RetrogeneDB ID:

retro_lcha_114

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH128855.1:306264..306853(-)
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_114
TGGCTTAACAAAGGACTTTACAGGATTGGGGACCTCTTTCAAGGTACAGTCCTGAAGTCCTTTAATGATCTCCACAGGAA
GTTTTCCCTAGATTCCAAAGAAGTATGGTGGTGGTTCAAAAAAAAAAAGACATTGTATCCCTCAGATTTTTGGTGTGCGA
GGTAGTGTTCCCTCGATAGGTAAATTTCAAACTTACTAAAAAACTGGCAAGATGTCTCCCTCATACTGCTGCACTCATTT
ACTCTCACCTTATTTCTACCCCTTGGCAGGACTGAAAGGTTGATTTGGTTACTGGTTGAGAGAGTTGGACTTGGAGCTGG
ATGAGGAAGAAAGGGAGAATCTGATGGAAAAAAATTATCTTCCCCTCCGGGAAGCTAGACTAAAACTTCAACAATTTAAA
ATTGTAAATAGACTGCATTGGGCTCCTGCTCATCTTGGGGAGGCAGGACTGTGGGTTGCACAGGGATGCTGGTTCTGCAC
AGACCAGGTGGGTGGTCATCAGCACATGTTATGAGGTTGTGAAAACATTGCGCGATGCTGGGAAGACGTTTTACAGTTTT
GTAGTGATGTGCTGGATAGACCCATTCCC

ORF - retro_lcha_114 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.79 %
Parental protein coverage: 87.84 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalWCAESLSLLSVKYNCTTLKPFSDLHRQFCLDSKDI-WRFFQLR-HCIVQLYRDQGKVPLLGELLPF-YEL
W....L.........T.LK.F.DLHR.F.LDSK...W.F.....HCI.Q.....G.VP..G........L
RetrocopyWLNKGLYRIGDLFQGTVLKSFNDLHRKFSLDSKEVWWWFXXXX>HCIPQIFGVRGSVPSIGKFQTY>KKL
ParentalTRCLPHTAALIYSHLISIP-PASMIGPLEYWVRELELELEEGERESLMRNMYLPLREARLKLQHFKIVNR
.RCLPHTAALIYSHLIS.P..A...G...YW.REL.LEL.E.ERE.LM...YLPLREARLKLQ.FKIVNR
RetrocopyARCLPHTAALIYSHLISTP<LAGLKG*FGYWLRELDLELDEEERENLMEKNYLPLREARLKLQQFKIVNR
ParentalLYWTPSHLGVAGLQEGRGCWFCSAQVGDLQHMLWECENLTRFWDEVLQFCGKVLDRPIP
L.W.P.HLG.AGL....GCWFC..QVG..QHML..CEN..R.W..VLQFC..VLDRPIP
RetrocopyLHWAPAHLGEAGLWVAQGCWFCTDQVGGHQHML*GCENIARCWEDVLQFCSDVLDRPIP

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_114 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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