGAACAATGGAGTTGACTTGCTCTTTCTTTCTGAACTCCAAGTGCTACA
TGATATTTCAAGCTTGGTGTCTTGTCATAAGCATCTAGCCAAGGATCATTCTCCTGATTTATATTCACTGGAGCTGGCAG
GTTTGGATGAAATTGGGAAGCATTACAGGGAAGACTCTGAACAATTCATAGTTGCTTCTAAAATCCTGTTGACGCTCTGC
AAGAGTTTGCAGATAACATGTACAATCTTTACAGTGGGAATGCAGTGGTAGAGTTAGTCACTATTAAGTCATTTGACACC
TCCCTTATGAGGAAGACAAGGACTATCTTTGAGGCAAAATAAGTGAAGAACCCAGCAAGTCCCTATAACCTTGCGTATAA
TTTTGAATATTCAGTGATTTTCAACATGATACTTTGGATAATGATTGCCTTGGCCCTGGCTGTGATTATCACTTCTTACA
ATATTTGGAACATGGATCCTGGATATGATAGCATCATTTATAGGATTACAAACCAGAAGATTCGAATAGAT

ORF - retro_hsap_280 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.04 %
Parental protein coverage: 100.0 %
Number of stop codons detected: 3
Number of frameshifts detected: 1


Retrocopy - Parental Gene Alignment:

ParentalMAVFVVLLALVAGVLGNEFSILKSPGSVVFRNGNWPIPGERIPDVAALSMGFSVKEDLSWPGLAVGNLFH
M.VF.VLL.LVAGV.GNEF....S..SV.FRNGNWPIPGE.IPDVAALSM.FSVKE.LSWPGLAVG.LFH
RetrocopyMIVFAVLLSLVAGV*GNEF----SSWSVIFRNGNWPIPGE*IPDVAALSMAFSVKENLSWPGLAVGDLFH
ParentalRPRATVMVMVKGVNKLALPPGSVISYPLENAVPFSLDSVANSIHSLFSEETPVVLQLAPSEERVYMVGKA
RPRATVMVMVKGV.KLALPPGSVISYPLENAVPF.L.SVANSI.SLFS.ETPVVLQLAPSEERVY.VGKA
RetrocopyRPRATVMVMVKGVDKLALPPGSVISYPLENAVPFGLGSVANSIRSLFSDETPVVLQLAPSEERVYLVGKA
ParentalNSVFEDLSVTLRQLRNRLFQENSVLSSLPLNSLSRNNEVDLLFLSELQVLHDISSLLSRHKHLAKDHSPD
NSVFEDLSVTL.QL.N.LFQENS.LSS.PLNSLSRNN.VDLLFLSELQVLHDISSL.S.HKHLAKDHSPD
RetrocopyNSVFEDLSVTLGQLHNYLFQENSILSSFPLNSLSRNNGVDLLFLSELQVLHDISSLVSCHKHLAKDHSPD
ParentalLYSLELAGLDEIGKRYGEDSEQFRDASKIL-VDALQKFADDMYSLYGGNAVVELVTVKSFDTSLIRKTRT
LYSLELAGLDEIGK.Y.EDSEQF..ASKIL.VDALQ.FAD.MY.LY.GNAVVELVT.KSFDTSL.RKTRT
RetrocopyLYSLELAGLDEIGKHYREDSEQFIVASKIL<VDALQEFADNMYNLYSGNAVVELVTIKSFDTSLMRKTRT
ParentalILEAKQAKNPASPYNLAYKYNFEYSVVFNMVLWIMIALALAVIITSYNIWNMDPGYDSIIYRMTNQKIRM
I.EAK..KNPASPYNLA..YNFEYSV.FNM.LWIMIALALAVIITSYNIWNMDPGYDSIIYR.TNQKIR.
RetrocopyIFEAK*VKNPASPYNLA--YNFEYSVIFNMILWIMIALALAVIITSYNIWNMDPGYDSIIYRITNQKIRI
ParentalD
D
RetrocopyD

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 121 .32 RPM
bodymap2_adrenal 0 .08 RPM 115 .88 RPM
bodymap2_brain 0 .00 RPM 238 .46 RPM
bodymap2_breast 0 .12 RPM 161 .66 RPM
bodymap2_colon 0 .00 RPM 168 .43 RPM
bodymap2_heart 0 .00 RPM 45 .82 RPM
bodymap2_kidney 0 .00 RPM 237 .04 RPM
bodymap2_liver 0 .00 RPM 85 .30 RPM
bodymap2_lung 0 .00 RPM 194 .16 RPM
bodymap2_lymph_node 0 .00 RPM 137 .67 RPM
bodymap2_ovary 0 .13 RPM 145 .69 RPM
bodymap2_prostate 0 .00 RPM 157 .49 RPM
bodymap2_skeletal_muscle 0 .00 RPM 28 .63 RPM
bodymap2_testis 0 .21 RPM 124 .98 RPM
bodymap2_thyroid 0 .04 RPM 267 .05 RPM
bodymap2_white_blood_cells 0 .00 RPM 332 .35 RPM

ChIP-Seq - click to see more details

RNA Polymerase II activity may be related with retro_hsap_280 in 2 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF002DBO POLR2A 1:197191118..197191502
ENCFF002DBP POLR2A 1:197191147..197191477

EST - click to see more details

No EST(s) were mapped for retro_hsap_280 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_280 retrocopy 5' end.

Lab - click to see more details

retro_hsap_280 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_280 has 4 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_233
Gorilla gorilla retro_ggor_323
Pongo abelii retro_pabe_389
Macaca mulatta retro_mmul_561
Parental genes homology:
Parental genes homology involve 8 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Dasypus novemcinctus ENSDNOG000000061091 retrocopy
retro_dnov_2102,
Homo sapiens ENSG00000182220 1 retrocopy
retro_hsap_280 ,
Gorilla gorilla ENSGGOG000000005321 retrocopy
retro_ggor_323,
Myotis lucifugus ENSMLUG000000011591 retrocopy
retro_mluc_1613,
Macaca mulatta ENSMMUG000000127621 retrocopy
retro_mmul_561,
Nomascus leucogenys ENSNLEG000000014411 retrocopy
retro_nleu_1491,
Pongo abelii ENSPPYG000000202511 retrocopy
retro_pabe_389,
Pan troglodytes ENSPTRG000000218031 retrocopy
retro_ptro_233,

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 .00 RPM
FIN_HG00315 0 .06 RPM
FIN_HG00321 0 .00 RPM
FIN_HG00328 0 .05 RPM
FIN_HG00338 0 .02 RPM
FIN_HG00349 0 .00 RPM
FIN_HG00375 0 .02 RPM
FIN_HG00377 0 .00 RPM
FIN_HG00378 0 .02 RPM
GBR_HG00099 0 .00 RPM
GBR_HG00111 0 .02 RPM
GBR_HG00114 0 .03 RPM
GBR_HG00119 0 .05 RPM
GBR_HG00131 0 .03 RPM
GBR_HG00133 0 .05 RPM
GBR_HG00134 0 .00 RPM
GBR_HG00137 0 .00 RPM
GBR_HG00142 0 .06 RPM
GBR_HG00143 0 .00 RPM
TSI_NA20512 0 .03 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 .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 .04 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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