RetrogeneDB ID:

retro_lcha_7

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH126814.1:964267..964606(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000014113
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:rplp1 (1 of 2)
Ensembl ID:ENSLACG00000012630
Aliases:None
Description:ribosomal protein, large, P1 [Source:ZFIN;Acc:ZDB-GENE-030131-8663]


Retrocopy-Parental alignment summary:






>retro_lcha_7
ATGGCTTCCGTGTCCGAGCTGGCTTGTATTTATTCTGCTCTCATCCTCCACGGCGATGAGGTCACCGTCACGGAGGATAA
AATCAATGCCCTCATCAAGGCTGCTGGAGTGAATGTTGAGCCTTTCTGGCCTAGCCTGTTTGCTAAGGCCCTGTCTAGCA
TTGACATTGGCAGCCTGATCTGTAACGTTGGTGCTGGTGGCCCTGTGGCTGCTGGTAGTGCTCCTGCAGGTGGTGCCCCT
GCTGCTAGTGCTGCGCCAGCTGAAGAAAAGAAGGAAGAGGAGAAGAAGGAAGAATCTGAGGAGTCCGATGATGACATGGG
CTTTGGTCTCTTCGACTAA

ORF - retro_lcha_7 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.11 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA
MASVSELACIYSALILH.DEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA
RetrocopyMASVSELACIYSALILHGDEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA
ParentalAGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD
AGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD
RetrocopyAGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD

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 2 .55 RPM 385 .48 RPM
DRP000627_kidney 2 .77 RPM 368 .32 RPM
DRP000627_pectoral_fin 8 .20 RPM 527 .20 RPM
DRP000627_pelvic_fin 4 .25 RPM 732 .34 RPM
DRP000627_pharynx 1 .40 RPM 278 .31 RPM
DRP000627_tail_muscle 1 .22 RPM 185 .38 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_7 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 34 parental genes, and 332 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001425120 retrocopies
Bos taurus ENSBTAG000000183204 retrocopies
Choloepus hoffmanni ENSCHOG0000000594410 retrocopies
Callithrix jacchus ENSCJAG0000003291919 retrocopies
Cavia porcellus ENSCPOG000000043216 retrocopies
Dasypus novemcinctus ENSDNOG0000001422426 retrocopies
Equus caballus ENSECAG000000085424 retrocopies
Felis catus ENSFCAG0000003203723 retrocopies
Homo sapiens ENSG0000013781818 retrocopies
Gorilla gorilla ENSGGOG0000000398013 retrocopies
Latimeria chalumnae ENSLACG00000012630 1 retrocopy
retro_lcha_7 ,
Loxodonta africana ENSLAFG000000320603 retrocopies
Macropus eugenii ENSMEUG000000152776 retrocopies
Macropus eugenii ENSMEUG000000152822 retrocopies
Myotis lucifugus ENSMLUG0000001054233 retrocopies
Macaca mulatta ENSMMUG000000148887 retrocopies
Monodelphis domestica ENSMODG000000092091 retrocopy
Monodelphis domestica ENSMODG000000092184 retrocopies
Mustela putorius furoENSMPUG0000000020413 retrocopies
Mustela putorius furoENSMPUG000000170962 retrocopies
Mus musculus ENSMUSG000000078926 retrocopies
Oryctolagus cuniculus ENSOCUG000000150878 retrocopies
Otolemur garnettii ENSOGAG0000002964119 retrocopies
Ochotona princeps ENSOPRG0000000116311 retrocopies
Procavia capensis ENSPCAG000000145957 retrocopies
Pongo abelii ENSPPYG000000066015 retrocopies
Pan troglodytes ENSPTRG000000072281 retrocopy
Rattus norvegicus ENSRNOG000000119556 retrocopies
Rattus norvegicus ENSRNOG000000138743 retrocopies
Sarcophilus harrisii ENSSHAG000000148186 retrocopies
Sus scrofa ENSSSCG0000000497016 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278938 retrocopies
Tarsius syrichta ENSTSYG000000139271 retrocopy
Tursiops truncatus ENSTTRG0000001365620 retrocopies



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