RetrogeneDB ID:

retro_ttru_188

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:GeneScaffold_1515:96775..98288(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:LPCAT2
Ensembl ID:ENSTTRG00000001182
Aliases:None
Description:lysophosphatidylcholine acyltransferase 2 [Source:HGNC Symbol;Acc:26032]


Retrocopy-Parental alignment summary:






>retro_ttru_188
TCCCTGTACCCACCGGCCGTGGACAACCCCTTCACGCAGCAGACGCACATCAGCGCGTGGCGCTGGGCCTACATCGTCCT
CATGGGGGCTGTGCTGGTGCCGGTGCGCGTGTCCTACATCGCCGTCCTCTTCATCTTCCTCTGGCCGGTGGCTGCGCTTT
CCACCATAGGTCGTCGTGCTCGACCAACCAAGCCCGCCAGGAGTTGGAGAAGAAGACTGGTGCAGCCAACTCTCAAGTTC
TTGTTTCAGGTGACTTTTTTTCAGCAGGGTTCCTGGTTAAAGTGAAAGGGATAAAGGCAACCCGAGACGAGGCCTGCATC
TTCGTTGCAGCACCGCACTCCAGTTTCTTTGACGCAGTCGCCTGTGTCGTAGCAGGGTTCCCCTCGGTGGTCTCTGCGAG
TCAAAATGTGTGTATCCCCGTGGCTGGGAAATTCTTACTGTCAACGCAGCCGGTGCTTGTGACCTGAGATGACCCCAATT
CGAGGAAGAATACCCGGGAGGAAATCCTGAGGCCAGTGACATCTGATAGGAAGTGGCCACAGATCCTGATTTTCCTGGAA
GGAGTGTGTACCAACCGCAGCTGTCTGGTCACTTTAAACTAGGGGCCTTCTCTCCAGGTGTTCCTGTGCAGCCAGTGCTG
CTCAGGTAGCCAAACACCCTGGACACCGTGACCTGGACCTGGCAGGGGTTTACAGGCTTCCAGACCTGTATATTGACCCT
GAGTCAACTCTTCACCAGGGTAGAAGTTGAGTTTATGCCCGTTTATATCCCAAATGACCGAGAAAAAAAAGACCCCGTCC
TTTTTGCCAATAATACAGTGAGGATCATCATGGCCAATGCTCTTGGGGTGCCTGTGACAGATCACACTTATGAAGATTGC
AGACTGATGATTTCTGCAGGTAACCTTCGACTACCCATGGAAGGCGGTTTGGTTGAATTTACAAAAATTAGCCAGAAATT
AATGTTAGATTGGGATAATATTCATCAGTGTTTGGATGAATGTGCTACAATTGCAGCTGCCTCAAAAGGAGGGAAGATAG
GAATTACAGAGTTGGCGAACTATTTGAAACTCCCAATTTCAGAGCCCTTGAGACAACTTTTTGCCCTCTTTGACAGGAAT
AATGATGGCAGCATAGACTTCAGAGAGTATGTGATAGGTCTGACTGTCCTATGCAATCCTGCCAACACTGAAAAGATTCT
GCACATGTCATTTAAGCTTTTTGATCTTGATAGTGATGGTTTCATAACCGAACAGGAGTTAGCTGCTATACTTCGGGCAG
CTTTTGGAGTGCCAAATCTTGATGTTTCCAGACTCTTTCGATAGATAGCTGGACAGAACTCAGAGTACATTTCATACAGG
ACCTTTAAGAACTTTGCCCTGAAGCATCCAGGATATGCCAAGTTATTTAGTTCATACTTAGACCTCCAGGCAGCCTATAT
ATATTCATTACCACAGCAAGTACAGGTTTGATGGTTGTATTCAGATGTTAAAGGCAGCCCTGAAAATGGTGAA

ORF - retro_ttru_188 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.74 %
Parental protein coverage: 92.28 %
Number of stop codons detected: 4
Number of frameshifts detected: 2


Retrocopy - Parental Gene Alignment:

ParentalSFFPPPVRNPFVQQTRLGAARRIQIFFLGIILLPIRALLLALILLLAWLFAAISTTCCPEKLTHPITGWK
S..PP.V.NPF.QQT...A.R...I...G..L.P.R....A......W..AA.ST.......T.P...W.
RetrocopySLYPPAVDNPFTQQTHISAWRWAYIVLMGAVLVPVRVSYIAVLFIFLWPVAALSTIGRRARPTKPARSWR
ParentalRTITQPVLKFLGHAMFF-SMGFIVTVKGKIASPVEAPIFVVAPHSTFFDGIACVVAGLPSIVSRHENVQV
R...QP.LKFL....FF.S.GF.V.VKG..A...EA.IFV.APHS.FFD..ACVVAG.PS.VS...NV..
RetrocopyRRLVQPTLKFLFQVTFF<SAGFLVKVKGIKATRDEACIFVAAPHSSFFDAVACVVAGFPSVVSASQNVCI
ParentalPLIGRILRALQPVLVSRVDPDSRKNTINEIIRRATSGGEWPQILVFPEGTCTNRSCLIT-FKPGAFIPGV
P..G..L...QPVLV...DP.SRKNT..EI.R..TS...WPQIL.F.EG.CTNRSCL.T.FK.GAF.PGV
RetrocopyPVAGKFLLSTQPVLVT*DDPNSRKNTREEILRPVTSDRKWPQILIFLEGVCTNRSCLVT<FKLGAFSPGV
ParentalPVQPVLLRYPNKLDTVTWTWQGYKFIQLCVLTCCQPFTKVEVEFMPVQIPNDEEKSDPVLFAS-TVRNLM
PVQPVLLR.PN.LDTVTWTWQG....Q.C.LT..Q.FT.VEVEFMPV.IPND....DPVLFA..TVR..M
RetrocopyPVQPVLLR*PNTLDTVTWTWQGFTGFQTCILTLSQLFTRVEVEFMPVYIPNDRXXXDPVLFANNTVRIIM
ParentalAEALRIPVTDHTYEDCRLMISAGQLTLPMEAGLVEFTKISRKLKLDWDGIRKHLDEYAAIASSSKGGRIG
A.AL..PVTDHTYEDCRLMISAG.L.LPME.GLVEFTKIS.KL.LDWD.I...LDE.A.IA..SKGG.IG
RetrocopyANALGVPVTDHTYEDCRLMISAGNLRLPMEGGLVEFTKISQKLMLDWDNIHQCLDECATIAAASKGGKIG
ParentalIEEFAEYLKLPVSDVLRQLFALFDRNHDGSIDFREYVIGLAVLCNPANTEEIIQVAFKLFDVDKDGFITE
I.E.A.YLKLP.S..LRQLFALFDRN.DGSIDFREYVIGL.VLCNPANTE.I....FKLFD.D.DGFITE
RetrocopyITELANYLKLPISEPLRQLFALFDRNNDGSIDFREYVIGLTVLCNPANTEKILHMSFKLFDLDSDGFITE
ParentalEEFATIMQASLGVPDLDVSGLFKEIAQGDS--VSYEEFKSFALKHPEYAKIFTTYLDLQTCHVFSLPKEV
.E.A.I..A..GVP.LDVS.LF..IA...S...SY..FK.FALKHP.YAK.F..YLDLQ.....SLP..V
RetrocopyQELAAILRAAFGVPNLDVSRLFR*IAGQNSEYISYRTFKNFALKHPGYAKLFSSYLDLQAAYIYSLPQQV
ParentalQATSSVVSNKVSPESHE
Q........K.SPE..E
RetrocopyQV*WLYSDVKGSPENGE

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






RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_188 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_188 was not experimentally validated.

Retrocopy orthology:
Tursiops truncatus 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 ENSSHAG000000123831 retrocopy
retro_shar_116,
Tursiops truncatus ENSTTRG00000001182 1 retrocopy
retro_ttru_188 ,


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