RetrogeneDB ID:

retro_shar_116

Retrocopy
location
Organism:Tasmanian devil (Sarcophilus harrisii)
Coordinates:GL856730.1:921729..923319(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSHAG00000011876
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:LPCAT2
Ensembl ID:ENSSHAG00000012383
Aliases:None
Description:lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]


Retrocopy-Parental alignment summary:






>retro_shar_116
GACCATCGGCTGCAGCCCCTGCGCTCCCTCCGCGAGCGCTCGCTGTTCCCGCCCCCCGTGGAGAACCCCTTCGTGGCCGA
GAGGCACTTCAGTCCATCGCGCTGGCTCTGCATCTGGCTGAGCGGCCTCATCCTGGTGCCCCTGCGCGTCGTGCTCCTGC
TGCTGCTGGTCATCCTCTCGTGGCCCTTGGTGTTCGCGGCCACGGCCTTCCACCCGCTGAAGCGGGCCCAGCCGCTGCCG
CGGTGGAGGCGGCGGCTCACGCACCCGCTGTTGCAGGTGCTGGGCCGCATCTTCTTCTTCTTCTTCGGCTTCATTGTGAA
GGTGAGGGGCACCGCGGCCAATTCCCGCGAGGCGCCCCTGCTGGTGGCCGCCCCGCACTCCAGCTTCTTCGACGGCATCG
CCTGGATCTTCGCCGGTTTGCCGTCCGTTGTGTCTCGGGAGGAGAACGCCAGCTATCCGTTCGTCGGCAGGCTGCTCCTG
GCCGGGCAGCCGGTGCTGGTGTCCCGGGGAGACCCCGATTCCAGGAAGAACACGGTTAACGAAATTAAAAGGCGCGCCAC
CTCCAAAGGGCGGTGGCCGCAGATCCTGATTTTCCCCGAAGCCACCTGCACCAACCGCACGTGCCTGATCACTTTCAAAC
CGGGAGCCTTCGTCCCCGGAGTCCCCGTGCAGCCGCTGCTGCTCCGCTATCCCAACAAGCTCGACACGGTGACCTGGACC
TGGCAGGGGACTTCGGCCTTCCAGCTGCTCCTGCTGACCCTCACGCAGCCTTACACAAACATGGAAATGGAGTTCCTGCC
TATTTATGTCCCCGACGAGGAAGAGAGAAGCGATCCTGCCCTTTATGCCCGAAGAGTACGGAACGTCATGGCCAATGCCT
TACAGTTGCCTGTCACAGATCATACCTATGAAGACTGCAGACTGATGATTTCTGCAGGAAAGCTGACCTTGCCTATGGAA
GCGGGCTTGGTGGAATTTACCAAAATCAGCCAGAAGTTAAATTTGGATTGGGATACTGTCAGAAAACATTTGGATGAATA
TGCCACAATTGCAACTTCCGCAAAAGGAGGCAGAATTGGAATTGAAGAATTTTCCAAGTACTTAATGCTTCCCATTTCTG
ACACCCTGAAGCAACTCTTTGGCCTCTTTGACCGGAACCAAGATGGTACCATAGATTTCAGAGAATATGTGATTGGGCTG
TCGGTCCTGTGCAACCCTGTCAACACAGAAGACCTTATCCGCATGGCTTTCAAGCTCTTTGACTTGGACGAGGATGGCTA
CATAACAGAGTTAGAGTTTGCCAGTATTCTCCAGGCTTCTCTTGGCGTTAGAAACCTAGAAGTTTCAGGTCTCTTCCAAG
AAATAGCCAAAGAAAGCGCAGATCACATTTCCTATACAGAATTTAAAAGTTTTGCTATGAAGAATCCAGAATATGCCAGA
TTGTTTACTACTTACCTAGAACTCCAGGCGAGCCACGTGTTTTCATTACCCAAAGACGTTAAGTTTCCAAGTTTGAATTC
AACAACTTTGAATAACAAAGTCATCTGTGAGAATGCCGATGAAGATTTCTCAGATAAAAAAGATAACTGA

ORF - retro_shar_116 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.55 %
Parental protein coverage: 94.04 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalRQASFFPPPVPNPFVQDTRISASSRFLILLLGSILLPIRAICVALILIMAWPFAAVATVGLPEKLTHPVI
R..S.FPPPV.NPFV.....S.S....I.L.G.IL.P.R.....L..I..WP....AT...P.K...P..
RetrocopyRERSLFPPPVENPFVAERHFSPSRWLCIWLSGLILVPLRVVLLLLLVILSWPLVFAATAFHPLKRAQPLP
ParentalGWRRTLTHPALKFLGRAMFFSMGFMVRVKGKIASPMEAPIFIVAPHSTFFDGIACIVAGLPSIVSRTENI
.WRR.LTHP.L..LGR..FF..GF.V.V.G..A...EAP....APHS.FFDGIA.I.AGLPS.VSR.EN.
RetrocopyRWRRRLTHPLLQVLGRIFFFFFGFIVKVRGTAANSREAPLLVAAPHSSFFDGIAWIFAGLPSVVSREENA
ParentalYVPLIGRVLRAIQPVLVSRVDPDSRKTTINEIRKRATSRGEWPQLLVFPEGTCTNRTCLITFKPVLGAFI
..P..GR.L.A.QPVLVSR.DPDSRK.T.NEI..RATS.G.WPQ.L.FPE.TCTNRTCLITFKP..GAF.
RetrocopySYPFVGRLLLAGQPVLVSRGDPDSRKNTVNEIKRRATSKGRWPQILIFPEATCTNRTCLITFKP--GAFV
ParentalPGVPVQPILLRYPNKLDTVTWTWQGYTFIRLCMLTFSQLFTKVEVEFMPVTLPHDSYVEKKEKMLVFANH
PGVPVQP.LLRYPNKLDTVTWTWQG.....L..LT..Q..T..E.EF.P...P.....E........A..
RetrocopyPGVPVQPLLLRYPNKLDTVTWTWQGTSAFQLLLLTLTQPYTNMEMEFLPIYVPDE---EERSDPALYARR
ParentalIRNIMANALGVPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISQKLKLDWESIRKHLDEYAAIATASK
.RN.MANAL..PVTDHTYEDCRLMISAG.LTLPMEAGLVEFTKISQKL.LDW...RKHLDEYA.IAT..K
RetrocopyVRNVMANALQLPVTDHTYEDCRLMISAGKLTLPMEAGLVEFTKISQKLNLDWDTVRKHLDEYATIATSAK
ParentalGGRIGIDEFAAYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLAVLCNPANTEELIQVAFKLFDVDED
GGRIGI.EF..YL.LP.SD.L.QLF.LFDRN.DG.IDFREYVIGL.VLCNP.NTE.LI..AFKLFD.DED
RetrocopyGGRIGIEEFSKYLMLPISDTLKQLFGLFDRNQDGTIDFREYVIGLSVLCNPVNTEDLIRMAFKLFDLDED
ParentalGYITEEEFATILQASLGVPDLNVSGLFREIAKGDSTHVSYVEFRSFALKHPEYAKIFTTYLDLQACHVFS
GYITE.EFA.ILQASLGV..L.VSGLF.EIAK....H.SY.EF.SFA.K.PEYA..FTTYL.LQA.HVFS
RetrocopyGYITELEFASILQASLGVRNLEVSGLFQEIAKESADHISYTEFKSFAMKNPEYARLFTTYLELQASHVFS
ParentalLPKEVE---MAPSIAHNKVCPGPIEDGTSDKKDD
LPK.V...........NKV.........SDKKD.
RetrocopyLPKDVKFPSLNSTTLNNKVICENADEDFSDKKDN

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_116 was not experimentally validated.

Retrocopy orthology:
Sarcophilus harrisii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
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 ENSRNOG000000166431 retrocopy
retro_rnor_309,
Sorex araneus ENSSARG000000119141 retrocopy
retro_sara_88,
Sarcophilus harrisii ENSSHAG00000012383 1 retrocopy
retro_shar_116 ,
Tursiops truncatus ENSTTRG000000011821 retrocopy
retro_ttru_188,


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