RetrogeneDB ID:

retro_lcha_117

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH129451.1:67373..68045(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLAUR
Ensembl ID:ENSLACG00000022222
Aliases:None
Description:plasminogen activator, urokinase receptor [Source:HGNC Symbol;Acc:9053]


Retrocopy-Parental alignment summary:






>retro_lcha_117
ATGAAGGCTTTACTTTTCACGGTCTGCGTTTTGCACGCTTTGGCCGTCGAAGTGTCCACGCTGGTTTGCAAGAGCTGCTT
CTCTATCCAGTCCTCGTGTCCTACAATGAAGGAAGTCACTTGCTTACCTAAGGAAAACGTTTGCTACTCTACATCCGTGG
AGATGAAAAATACATTATTAGCCAAGACATTTAAGTCCTTCTCGAAGGGATGTGCAGCCAGTAACGTCTGCAGGGCCACC
CAGCTCACCAACATTACCGGCATCCAAACAGTCACTAGCGTTCAATGCTGCAATAAAGACCTCTGCAATGTTGGAGAATT
CTCTGTCCCGGCTCTGAAGCAAGCAGCTAATACTTTGCACTGTTACTCTTGTGCTAGCAGAACTGCTCAATATTGTTCTG
CCAAAAGTAAACTAAAGTGTACCGGGGACCAGGCCATGTGCTTCAAACTGACTGAGGAATTTGATACGGAGGGCAAAAGA
CAACCTTACATACTAAAGGGGTGCGTTTCTCAGCGAGCCTGCGGCGAGGGATTTTTATTTACCACTCCCGGCGGAATGAG
GCTGCTTAACAAAGTTTACTGTTGTAAAAGCAAGCTGTGCAACAGCGGCGTGCGTCTTCCATACAGCTGGATCCTGCTGG
TGGTGGCAAGCGTCTTCCTACTCATCAAGCCA

ORF - retro_lcha_117 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 50.22 %
Parental protein coverage: 99.11 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMKALFFTIYILCTLSVEVSTLVCKSCFAIKKECDEMQNVNCTAKENVCYDMSVEMKN-MKGEEFQSVMKG
MKAL.FT...L..L.VEVSTLVCKSCF.I...C..M..V.C..KENVCY..SVEMKN......F.S..KG
RetrocopyMKALLFTVCVLHALAVEVSTLVCKSCFSIQSSCPTMKEVTCLPKENVCYSTSVEMKNTLLAKTFKSFSKG
ParentalCGMGNICKPAQSIIIHGVQTITAVKCCKTNLCNSASFLVSVPKSTFNGMKCYSCTDKSSKVCQSVKTTVE
C...N.C...Q...I.G.QT.T.V.CC...LCN...F.V...K...N...CYSC.......C.S.K....
RetrocopyCAASNVCRATQLTNITGIQTVTSVQCCNKDLCNVGEFSVPALKQAANTLHCYSCASRTAQYC-SAKSKLK
ParentalCSGDQTVCFKLTEEIDKDGNKKPYITKGCASKGVC-KGFLFSTSKGITVIDNVHCCEGSLCNNGDCFSYN
C.GDQ..CFKLTEE.D..G...PYI.KGC.S...C..GFLF.T..G......V.CC...LCN.G....Y.
RetrocopyCTGDQAMCFKLTEEFDTEGKRQPYILKGCVSQRACGEGFLFTTPGGMRLLNKVYCCKSKLCNSGVRLPYS
ParentalWILLAVASI-LLLKP
WILL.VAS..LL.KP
RetrocopyWILLVVASVFLLIKP

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






(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
DRP000627_gill 0 .00 RPM 0 .00 RPM
DRP000627_kidney 0 .00 RPM 0 .00 RPM
DRP000627_pectoral_fin 0 .12 RPM 0 .00 RPM
DRP000627_pelvic_fin 0 .00 RPM 0 .00 RPM
DRP000627_pharynx 0 .02 RPM 0 .00 RPM
DRP000627_tail_muscle 0 .02 RPM 0 .02 RPM
Latimeria chalumnae was not studied using ChIP-Seq data.
Latimeria chalumnae was not studied using EST data.
Latimeria chalumnae was not studied using FANTOM5 data.
retro_lcha_117 was not experimentally validated.

Retrocopy orthology:
Latimeria chalumnae 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
Latimeria chalumnae ENSLACG00000022222 1 retrocopy
retro_lcha_117 ,



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