RetrogeneDB ID:

retro_rnor_309

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:14:3359474..3361028(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSRNOG00000048507
Aliases:Lpcat2b, Aytl1b, Lpcat2bp, RGD1310837
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:Lpcat2
Ensembl ID:ENSRNOG00000016643
Aliases:Lpcat2, LPCAT-2, RGD1563994
Description:lysophosphatidylcholine acyltransferase 2 [Source:RefSeq peptide;Acc:NP_001258273]


Retrocopy-Parental alignment summary:






>retro_rnor_309
ATGGCTCATCAAACCCAACGCAGAGATACCGCAGACACTATGACGGAGGTGGAGGTGTGGGACAGCAGGACTGCACAGGA
GGTGAATAAGTCTTTATATCCGCCGGCAGTGACCAACCCCTTCACTCACCACACGCAGCTGAGTGCTTGGCAGTTGGCCT
GCAGCATCTTCCTGGGGACTGTGCTGGTACCCGTGCGGGTGTCCTGCATTGTCTTCCTCTTCCTCCTCCTCTGGCCAGTG
GCCCTACTCTCCACCATTAACTTGCCTATTCAACCTACCGAACCCGTGAAGAGTTGGAGGAAACATTTGATAAAGCCGGT
CTTCATATTCTTGCTCCGTTTGGCGTTCTTTTGTGCCGGGTTCCTAATTAAGGTCAAAGGGAAAAAGGCCACCAGAGAGG
AGGCCCCCATCTTCGTCGTCGCACCACACTCCACCTTCTTTGATGCCATCGCCGTTATTGTGGCGGGGCTCCCTTCAGTG
GTCTCTGATACCCAGCACGTGCGCATCCCATTGGTTGGGCAATGCATCCTTTTAACTCAGCCTGTGCTTGTGCGACGAGA
AGACCCGAATTCTAGAAAGACTACCCGGAATGAGATCCTCTCGCGGGTGAAATCTAAAATGAAGTGGCCACAGATTCTGA
TTTTTCCAGAAGGATTGTGCACCAACCGCTCCTGTCTTGTCACTTTTAAACTAGGAGCCTTCTCCCCAGGTGTCCCTGTG
CAACCCGTACTGCTTAGGTACCCCAACACCCTGGACACCGTGACCTGGACGTGGCATGGGTTCTCGGGCTTCCAGGTATG
TATGCTCACCCTGAGTCAGCCCTTCACTAGAATGGAAGTTGAGTTCATGCCTGTTTACATCCCAAATGAAGACGAAAAGA
AAGACCCCATCCTTTTTGCCAACACAGTCCGAATCAACATGGCAAACGCTTTGAAGCTGCCGGTAACGGATCACAGTTTC
GAAGATTGCAAACTGATGATCTCTGCTGGTGCCCTTCGGCTACCCATGGAAGCTGGCCTGGTGGAATTCACAAAAATCAG
TCAGAAATTGAAATTAGATTGGGACAACATCCACACGCACTTGGACAAGTACGCTTCGGTTGCAGTCTCCTCCAAAGGAG
GCAAGATTGGGATCGAAGAGTTCTCAAGATACTTAAAACTCCCCATTTCAGAGCCCCTGAGACAGCTTTTCTCCCTCTTT
GATAGGAATCAGGACGGCACCATAGACTTCCGAGAGTATGTGATAGGTCTAACCGTCCTGTGCAACCCAGCCAACACAGA
GAAGATTCTGCAAATGTCATTTAAGCTTTTTGATCTCGACGAGGATGGTTATATAACAGAACAGGAGCTGACAACCATGC
TCCGGGCAGCTTTCGGAGTGCCAGACCTAGATGTCTCCACACTCTTCCAGCAGATGGCTGGCAAGGATTCAGCTCAGGTT
TCCTACAGGACTTTTAGGAGGTTTGCCCTGAAGCATCCAGCATACGCCAAGCTATTTCACTCATACATAGACCTCCAGGC
GGCCTATATATACTCATTACCGGGAGAGGTATAA

ORF - retro_rnor_309 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.63 %
Parental protein coverage: 89.15 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSFFPPPVPNPFVQQTRISAARRLQMILLGIILLPVRALLVGLVLLLAWPFAVISTVCCPKKLTHPISDWR
S..PP.V.NPF...T..SA......I.LG..L.PVR........LL.WP.A..ST...P...T.P...WR
RetrocopySLYPPAVTNPFTHHTQLSAWQLACSIFLGTVLVPVRVSCIVFLFLLLWPVALLSTINLPIQPTEPVKSWR
ParentalRKITQPALKFLGRAMFFSMGFRVTVKGKVASPLEAPIFVVAPHSTFFDGIACVVAGLPSLVSRNENAQTP
.....P...FL.R..FF..GF...VKGK.A...EAPIFVVAPHSTFFD.IA..VAGLPS.VS.......P
RetrocopyKHLIKPVFIFLLRLAFFCAGFLIKVKGKKATREEAPIFVVAPHSTFFDAIAVIVAGLPSVVSDTQHVRIP
ParentalLVGRLLRALQPVLVSRVDPDSRKNTINEIKKRAMSGGEWPQILVFPEGTCTNRSCLITFKPGAFIPGVPV
LVG......QPVLV.R.DP.SRK.T.NEI..R..S...WPQIL.FPEG.CTNRSCL.TFK.GAF.PGVPV
RetrocopyLVGQCILLTQPVLVRREDPNSRKTTRNEILSRVKSKMKWPQILIFPEGLCTNRSCLVTFKLGAFSPGVPV
ParentalQPVLLRYPNKLDTVTWTWQGYTFIQLCVLTFCQLFTKVEVEFMPVQAPSEEERNDPVLFASRVRNLMAEA
QPVLLRYPN.LDTVTWTW.G....Q.C.LT..Q.FT..EVEFMPV..P.E.E..DP.LFA..VR..MA.A
RetrocopyQPVLLRYPNTLDTVTWTWHGFSGFQVCMLTLSQPFTRMEVEFMPVYIPNEDEKKDPILFANTVRINMANA
ParentalLEIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISRKLKLDWDGIRKHLDEYASIASSAKGGRIGIEE
L..PVTDH..EDC.LMISAG.L.LPMEAGLVEFTKIS.KLKLDWD.I..HLD.YAS.A.S.KGG.IGIEE
RetrocopyLKLPVTDHSFEDCKLMISAGALRLPMEAGLVEFTKISQKLKLDWDNIHTHLDKYASVAVSSKGGKIGIEE
ParentalFAEYLKLPVSDVLRQLFALFDRNNDGSIDFREYVIGLAVLCNPANTEDIIQVAFKLFDVDEDGYITEEEF
F..YLKLP.S..LRQLF.LFDRN.DG.IDFREYVIGL.VLCNPANTE.I.Q..FKLFD.DEDGYITE.E.
RetrocopyFSRYLKLPISEPLRQLFSLFDRNQDGTIDFREYVIGLTVLCNPANTEKILQMSFKLFDLDEDGYITEQEL
ParentalCTILQASLGVPDLNVSGLFREIAQGDS--VSYEEFKSFALKHPEYAKIFTTYLDLQTCHVFSLPEDV
.T.L.A..GVPDL.VS.LF...A..DS..VSY..F..FALKHP.YAK.F..Y.DLQ.....SLP..V
RetrocopyTTMLRAAFGVPDLDVSTLFQQMAGKDSAQVSYRTFRRFALKHPAYAKLFHSYIDLQAAYIYSLPGEV

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
SRP017611_brain 1 .44 RPM 7 .55 RPM
SRP017611_kidney 0 .00 RPM 4 .33 RPM
SRP017611_liver 0 .00 RPM 0 .54 RPM

ChIP-Seq - click to see more details

Rattus norvegicus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_rnor_309 retrocopy.

TSS - click to see more details

Rattus norvegicus was not studied using FANTOM5 data.

Lab - click to see more details

retro_rnor_309 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_309 has 3 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Bos taurus retro_btau_64
Equus caballus retro_ecab_865
Mus musculus retro_mmus_270
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 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 ENSRNOG00000016643 1 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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