RetrogeneDB ID:

retro_dnov_183

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_24:129336..129771(-)
Located in intron of:ENSDNOG00000013598
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL23A
Ensembl ID:ENSDNOG00000019487
Aliases:None
Description:ribosomal protein L23a [Source:HGNC Symbol;Acc:10317]


Retrocopy-Parental alignment summary:






>retro_dnov_183
GCCCCTCCCAAAACTGAAGCCAGAGCAAAAGCTTTGAAAGCCAAGAAGGCAGTACTGAAAGGCATCCACAGTCACATAAA
AAAAGAGAAGATCCACACATCACCCACCTTCCAGCGGCCTTAAGTGCTGCGTCTCAGGAGAGAGCCCAAATATCCTCGGA
AAAGCACCCCCAGGAGAAACAAGCCTGACCACTCTGCCATCATCAGTCTTCCCCTGACCACTGTGTCAGCCAAGAAGACT
GAAGTCAACGACACACTGTGTTCATTGTGGATGTCAAGGCCAACAAGCACCAGATCAACAGGCTGTGAAGAGGCTCTGTG
ACATCACTGTGGCCAAGGTCAACACCTTATCAGGCCTGAAGCAGAGAAGAAGGCGTATGTTCAGCTGGCTCCTGACTATG
ATGCTTTGGATGTTGCCAACAGAATTGGGATCATC

ORF - retro_dnov_183 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80. %
Parental protein coverage: 78.49 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalAPPKTEAKAKALKAKKAVLKGVHSH-KKKKIRTSPTFRRPKTLRLRRQPKYPRKSAPRRNKLDHYAIIKF
APPKTEA.AKALKAKKAVLKG.HSH.KK.KI.TSPTF.RP..LRLRR.PKYPRKS.PRRNK.DH.AII..
RetrocopyAPPKTEARAKALKAKKAVLKGIHSHIKKEKIHTSPTFQRP*VLRLRREPKYPRKSTPRRNKPDHSAIISL
ParentalPLTTESAMKKIEDNNTL-VFIVDVKANKHQI-KQAVKKLYDIDVAKVNT-LIRPDGEKKAYVRLAPDYDA
PLTT.SA.KK.E.N.TL.VFIVDVKANKHQI..QAVK.L.DI.VAKVNT.LIRP..EKKAYV.LAPDYDA
RetrocopyPLTTVSA-KKTEVNDTL<VFIVDVKANKHQI<QQAVKRLCDITVAKVNT<LIRPEAEKKAYVQLAPDYDA
ParentalLDVANKIGII
LDVAN.IGII
RetrocopyLDVANRIGII

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
SRP012922_ascending_colon 0 .00 RPM 146 .05 RPM
SRP012922_cerebellum 0 .00 RPM 82 .62 RPM
SRP012922_heart 0 .00 RPM 77 .96 RPM
SRP012922_kidney 0 .00 RPM 124 .03 RPM
SRP012922_liver 0 .00 RPM 87 .00 RPM
SRP012922_lung 0 .00 RPM 200 .07 RPM
SRP012922_quadricep_muscle 0 .00 RPM 140 .03 RPM
SRP012922_spleen 0 .00 RPM 210 .72 RPM
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_183 was not experimentally validated.

Retrocopy orthology:
Dasypus novemcinctus 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 22 parental genes, and 446 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000468431 retrocopies
Bos taurus ENSBTAG000000463946 retrocopies
Callithrix jacchus ENSCJAG000000131267 retrocopies
Cavia porcellus ENSCPOG000000014526 retrocopies
Dasypus novemcinctus ENSDNOG00000019487 65 retrocopies
Equus caballus ENSECAG000000089281 retrocopy
Felis catus ENSFCAG0000000402135 retrocopies
Gorilla gorilla ENSGGOG0000001673626 retrocopies
Loxodonta africana ENSLAFG0000001338716 retrocopies
Myotis lucifugus ENSMLUG000000124484 retrocopies
Monodelphis domestica ENSMODG000000192973 retrocopies
Mustela putorius furoENSMPUG0000001417912 retrocopies
Mus musculus ENSMUSG000000585468 retrocopies
Nomascus leucogenys ENSNLEG0000000287260 retrocopies
Procavia capensis ENSPCAG0000001700230 retrocopies
Pongo abelii ENSPPYG0000000810849 retrocopies
Pteropus vampyrus ENSPVAG0000000292232 retrocopies
Rattus norvegicus ENSRNOG000000233446 retrocopies
Sarcophilus harrisii ENSSHAG0000001454913 retrocopies
Sus scrofa ENSSSCG000000177689 retrocopies
Sus scrofa ENSSSCG000000298024 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000001132823 retrocopies



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