RetrogeneDB ID:

retro_mmus_270

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:5:107432806..107434357(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000033794
Aliases:Lpcat2b, 4921521K07Rik, Aytl1b
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Lpcat2
Ensembl ID:ENSMUSG00000033192
Aliases:Lpcat2, A330042H22, Aytl1, Aytl1a, lpafat1
Description:lysophosphatidylcholine acyltransferase 2 [Source:MGI Symbol;Acc:MGI:3606214]


Retrocopy-Parental alignment summary:






>retro_mmus_270
ATGGCTCATCAGAACCAGCACCAGGATACCATAGACTCCACAGAGGTGGAGGTGTGGGACAGCAGGACTGCGCAGGAGGT
GAACAAGTCCTTATATCCTCCGGCAGTGGACAGTCCCTTCACTCTCAACACTCACCTGAGTGCTTGGCGCTGGGCCTGCA
CCATCATCCTGGGGACTGTGCTGGTACCCGTGCGGGTGTCCTGCATTGTCTTCCTCCTCATCCTTCTCTGGCCAGTGGCC
GTACTCTCCGCCATTAACTTGCCTACTCAACCTACCAAACCCATAAGGAGATGGAGGAAACATCTGATAAAGTCGGCCCT
GGTATTCTTGTTTCGTTTGGGGTTCTTTTTTGCTGGGTTCCTGGTTAAGGTCAAAGGGAAAAAGGCTACCAGAGAGGAGG
CCCCCATCTTTGTCTCCGCACCACACTCCACCTTCTTTGATGCAATCGCCGTTGTTGTGGCGGGGCTCCCTTCGGTGGTC
TCTGATAGTCAGCTTGCGAGGGTCCCATTGGCTGGGAAATGCATCCTGGTAACTCAGCCTGTGCTTGTGAAACGAGAAGA
CCCGAATTCTAGAAAGACTACCCGGAATGAAATCCTCAGACGAGTGAAATCTAAAATGAAGTGGCCACAGATTCTGATTT
TTCCGGAAGGATTGTGCACCAACCGCTCCTGTCTCGTCACTTTTAAACTAGGAGCCTTCTCCCCAGGTGTCCCTGTGCAG
CCAGTGCTGCTTAGGTACCCCAACAGCCTGGACACAGTGACCTGGACTTGGAATGGGTTCTCAGGCTTCCAGGTATGTAT
GCTTACTCTGAGTCAGCTCTTCACTAGAGTGGAAGTCGAGTTCATGCCTGTTTATATCCCAAGTGAAGAAGAAAAGAAAG
ACCCCATCCTTTTTGCCAACACAGTCCGAATCAAGATGGCAAACGCTTTGAAGCTGCCTGTAACCGATCACAGCTTGGAA
GACTGTAAACTGATGATATCTGCGGGTGCCCTTCAACTACCCATGGAAGCTGGCTTGGTGGAATTTACAAAAATCAGTCA
GAAATTGAAATTAGATTGGGACAACATCCACAAGCACTTGGACCAATATGCTTCGTTTGCGGTCTCCTCAAAAGGAGGCA
AGATTGGAATTGAAGCATTCTCACGTTATTTAAAACTCCCAATTTCAGAGCCCTTGAGACAGCTTTTCTCTCTCTTTGAC
AGGAATCAGGATGGCACCATAGACTTCCGAGAGTATGTGATAGGTCTAACTGTCCTGTGCAACCCATCCAATACGGAGAA
GATTCTGCAAATGTCATTTAAACTTTTTGATCTTGATGAGGATGGTTATGTAACAGAACGGGAGTTGACAACTATGCTTC
AGGCAGCTTTCGGAGTGCCAGACCTAGATGTTTCCACACTCTTCCAGCAGATGGCTGGCAAGGATTCAGATCAGGTTTCA
TACAGAACTTTTCGGAGGTTTGCCCTGAAGCATCCAGCATATGCCAAATTATTTCATTCATACATAGATCTCCAGGCAGC
CTATATATACTCATTACCAAGAGAAGTATAA

ORF - retro_mmus_270 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.66 %
Parental protein coverage: 89.15 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalSFFPPPVPNPFVQQTTISASRRLQMFLLGIILLPVRALLVGIILLLAWPFAVISTACCPEKLTHPISNWR
S..PP.V..PF...T..SA.R......LG..L.PVR.......L.L.WP.AV.S....P...T.PI..WR
RetrocopySLYPPAVDSPFTLNTHLSAWRWACTIILGTVLVPVRVSCIVFLLILLWPVAVLSAINLPTQPTKPIRRWR
ParentalRKITRPALTFLARAMFFSMGFTVTVKGKVASPLEAPIFVVAPHSTFFDGIACVVAGLPSLVSRNENAQTP
......AL.FL.R..FF..GF.V.VKGK.A...EAPIFV.APHSTFFD.IA.VVAGLPS.VS....A..P
RetrocopyKHLIKSALVFLFRLGFFFAGFLVKVKGKKATREEAPIFVSAPHSTFFDAIAVVVAGLPSVVSDSQLARVP
ParentalLVGRLLRALQPVLVSRVDPDSRKNTINEIKKRATSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVPV
L.G......QPVLV.R.DP.SRK.T.NEI..R..S...WPQIL.FPEG.CTNRSCL.TFK.GAF.PGVPV
RetrocopyLAGKCILVTQPVLVKREDPNSRKTTRNEILRRVKSKMKWPQILIFPEGLCTNRSCLVTFKLGAFSPGVPV
ParentalQPVLLRYPNKLDTVTWTWQGYTFLQLCVLTFCQLFTKVEIEFMPVQAPSEEEKNDPVLFASRIRNLMAEA
QPVLLRYPN.LDTVTWTW.G....Q.C.LT..QLFT.VE.EFMPV..PSEEEK.DP.LFA...R..MA.A
RetrocopyQPVLLRYPNSLDTVTWTWNGFSGFQVCMLTLSQLFTRVEVEFMPVYIPSEEEKKDPILFANTVRIKMANA
ParentalLEIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFSKISRKLKLDWDGIRKHLDEYASIASSSKGGRIGIEE
L..PVTDH..EDC.LMISAG.L.LPMEAGLVEF.KIS.KLKLDWD.I.KHLD.YAS.A.SSKGG.IGIE.
RetrocopyLKLPVTDHSLEDCKLMISAGALQLPMEAGLVEFTKISQKLKLDWDNIHKHLDQYASFAVSSKGGKIGIEA
ParentalFAEYLKLPVSDVLRQLFALFDRNNDGSIDFREYVIGLAVLCNPANTEEIIQVAFKLFDVDEDGYITEEEF
F..YLKLP.S..LRQLF.LFDRN.DG.IDFREYVIGL.VLCNP.NTE.I.Q..FKLFD.DEDGY.TE.E.
RetrocopyFSRYLKLPISEPLRQLFSLFDRNQDGTIDFREYVIGLTVLCNPSNTEKILQMSFKLFDLDEDGYVTEREL
ParentalCTILQASLGVPDLNVSGLFREIAQRDS--VSYEEFKSFALKHPEYAKIFTTYLDLQTCHVFSLPEEV
.T.LQA..GVPDL.VS.LF...A..DS..VSY..F..FALKHP.YAK.F..Y.DLQ.....SLP.EV
RetrocopyTTMLQAAFGVPDLDVSTLFQQMAGKDSDQVSYRTFRRFALKHPAYAKLFHSYIDLQAAYIYSLPREV

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
SRP007412_brain 0 .02 RPM 8 .34 RPM
SRP007412_cerebellum 0 .00 RPM 4 .52 RPM
SRP007412_heart 0 .00 RPM 1 .49 RPM
SRP007412_kidney 0 .06 RPM 2 .04 RPM
SRP007412_liver 0 .05 RPM 3 .36 RPM
SRP007412_testis 121 .57 RPM 0 .59 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_270 was not detected

EST - click to see more details

1 EST(s) were mapped to retro_mmus_270 retrocopy
EST ID Start End Identity Match Mis-match Score
BX635238 107433481 107433672 97.4 189 2 186

TSS - click to see more details

No TSS is located nearby retro_mmus_270 retrocopy 5' end.

Lab - click to see more details

retro_mmus_270 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_270 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_64
Equus caballus retro_ecab_865
Rattus norvegicus retro_rnor_309
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 ENSG000000872531 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 ENSMUSG00000033192 1 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,




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