RetrogeneDB ID:

retro_lcha_66

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH127164.1:433436..433977(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MAD1L1
Ensembl ID:ENSLACG00000017346
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_66
TGGTTTAATAAGGGGTTGTATAGGATTGGGGACCTTTTTCGAGGTACCACTTTGAAATCTTTTAGTGATCTCCAGAAGGA
ATTTTCCCTGGACTCTAAGGATATATGGCGATTTTTCCAGTTAAGACACTGTATTGTGCAGCTTTATAGGGATCGGGGCA
AGGCTCCCTTATTAGGGGAGTTTTTACTGTTTTATGAATTGGCAAGGTGCTTGCCACATACTGCGGCACTTATCTACTCC
CATCTTATTTCCATTCCACCAGCAAGTATGATAGGTCTGCTAGAGTATTGGGTGAGGGAGCTGCAGCTAGAACTGGAGGA
AGGAGCAAGAGAGCCTCATGAGAAACATGTATCTCCCTTTGAGAGAAGCCAGGCTAAAACTCCAGCAATTTAAGATTGTC
AACAGGCTTTATTGGACACCATCACGTCTTGGGGTGGCTGGGCTACGAGAAGGAAGAGGTTGCTGGTTCTGTTCAGCACA
GGTGGGAGATCTCCAACGCATGCTGTGGGGATGTGAAAATTTAACACGATTCTGTGATGAG

ORF - retro_lcha_66 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.18 %
Parental protein coverage: 81.53 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalWCAESLSLLSVKYNCTTLKPFSDLHRQFCLDSKDIWRFFQLRHCIVQLYRDQGKVPLLGELLPFYELTRC
W....L.........TTLK.FSDL...F.LDSKDIWRFFQLRHCIVQLYRD.GK.PLLGE.L.FYEL.RC
RetrocopyWFNKGLYRIGDLFRGTTLKSFSDLQKEFSLDSKDIWRFFQLRHCIVQLYRDRGKAPLLGEFLLFYELARC
ParentalLPHTAALIYSHLISIPPASMIGPLEYWVRELELELEEGERESLMRNMYLPLREARLK-LQHFKIVNRLYW
LPHTAALIYSHLISIPPASMIG.LEYWVREL.LELEEG.RE........P......K.LQ.FKIVNRLYW
RetrocopyLPHTAALIYSHLISIPPASMIGLLEYWVRELQLELEEGAREPHEKHV-SPFERSQAK>LQQFKIVNRLYW
ParentalTPSHLGVAGLQEGRGCWFCSAQVGDLQHMLWECENLTRFWDE
TPS.LGVAGL.EGRGCWFCSAQVGDLQ.MLW.CENLTRF.DE
RetrocopyTPSRLGVAGLREGRGCWFCSAQVGDLQRMLWGCENLTRFCDE

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 1 .12 RPM
DRP000627_kidney 0 .00 RPM 0 .58 RPM
DRP000627_pectoral_fin 0 .00 RPM 3 .42 RPM
DRP000627_pelvic_fin 0 .00 RPM 3 .94 RPM
DRP000627_pharynx 0 .02 RPM 0 .51 RPM
DRP000627_tail_muscle 0 .00 RPM 0 .43 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_66 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 2 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Equus caballus ENSECAG000000142421 retrocopy
Latimeria chalumnae ENSLACG00000017346 17 retrocopies



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