RetrogeneDB ID:

retro_lcha_60

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH127054.1:1040132..1040735(+)
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_60
CCCTTTTTATGGAGTAAGTGGCTTAATAAAGGCCTCTATAGGATTGGAGACCTTTATCAAGGCATGATTCTTAAATCATT
TGGTGACCTCCAGAGGGAGTTCTCTCTTGATTCCAGAGAGATTTGGCGGTTCTTCCAACTAAGACATTGCATTTCCCAGT
TTTTCGATGGGAGGGAGAGGGCTCCTGTACTTGGCAAATTTCAGCCTTATTTTGATTCAGCAAGATGTCTACCACATACA
GCAGCACTCATCTACTCCCACCTTATTTCGACCCCTCAGACAGGCTTGAAAGGTCCAATGAGTTATTGGATGAGGGAATG
TAAATTAGAAATGGAAGAGAGAGAATAGGAGAATCACATGAAAAATATGTATCTTCCCCTCCGAGAAGCTAGATTAAAGC
TCCAACAATTTAAAATTATTAATAAGTTATATTGGACTCCCTCACACCTAAGAGCGGTGGGTCTACGAGATAGCAAGAGG
TGTTGGTTTTGTACGGAACAAATAGGCAACCTCCAGCATATGTTATGGAGTTGTAGAAACCTGTCGAGATACTGGGAGGA
AATATTGCAATTTTGTGGTGTGGTGCTTAAAACATCAATTCCC

ORF - retro_lcha_60 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.07 %
Parental protein coverage: 92.34 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPHLWGNMLPLWCAESLSLLSVKYNCTTLKPFSDLHRQFCLDSKDIWRFFQLRHCIVQLYRDQGKVPLLGE
P.LW......W....L......Y....LK.F.DL.R.F.LDS..IWRFFQLRHCI.Q........P.LG.
RetrocopyPFLWSK----WLNKGLYRIGDLYQGMILKSFGDLQREFSLDSREIWRFFQLRHCISQFFDGRERAPVLGK
ParentalLLPFYELTRCLPHTAALIYSHLISIPPASMIGPLEYWVRELELELEEGERESLMRNMYLPLREARLKLQH
..P.....RCLPHTAALIYSHLIS.P.....GP..YW.RE..LE.EE.E.E..M.NMYLPLREARLKLQ.
RetrocopyFQPYFDSARCLPHTAALIYSHLISTPQTGLKGPMSYWMRECKLEMEERE*ENHMKNMYLPLREARLKLQQ
ParentalFKIVNRLYWTPSHLGVAGLQEGRGCWFCSAQVGDLQHMLWECENLTRFWDEVLQFCGKVLDRPIP
FKI.N.LYWTPSHL...GL.....CWFC..Q.G.LQHMLW.C.NL.R.W.E.LQFCG.VL...IP
RetrocopyFKIINKLYWTPSHLRAVGLRDSKRCWFCTEQIGNLQHMLWSCRNLSRYWEEILQFCGVVLKTSIP

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 .00 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_60 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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