RetrogeneDB ID:

retro_lcha_118

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH129548.1:57611..57943(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS25
Ensembl ID:ENSLACG00000017531
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_118
CAGCAACAAAAAGAGGAGAAGAATGCTGGGAAAGGTGCCAAGAAGAATAAGGATCCAATAAACTAATCCAGTGGCGTTGT
GGCTAAACTAACAAGGAGAAAGGAGAAAGGTGAGGGACAAGCTTAATAAAATCCTTGTCCTCTTTGAAAAGTCCACTTAC
TATAAAATATGCAGGGAACTGTCCAACTACAAGCTCATCAGACTTGCCAGGGTGTCAGAGAGACTGAAGGTAAGAGGATC
TCCTGTCAGGGTCTGCCCTTCAGGAACTGTTCAACCAGACAAGATTGGTACCTAAATACAGAGCCCAGATTTGCTACACA
AGAAATATCAAG

ORF - retro_lcha_118 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 57.02 %
Parental protein coverage: 89.52 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalKDDKKKKDAGKGAKKDKDPVNKSGGKAKKK-KWSKGKVRDKLNN-LVLFDKATYDKLYKEVPNYKLITPA
...K..K.AGKGAKK.KDP.N.S.G...K.......KVRDKLN..LVLF.K.TY.K...E..NYKLI..A
RetrocopyQQQKEEKNAGKGAKKNKDPIN*SSGVVAKL>QGERRKVRDKLNKILVLFEKSTYYKICRELSNYKLIRLA
ParentalVVSERLKIRGS-LARAALQELLNKGMIKLVSKHRAQVIYTRNTK
.VSERLK.RGS.L...ALQEL.N.....LV.K.RAQ..YTRN.K
RetrocopyRVSERLKVRGS>LSGSALQELFNQ--TRLVPKYRAQICYTRNIK

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 1027 .91 RPM
DRP000627_kidney 0 .00 RPM 1234 .29 RPM
DRP000627_pectoral_fin 0 .00 RPM 1856 .97 RPM
DRP000627_pelvic_fin 0 .00 RPM 1759 .00 RPM
DRP000627_pharynx 0 .00 RPM 695 .42 RPM
DRP000627_tail_muscle 0 .00 RPM 445 .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_118 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 23 parental genes, and 132 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000000515 retrocopies
Bos taurus ENSBTAG000000277722 retrocopies
Canis familiaris ENSCAFG000000123953 retrocopies
Callithrix jacchus ENSCJAG000000136911 retrocopy
Cavia porcellus ENSCPOG000000132982 retrocopies
Equus caballus ENSECAG000000209782 retrocopies
Felis catus ENSFCAG000000011513 retrocopies
Latimeria chalumnae ENSLACG00000017531 4 retrocopies
Loxodonta africana ENSLAFG000000171176 retrocopies
Macropus eugenii ENSMEUG000000141853 retrocopies
Microcebus murinus ENSMICG000000026878 retrocopies
Myotis lucifugus ENSMLUG0000000475215 retrocopies
Macaca mulatta ENSMMUG000000168942 retrocopies
Mus musculus ENSMUSG0000000992715 retrocopies
Oryctolagus cuniculus ENSOCUG0000001725611 retrocopies
Otolemur garnettii ENSOGAG000000072653 retrocopies
Ochotona princeps ENSOPRG000000161949 retrocopies
Pongo abelii ENSPPYG000000259156 retrocopies
Rattus norvegicus ENSRNOG000000275035 retrocopies
Sorex araneus ENSSARG000000022844 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000207833 retrocopies
Tupaia belangeri ENSTBEG0000001024416 retrocopies
Vicugna pacos ENSVPAG000000002664 retrocopies



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