RetrogeneDB ID:

retro_hsap_1537

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:15:22691018..22692943(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000259689
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:ABCB10
Ensembl ID:ENSG00000135776
Aliases:ABCB10, EST20237, M-ABC2, MTABC2
Description:ATP-binding cassette, sub-family B (MDR/TAP), member 10 [Source:HGNC Symbol;Acc:41]


Retrocopy-Parental alignment summary:






>retro_hsap_1537
GGGCCCGGCAGCTGCAGGTGCGGGGCTCTTGCCGGCCGGGCGCTCCTCGGCTCCCGCGCGCCGGGTTCCCGGGCGGTCCC
ACCGCCACTGCCTGGGCAGGGGAGGAGGCCTGGCGGAGCGGGCGGGCGGCGCCTTCCCGGGACGACCAGCGGCTACGACC
CATGGCGCCCGGACTCTCGGAGGCCGGGAAGCTCCTGGGGCTGGAGTTCCCTGAGCGCCAGAGGCTGGCAGCTGCGGTTG
GATTTCTCCGATGTCCGGTGTTATCTCCATGTCTGCCCCTTTCTTCCTGGGGAAGATCATCGATGCCATCTATACCAACC
CCACTGTGGACTACAGCGACAACCTGACCCGCCTCTGCCTTGGCCTCAGTGGCGTGTTTCTGTGTGGTGCTGCCGCCAAT
GCCATTCGTGTCTACCTCATGCAAACTTCACGTCAGCGCGTTGTGAAGAGGCTGAGAACTTCGTTATTCTCCTCCATTCT
GGGGCAGGAGGTTGCTTTCTCTGACAAGGCTGGCACAGGGGAATTGATTAACCGCCTCTCATCGGACACTGCACTCCTGG
GGCGCTCAGTGACTGAAAACCTCTCAGATGGGCTCAGGGCCGGGGCCCGGGCTTCTGTAGGCATCAGGACGATGTTTTGT
GTCTCACCTAATCGGGCCACCTTTGTTGTGAGTGTGGTGCCTCTAGTGTCAATCATTGATGTAATTTATGGACGATATCT
ACGGAAACTGACCAAAGTCACCCAGGATTCGCTGGCACAAGCCACTCAGGAGGAACGTATTGGAAATGTTAAGAACTGTT
CGAGCTTTTGGGAAAGAAATGACTGAAATAGAAAAATAGGCCAGCAAAGTGGACCATGTGATGTAGTCAGCAAGGAAAGC
GGCATTCGCTCAGGCTGGCTTCTTTGGAGAACTAGGCTGTCCGGAAACCTGATTGTGCTTTCTGTCCTGTACAAAGGGGG
GCTGCTGATGGGCAGTGCCCACATGACCATGGGTGAACTCTCTTCCTTCCTATGTATGCTTTCGGGGTTGGAATAAGCAT
TGGAGGTCTGAGCTTTTTCTACTCGGAGCTGATGAAAGGACTGGGTGCCGGGGGGCGCCTCTGGGAGCTCCTGGAGAGAG
AGCCCAATCTGCCTTTTAAGGAGGGGGAAGGGTTATCTTAAATGAGAAAAGCTTCCAGGGTGCTTTGGAGTTTAAGAACG
TGCATTTTGCCGATCCCGCTTGCCCAGAGGCGCCCATATTTCAGGATTTCAGCCTTTCCATTCCGTCAGGATCTGTCACG
GCACTGGTTGGCCCAGGTGGTTCTGGCAAATCAACAGTGCTTTCGCTCCTGCTGAGGTTGTTCGACCCTGCTTCTGGAAC
TATCAGTCTTGATGGCCATGACATCCGTCAGCTAAACCCAGTGTGGCTGAGATCCAAGATTGGGACAGTGAGACAGGAAA
CCCATTTTGTTTTCTTGCTCTATCACTGAGAACATTGCTTATGGTGCTGATGGCCTTCCTCTGTGACCGCTGAGCAAGTC
CAGAGAGTGGCTGAAGTGGCCAATGCAGTGGTCTTGATCCGGAATTTCCCCCAAGGGTTCAACACTGTGGTTGGAGAAAA
GGGTGTTCTCCTCTCAGGTGGGCAGAAACAGCGGATTGCAATTGCCCGTGCTCTGCTGAAGAATCCCAAAATTCTTCTCC
TAGATGAAGCAACCAGTGCGCTGGATGCTGAAAATGAGTACCTTGTTCAAGAAGCTCTAGATCCACTGATGGATGGAAGA
ACAGCGTTAGTTATTGCCCATCATCTCTCCACCATTAAGAATGCTAATATGGTTGCTGTTCTTGACCAAGGAAAAATTAC
TGAATATGGAAAACACGAAGAGCTGCTTTCAAAACCAAATGGGATATACAGAAAACTAATGAACAAGCAAAGTTTTATTT
CAGCC

ORF - retro_hsap_1537 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.36 %
Parental protein coverage: 87.13 %
Number of stop codons detected: 2
Number of frameshifts detected 8


Retrocopy - Parental Gene Alignment:

ParentalGPGSCRCGAFAG-PGAPRLPRARFPGGPAAAAWAGDEAWRRGPAAPPGDKGRLRPAAAGLPEARKLLGLA
GPGSCRCGA.AG.PGAPRLPRA.FPGGP.A.AWAG.EAWR.G.AAP..D..RLRP.A.GL.EA.KLLGL.
RetrocopyGPGSCRCGALAG<PGAPRLPRAGFPGGPTATAWAGEEAWRSGRAAPSRDDQRLRPMAPGLSEAGKLLGLE
ParentalYPERRRLAAAVGFLT-MSSVISMSAPFFLGKIIDVIYTNPTVDYSDNLTRLCLGLSAVFLCGAAANAIRV
.PER.RLAAAVGFL..MS.VISMSAPFFLGKIID.IYTNPTVDYSDNLTRLCLGLS.VFLCGAAANAIRV
RetrocopyFPERQRLAAAVGFLR<MSGVISMSAPFFLGKIIDAIYTNPTVDYSDNLTRLCLGLSGVFLCGAAANAIRV
ParentalYLMQTSGQRIVNRLRTSLFSSILRQEVAFFDKTRTGELINRLSSDTALLGRSVTENLSDGLRAGAQASVG
YLMQTS.QR.V.RLRTSLFSSIL.QEVAF.DK..TGELINRLSSDTALLGRSVTENLSDGLRAGA.ASVG
RetrocopyYLMQTSRQRVVKRLRTSLFSSILGQEVAFSDKAGTGELINRLSSDTALLGRSVTENLSDGLRAGARASVG
ParentalISMMFFVSPNLATFVLSVVPPVSIIAVIYGRYLRKLTKVTQDSLAQATQLAEERIGNV-RTVRAFGKEMT
I..MF.VSPN.ATFV.SVVP.VSII.VIYGRYLRKLTKVTQDSLAQATQ..EERIGNV.RTVRAFGKEMT
RetrocopyIRTMFCVSPNRATFVVSVVPLVSIIDVIYGRYLRKLTKVTQDSLAQATQ--EERIGNV>RTVRAFGKEMT
ParentalEIEKYASKVDHVMQLARKEAFARAGFFGATG-LSGNLIVLSVLYKGGLLMGSAHMTVGELSSFL-MYAFW
EIEK.ASKVDHVM..ARK.AFA.AGFFG..G.LSGNLIVLSVLYKGGLLMGSAHMT.GELSSFL.MYAF.
RetrocopyEIEK*ASKVDHVM*SARKAAFAQAGFFGELG<LSGNLIVLSVLYKGGLLMGSAHMTMGELSSFL<MYAFG
ParentalVGISIGGLSSFYSELMKGLGAGGRLWELLEREPKLPFN--EG-VILNEKSFQGALEFKNVHFAYPARPEV
VGISIGGLS.FYSELMKGLGAGGRLWELLEREP.LPF...EG.VILNEKSFQGALEFKNVHFA.PA.PE.
RetrocopyVGISIGGLSFFYSELMKGLGAGGRLWELLEREPNLPFKEGEG<VILNEKSFQGALEFKNVHFADPACPEA
ParentalPIFQDFSLSIPSGSVTALVGPSGSGKSTVLSLLLRLYDPASGTISLDGHDIRQLNPVWLRSKIGTVSQE-
PIFQDFSLSIPSGSVTALVGP.GSGKSTVLSLLLRL.DPASGTISLDGHDIRQLNPVWLRSKIGTV.QE.
RetrocopyPIFQDFSLSIPSGSVTALVGPGGSGKSTVLSLLLRLFDPASGTISLDGHDIRQLNPVWLRSKIGTVRQE>
ParentalPILFSCSIAENIAYGADD-PSSVTAEEIQRVAEVANAVAFIRNFPQGFNTVVGEKGVLLSGGQKQRIAIA
PILFSCSI.ENIAYGAD..PSSVTAE..QRVAEVANAV..IRNFPQGFNTVVGEKGVLLSGGQKQRIAIA
RetrocopyPILFSCSITENIAYGADG<PSSVTAEQVQRVAEVANAVVLIRNFPQGFNTVVGEKGVLLSGGQKQRIAIA
ParentalRALLKNPKILLLDEATSALDAENEYLVQEALDRLMDGRTVLVIAHRLSTIKNANMVAVLDQGKITEYGKH
RALLKNPKILLLDEATSALDAENEYLVQEALD.LMDGRT.LVIAH.LSTIKNANMVAVLDQGKITEYGKH
RetrocopyRALLKNPKILLLDEATSALDAENEYLVQEALDPLMDGRTALVIAHHLSTIKNANMVAVLDQGKITEYGKH
ParentalEELLSKPNGIYRKLMNKQSFISA
EELLSKPNGIYRKLMNKQSFISA
RetrocopyEELLSKPNGIYRKLMNKQSFISA

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 19 .30 RPM
bodymap2_adrenal 0 .00 RPM 19 .83 RPM
bodymap2_brain 0 .14 RPM 11 .23 RPM
bodymap2_breast 0 .00 RPM 21 .65 RPM
bodymap2_colon 0 .00 RPM 14 .70 RPM
bodymap2_heart 0 .11 RPM 16 .91 RPM
bodymap2_kidney 0 .00 RPM 25 .04 RPM
bodymap2_liver 0 .00 RPM 18 .78 RPM
bodymap2_lung 0 .00 RPM 22 .31 RPM
bodymap2_lymph_node 0 .22 RPM 29 .22 RPM
bodymap2_ovary 0 .00 RPM 15 .88 RPM
bodymap2_prostate 0 .00 RPM 31 .21 RPM
bodymap2_skeletal_muscle 0 .00 RPM 20 .04 RPM
bodymap2_testis 0 .23 RPM 15 .55 RPM
bodymap2_thyroid 0 .00 RPM 20 .30 RPM
bodymap2_white_blood_cells 0 .00 RPM 32 .80 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_1537 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_1537 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_1537 retrocopy 5' end.

Lab - click to see more details

retro_hsap_1537 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_1537 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 3 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000110111 retrocopy
retro_cjac_3824,
Dasypus novemcinctus ENSDNOG000000237851 retrocopy
retro_dnov_2360,
Homo sapiens ENSG00000135776 3 retrocopies
retro_hsap_1470, retro_hsap_1537 , retro_hsap_1542,

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 = 0.05 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 .05 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 .02 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 .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 .03 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 .03 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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