RetrogeneDB ID:

retro_hsap_185

Retrocopy
location
Organism:Human (Homo sapiens)
Coordinates:1:92531992..92533059(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSG00000233228
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:LPCAT2
Ensembl ID:ENSG00000087253
Aliases:LPCAT2, AYTL1, LysoPAFAT
Description:lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]


Retrocopy-Parental alignment summary:






>retro_hsap_185
GTACGAATGTCCTGCATCGCCTTCCTCTTCATCTGGCCAGTGGCCATGCTTTCCACCTTTGGCTATCCTGCTCAAATCCT
GCAACCCTGCCAAGAGTTGGAGAAAAAAAACTGGTGAAACCAGTACTCAAGCTCATGCTTCAGGTGGCTTTCTTTTTACT
TGGGTTCCTGGCTAAAGTGAAAGGGAAAAAGGCAACCCAAGACAAGGCCCCTATCTTCGTTACAGCACCACGGTCCACTT
TCTTTGACTCAATCCCCTGTGTGGTGGCAGGGTTACCCTCAGTGGTCTCTGCAAGTCAAAATGTGCAGATCCCATTGGCT
GGGAAATTCCTACTGTCAACACAGCTGGTGCTTGTGATTTGAGAAGACTCCCATTCCAGGAAGAATACTAAGGATGAAAT
CCTGAAGTGAGTGACATTTGGAAAGAAGTGGCCACAGATTCTGATTTTCCTAGAAGGTGTGTGCATCAATCGCTCCCGTC
TAGTCACTTTTAAACCAGGGGCCTTCTGTCCAGGTGTTCCTGTGTAGCCAGTGCTGCTCAGGTACCCAAACACCCTGGAC
ATGGCAATCTGGACCTGGCAGGGATTCACAGCCTTACAGGCCTGTATGTTGACACTCAGTCAACTCTTCACCAGGGTAGA
AGTTGAGTTTATGCCTGTTTATATCCCAAATGATGAAGAAAAAAAAGACCCCATCCTTTTTGCCAATACAGCACACATCA
ACATGGCAAATGCTCTAGGGGTGCCTGGGACAGGGCACACTTACGAAGGCTGCAGAGTGATGATCTCCGCAGGTAACCTT
CAACTACCCGTAGAAGCTGGTTTGGTGGAATTTACAAACATTAGCCAGAAGTTGAAGTTAGACAGGGATAACATTCATCA
GCATTTGGATGAATATGCTGCAATTGCAGTTGCCTCAAAAGGAGGGAAGACAGGAATTGAAGAATTTTCAAGTTATTTAA
AACTCCCAATTTCAGAGCCCTTGAGACAACCCCCTGCCCACTTCGGCAGGAATAATGATGGCAACATAGACTTCAGAGAG
TATGTAATAGGTCTGAAAAGAGTCTGC

ORF - retro_hsap_185 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 59.66 %
Parental protein coverage: 65.26 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalVLLVALILLLAWPFAAISTVCCPEKLT-HPITGWRRKITQTA-LKFLGRAMFFSMGFIVAVKGKIASPLE
V.......L..WP.A..ST...P......P...W......T..LK......FF..GF...VKGK.A....
RetrocopyVRMSCIAFLFIWPVAMLSTFGYPAQIL>NPAKSWXXXXGETS>LKLMLQVAFFLLGFLAKVKGKKATQDK
ParentalAPVFVAAPHSTFFDGIACVVAGLPSMVSRNENAQVPLIGRLLRAVQPVLVSRVDPDSRKNTINEIIKRTT
AP.FV.AP.STFFD.I.CVVAGLPS.VS...N.Q.PL.G..L...Q.VLV...D..SRKNT..EI.K..T
RetrocopyAPIFVTAPRSTFFDSIPCVVAGLPSVVSASQNVQIPLAGKFLLSTQLVLVI*EDSHSRKNTKDEILK*VT
ParentalSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVPVQPVLLRYPNKLDTVTWTWQGYTFIQLCMLTFCQL
.G..WPQIL.F.EG.C.NRS.L.TFKPGAF.PGVPV.PVLLRYPN.LD...WTWQG.T..Q.CMLT..QL
RetrocopyFGKKWPQILIFLEGVCINRSRLVTFKPGAFCPGVPV*PVLLRYPNTLDMAIWTWQGFTALQACMLTLSQL
ParentalFTKVEVEFMPVQVPNDEEKNDPVLFANKVRNLMAEALGIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFT
FT.VEVEFMPV..PNDE...DP.LFAN.....MA.ALG.P.T.HTYE.CR.MISAG.L.LP.EAGLVEFT
RetrocopyFTRVEVEFMPVYIPNDEXXXDPILFANTAHINMANALGVPGTGHTYEGCRVMISAGNLQLPVEAGLVEFT
ParentalKISRKLKLDWDGVRKHLDEYASIASSSKGGRIGIEEFAKYLKLPVSDVLRQLFALFDRNHDGSIDFREYV
.IS.KLKLD.D....HLDEYA.IA..SKGG..GIEEF..YLKLP.S..LRQ..A.F.RN.DG.IDFREYV
RetrocopyNISQKLKLDRDNIHQHLDEYAAIAVASKGGKTGIEEFSSYLKLPISEPLRQPPAHFGRNNDGNIDFREYV
ParentalIGLAVLC
IGL...C
RetrocopyIGLKRVC

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 54 .80 RPM
bodymap2_adrenal 0 .00 RPM 19 .86 RPM
bodymap2_brain 0 .05 RPM 40 .11 RPM
bodymap2_breast 0 .00 RPM 38 .64 RPM
bodymap2_colon 0 .00 RPM 59 .69 RPM
bodymap2_heart 0 .00 RPM 19 .72 RPM
bodymap2_kidney 0 .00 RPM 46 .22 RPM
bodymap2_liver 0 .00 RPM 3 .42 RPM
bodymap2_lung 0 .00 RPM 25 .02 RPM
bodymap2_lymph_node 0 .00 RPM 39 .36 RPM
bodymap2_ovary 0 .00 RPM 71 .96 RPM
bodymap2_prostate 0 .00 RPM 64 .07 RPM
bodymap2_skeletal_muscle 0 .00 RPM 9 .57 RPM
bodymap2_testis 0 .00 RPM 48 .57 RPM
bodymap2_thyroid 0 .00 RPM 261 .08 RPM
bodymap2_white_blood_cells 0 .00 RPM 119 .70 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_hsap_185 was not detected

EST - click to see more details

No EST(s) were mapped for retro_hsap_185 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_hsap_185 retrocopy 5' end.

Lab - click to see more details

retro_hsap_185 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_hsap_185 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pan troglodytes retro_ptro_171
Gorilla gorilla retro_ggor_266
Macaca mulatta retro_mmul_392
Parental genes homology:
Parental genes homology involve 20 parental genes, and 21 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000192721 retrocopy
retro_btau_64,
Callithrix jacchus ENSCJAG000000129021 retrocopy
retro_cjac_2945,
Dasypus novemcinctus ENSDNOG000000068591 retrocopy
retro_dnov_1735,
Dipodomys ordii ENSDORG000000131931 retrocopy
retro_dord_399,
Equus caballus ENSECAG000000096491 retrocopy
retro_ecab_865,
Erinaceus europaeus ENSEEUG000000142771 retrocopy
retro_eeur_109,
Homo sapiens ENSG00000087253 1 retrocopy
retro_hsap_185 ,
Gorilla gorilla ENSGGOG000000051441 retrocopy
retro_ggor_266,
Loxodonta africana ENSLAFG000000039651 retrocopy
retro_lafr_66,
Myotis lucifugus ENSMLUG000000040081 retrocopy
retro_mluc_88,
Macaca mulatta ENSMMUG000000044781 retrocopy
retro_mmul_392,
Mus musculus ENSMUSG000000331921 retrocopy
retro_mmus_270,
Nomascus leucogenys ENSNLEG000000012581 retrocopy
retro_nleu_994,
Pongo abelii ENSPPYG000000073581 retrocopy
retro_pabe_445,
Pan troglodytes ENSPTRG000000081242 retrocopies
retro_ptro_171, retro_ptro_2928,
Pteropus vampyrus ENSPVAG000000078011 retrocopy
retro_pvam_173,
Rattus norvegicus ENSRNOG000000166431 retrocopy
retro_rnor_309,
Sorex araneus ENSSARG000000119141 retrocopy
retro_sara_88,
Sarcophilus harrisii ENSSHAG000000123831 retrocopy
retro_shar_116,
Tursiops truncatus ENSTTRG000000011821 retrocopy
retro_ttru_188,

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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