RetrogeneDB ID:

retro_ttru_1775

Retrocopy
location
Organism:Dolphin (Tursiops truncatus)
Coordinates:scaffold_91221:30939..33771(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SMG5
Ensembl ID:ENSTTRG00000001401
Aliases:None
Description:SMG5 nonsense mediated mRNA decay factor [Source:HGNC Symbol;Acc:24644]


Retrocopy-Parental alignment summary:






>retro_ttru_1775
CTGCGTGACCTCTGCGTCAAGCACCCGGTGGACTATGGGAGGAAGGCTAAGGAGCTGCTGTGGAGAAAGGTATGCTACGA
AGTTATCCAGCTCATCAAGTCTAACCAAAAGCATATCCACAGCCGGAGCACCTTAGAATGTGCCTACAGGACACACCTGG
TCGCTGGGATTGGCTTCTACCAGCATCTCCTTCTCTATATCCAGTCCCACTACCAGCTAGAACTGCAATGCTGCATCGAC
TGGACCCATGTCACCAACCCCCTCATAGGATGCAGGAAGCCAGTGTCTGCCTCAGGGAAGTAGATGGATTGAGCACAGAC
GGCATGCCACCAATGGCTAGTGTACCTGGGGGATTTGTCATGATATCAGAATGAATTAGCTGGCATAAACTCTGAGCTGC
TAGCTGAGAGATTTTACTACCAAGCCCTGTCAGTGGCTCCCCAGATTGGAACGCCTTCATCCAGCTGGGCACCCTTGCAG
GCAGCAAGTACTATAATGTGGAAGCCATGTATTGCTACCTGTGCTGCATCTAGTCGGAAGTGTCCTTTGAGGGGGCCTAT
GGGAATCTCAAGCGGCTGTGTGACAAGGCAGCCAAAATGTACCACAGCTGAAGAAGTGCGAGACTAGGAAACGCTCTCCC
AACAAGAAGCGATGTAAAGATATAAGAGGTTGCTGGTGAACTTTATGTGTCTGCAAAGCCTCCTGCAGCCCAAAAGTAGC
TCCCTGGACTCAAAGCTGATGTCACTTTGCCAGTCAGTCCTGAAGGACTTCAGCCTCTGTCTCTTCTACCTGCCCTCCCC
ACCCAACCTCAGCCTGGCCAGTGAGGATGAGAGTGGATATGATTTCCTCCCAGACCTTCTCATCTTTCAAATGGTCGTCA
TCTGCCTCATGTGTGTGCACAGCTTGAAGAGAGCAGATCCAAGCAGTAGAGTGCAGCTATTGCCTTCACCCTGGCCCTCT
TCTCCCACCTCGTCAGTCATGTCCACATAGGGCGGCAAGCTGAGCTGGAAGAGGGCGAGACTCCTGTCCCGGCATTCCAG
AGCGATGGCACATATGAACCAGAGTCCAAGGGACCCTTGGAGAAGGAGGGTCTTGAGCCTCTTCCTGCAGCACCTCAAGA
GGGCGAAGCCAGAAAGAACCAGAAGTTCTCCCACCTCTCCTGCCTCTACCGCCCACCCACAGCTGGTGATGACAGTGACA
TGAGTGAAGGCATTGACTAGGACTTGAGCCATGACTCAGTCCAGGCCAGCAAGGGCTTGGACAGTGGCTCTGACAGGAGT
CTTGAAGGTGGGGGAACGGCCTTTGATGCCAAGACAGATTCAGAAATGAAGAGCCAAGAGTCCAGATCAGACCTGGAAGA
TAAGGAGGATGAGGAAGGGACATGGTCCCCAGCCCTGGAGCCACCTTGGGCCAGGTCAGAGGCTCCTGAATCCTTCAGTG
GCCCACTGGACCCCAGCAAGGCCAGCATTGCCAGCAATCTACAAGCGATGTCCACCCAGATGTTGCAGACTAAACGCTGC
TTCCAACTGGCCCCCACCTTCAGCAACCTGCTCCTCCAGCCCACCACCAAAGCTCCCACATTGGCCAGCCCCAGGCCCTG
TGTCAGAGGGGATGTGGACAAGCCCTCAGAGCCAGCCTCTGAAGAGGGCTGTGAGTCGGAGGGAAGTGAGTCCAACAGTG
GGCGCGCCTGTTGGAATGAGCGCAGCATCCAGGAGAAGCTGCAAGTCCTCATGGCCAAAGGCCAGCTTCCTGCTGTGAAA
GTCTTCCTGGACTGGCTGCAAACCAACGGCAGCCTCATCACTGTATGTGCGTAGAGCTCTCTAAGTCTGTGGAACTGCCT
GTCTGTGTTGCTGAATCTGTTGCCAGCTGCTGGAGAACTCCAAGAGTCTGGCCTGGTCCTGTGTCCCAAGGTCCAGGATC
TTCTTGAAGGTTGTGAACTGCCTGACCTCCCGTCTAGCCTGCTGCTCCCAGAGGACATGGCACTTCACAATCTGCCTCCC
CTCCAGGCTGCCCACAGATTCTTTAACTTTGACACGGATCAGCTCTTGCTCAGCAGCTTAGAGGAGACAGTCGTGCACAT
CTGCTGCATCCACAGCTTTGGCCACTTCATTGCCCGCCTGCATGGCAGCATCCTACCGTTCAACCCAGAGGTCAGCATCT
TTGTCAGCATCTCCCAGTCTGAGCAAGAGAGCCTGCTGCAGCAGGCCCGGGCCCAGTTCCTCATGGCACAGGAGGAAGCT
CAGCGGAATGGGCTAATGAGAGACATGGCCCAGCTATGACTTCAGCTTGAGGTCTCTCGGCTGGAAGGGAGCCTGCAGCA
GCCCAAGGCCCGGTCAGCAATGTCTCCCTTCCTCGTCCCCAACACCCAAGCCCCTCTGCCACCACCACCCTATCATCCGC
CAGCTGGCCACCAGTGGCCTCTTCATTGTCATCATCCCAATGACAGTGATCGATGGCCTAGATCTGCTGAAGAAGGAAGA
CCCAGGGGCCCAGGATGGAATCCGATACCTGGAGGCAGAGTTTAAAAAAGGGAACAGGAACATTGGCTGCCAGAAAGAGG
TGGGGAAGAGCTTCAAGTGGCATAAGCTGAAGAGGCAGGATGCAGATGCCTGGATGCTCTATAAGATCCTGGACAGCTGC
AAACAGCTGACTCTGGCCCAGAGGGCAGGTGAGGAGGACCCGAGTGGCCTGGTGACCATCATCACAGGCCTTCCACTGGA
CAACCCTAGCACGCTCTCAGGCCCTATGCAGGCAGCCTTGCAGGCCACTGCAAATGCCAGTGTGGATATTAAGAATGTTC
TGGACTTCTACAAGCAGTGGAAGGAGATTGGC

ORF - retro_ttru_1775 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 81.64 %
Parental protein coverage: 94.28 %
Number of stop codons detected: 8
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalLRELCVKLMFLHPMDYGRKAEELLWRKVYYEVIQLIKTNKKHIHSRSTLECAYRTHLVAGIGFYQHLLLY
LR.LCVK....HP.DYGRKA.ELLWRKV.YEVIQLIK.N.KHIHSRSTLECAYRTHLVAGIGFYQHLLLY
RetrocopyLRDLCVK----HPVDYGRKAKELLWRKVCYEVIQLIKSNQKHIHSRSTLECAYRTHLVAGIGFYQHLLLY
ParentalIQSHYQLELQCCIDWTHVTDPLIGCKKPVSASGKEMDWAQMACHRCLVYLGDLSRYQNELAGVDTELLAE
IQSHYQLELQCCIDWTHVT.PLIGC.KPVSASGK.MD.AQ.ACH..LVYLGDLS.YQNELAG...ELLAE
RetrocopyIQSHYQLELQCCIDWTHVTNPLIGCRKPVSASGK*MD*AQTACHQWLVYLGDLS*YQNELAGINSELLAE
ParentalRFYYQALSVAPQIGMP-FNQLGTLAGSKYYNVEAMYCYLRCIQSEVSFEGAYGNLKRLYDKAAKMYH-QL
RFYYQALSVAPQIG.P.F.QLGTLAGSKYYNVEAMYCYL.CI.SEVSFEGAYGNLKRL.DKAAKMYH.QL
RetrocopyRFYYQALSVAPQIGTP<FIQLGTLAGSKYYNVEAMYCYLCCI*SEVSFEGAYGNLKRLCDKAAKMYH<QL
ParentalKKCETRKLSPSKKRCKDI-KRLLVNFMYLQSLLQPKSSSVDSELTSLCQSVLEDFNLCLFYLPSSPNLSL
KKCETRK.SP.KKRCKDI.KRLLVNFM.LQSLLQPKSSS.DS.L.SLCQSVL.DF.LCLFYLPS.PNLSL
RetrocopyKKCETRKRSPNKKRCKDI<KRLLVNFMCLQSLLQPKSSSLDSKLMSLCQSVLKDFSLCLFYLPSPPNLSL
ParentalASEDEEEYESGYAFLPDLLIFQMVIICLMGVHSLKRAG-SKQYSAAIAFTLALFSHLVNHVNIRLQAELE
ASED....ESGY.FLPDLLIFQMV.ICLM.VHSLKRA..SKQ.SAAIAFTLALFSHLV.HV.I..QAELE
RetrocopyASED----ESGYDFLPDLLIFQMVVICLMCVHSLKRAD<SKQ*SAAIAFTLALFSHLVSHVHIGRQAELE
ParentalEGENPVPAFQSDGTDEAESKEPLEKVEEPGPEPPPAASQDGEVRKSRKFSRLSCLRRRRHPPKAGDDSDL
EGE.PVPAFQSDGT.E.ESK.PLEK....G.EP.PAA.Q.GE.RK..KFS.LSCL.R...PP.AGDDSD.
RetrocopyEGETPVPAFQSDGTYEPESKGPLEK---EGLEPLPAAPQEGEARKNQKFSHLSCLYR---PPTAGDDSDM
ParentalSEGFDSDSSHDSARASEGSDSGSDKSLEGGGTAFDAETDSEMNSQESRSDLEDMEDEEGTRSPALEPPRA
SEG.D.D.SHDS..AS.G.DSGSD.SLEGGGTAFDA.TDSEM.SQESRSDLED.EDEEGT.SPALEPP.A
RetrocopySEGID*DLSHDSVQASKGLDSGSDRSLEGGGTAFDAKTDSEMKSQESRSDLEDKEDEEGTWSPALEPPWA
ParentalRSEAPESLNGPLGPSEASIASNLQAMSTQMFQTKRCFRLAPTFSNLLLQPTTEAPTLASRRPCVNGDVDK
RSEAPES..GPL.PS.ASIASNLQAMSTQM.QTKRCF.LAPTFSNLLLQPTT.APTLAS.RPCV.GDVDK
RetrocopyRSEAPESFSGPLDPSKASIASNLQAMSTQMLQTKRCFQLAPTFSNLLLQPTTKAPTLASPRPCVRGDVDK
ParentalPSEPASEEGSESEGSES-SGRSCRNERSIQEKLQVLMAEGLLPAVKVFLDWLRTNPDLIIVCAQSSQSLW
PSEPASEEG.ESEGSES.SGR.C.NERSIQEKLQVLMA.G.LPAVKVFLDWL.TN..LI.VCA.SS.SLW
RetrocopyPSEPASEEGCESEGSESNSGRACWNERSIQEKLQVLMAKGQLPAVKVFLDWLQTNGSLITVCA*SSLSLW
ParentalNRLSVLLNLLPAAGELQESGLVLCPEVQDLLEGCELPDLPSSLLLPEDMALRNLPPLRAAHRRFNFDTDR
N.LSVLLNLLPAAGELQESGLVLCP.VQDLLEGCELPDLPSSLLLPEDMAL.NLPPL.AAHR.FNFDTD.
RetrocopyNCLSVLLNLLPAAGELQESGLVLCPKVQDLLEGCELPDLPSSLLLPEDMALHNLPPLQAAHRFFNFDTDQ
ParentalLLLSTSEETVVRICCIRSFGHFVARLQGSILQFNPEVGIFVSIAQSEQESLLQQAQAQFRMAQEEARRNR
LLLS..EETVV.ICCI.SFGHF.ARL.GSIL.FNPEV.IFVSI.QSEQESLLQQA.AQF.MAQEEA.RN.
RetrocopyLLLSSLEETVVHICCIHSFGHFIARLHGSILPFNPEVSIFVSISQSEQESLLQQARAQFLMAQEEAQRNG
ParentalLMRDMAQLRLQLEVSQLE-SLQQ-PKAQSAMSPYLVPDTQA-CHHLPVXXXXXXXXXXXXXXXXXXIDGL
LMRDMAQL.LQLEVS.LE.SLQQ.P.......P...P.....CHH.P...................IDGL
RetrocopyLMRDMAQL*LQLEVSRLEGSLQQ>PRPGQQCLPSSSPTPKPLCHHHPIIRQLATSGLFIVIIPMTVIDGL
ParentalDLLKKEHPGARDGIRYLEAEFKKGNRYIRCQKEVGKSFERHKLKRQDADAWTLYKILDSCKQLTLAQGAG
DLLKKE.PGA.DGIRYLEAEFKKGNR.I.CQKEVGKSF..HKLKRQDADAW.LYKILDSCKQLTLAQ.AG
RetrocopyDLLKKEDPGAQDGIRYLEAEFKKGNRNIGCQKEVGKSFKWHKLKRQDADAWMLYKILDSCKQLTLAQRAG
ParentalEEDPSGMVTIITGLPLDNPSTLSGPMQAALQAAAHASVDIKNVLDFYKQWKEIG
EEDPSG.VTIITGLPLDNPSTLSGPMQAALQA.A.ASVDIKNVLDFYKQWKEIG
RetrocopyEEDPSGLVTIITGLPLDNPSTLSGPMQAALQATANASVDIKNVLDFYKQWKEIG

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_1775 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1775 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Tursiops truncatus ENSTTRG00000001401 1 retrocopy
retro_ttru_1775 ,


Copyright © RetrogeneDB 2014-2017