RetrogeneDB ID:

retro_lcha_124

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH130455.1:108293..108464(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:rps21 (1 of 2)
Ensembl ID:ENSLACG00000012753
Aliases:None
Description:ribosomal protein S21 [Source:ZFIN;Acc:ZDB-GENE-040426-1102]


Retrocopy-Parental alignment summary:






>retro_lcha_124
ATGCAAAATGACACTTGGTAATTATCTGGATCTATATGTCCCGCATAATTGCTCCACTAGCAACAGAATTGTTGATTTCA
AGGATCACATTTCCGTTCAGCTGAATCTTGCCGAGGTTGACAAGCGCACAGGCAGGTTAATTGGATATAAGACCTTGTTA
TCTGTGGAGCC

ORF - retro_lcha_124 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 63.33 %
Parental protein coverage: 69.88 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalMQNDA-GEFVDLYVPRKCSASNRIIGAKDHASIQLNLAEVDRLTGRFNGQFKT-YAICGA
MQND..G...DLYVP..CS.SNRI...KDH.S.QLNLAEVD..TGR..G..KT...ICGA
RetrocopyMQNDT>GNYLDLYVPHNCSTSNRIVDFKDHISVQLNLAEVDKRTGRLIG-YKT<LVICGA

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 314 .62 RPM
DRP000627_kidney 0 .00 RPM 459 .90 RPM
DRP000627_pectoral_fin 0 .00 RPM 593 .06 RPM
DRP000627_pelvic_fin 0 .00 RPM 478 .90 RPM
DRP000627_pharynx 0 .00 RPM 186 .07 RPM
DRP000627_tail_muscle 0 .00 RPM 121 .75 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_124 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 27 parental genes, and 112 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000173992 retrocopies
Bos taurus ENSBTAG000000207952 retrocopies
Canis familiaris ENSCAFG000000126764 retrocopies
Callithrix jacchus ENSCJAG000000141955 retrocopies
Cavia porcellus ENSCPOG000000019654 retrocopies
Erinaceus europaeus ENSEEUG000000045732 retrocopies
Homo sapiens ENSG000001718586 retrocopies
Gorilla gorilla ENSGGOG000000237457 retrocopies
Latimeria chalumnae ENSLACG00000012753 1 retrocopy
retro_lcha_124 ,
Loxodonta africana ENSLAFG000000157934 retrocopies
Macropus eugenii ENSMEUG000000158322 retrocopies
Microcebus murinus ENSMICG000000129975 retrocopies
Myotis lucifugus ENSMLUG000000003463 retrocopies
Macaca mulatta ENSMMUG000000050068 retrocopies
Monodelphis domestica ENSMODG000000167691 retrocopy
Mus musculus ENSMUSG0000003900111 retrocopies
Ornithorhynchus anatinus ENSOANG000000033612 retrocopies
Otolemur garnettii ENSOGAG0000001667312 retrocopies
Ochotona princeps ENSOPRG000000009371 retrocopy
Pongo abelii ENSPPYG000000112058 retrocopies
Pan troglodytes ENSPTRG000000137081 retrocopy
Pteropus vampyrus ENSPVAG000000035482 retrocopies
Rattus norvegicus ENSRNOG000000063252 retrocopies
Sus scrofa ENSSSCG000000218251 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000010295 retrocopies
Tarsius syrichta ENSTSYG000000070615 retrocopies
Tursiops truncatus ENSTTRG000000111056 retrocopies



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