RetrogeneDB ID:

retro_dnov_252

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:GeneScaffold_3025:82640..82990(+)
Located in intron of:ENSDNOG00000018918
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL34
Ensembl ID:ENSDNOG00000011179
Aliases:None
Description:ribosomal protein L34 [Source:HGNC Symbol;Acc:10340]


Retrocopy-Parental alignment summary:






>retro_dnov_252
ATGGTTCAGCGTTTGACATACCGTCGTAGGCTGTCCTACAGCACGGCTTCTAACACAAGTAGGCTTTCCCGGACCCCTGC
TAATAGAATTGTTTATCTTTACACCAAGAAGTTGGGAAAACACCAAAATCTACATGTGGTGTGTGTCTAGGTCGACTTCG
AGGGCTTCGTGCTGTGAGACTTAAAGTTCTTATGAAGTTATCTAAAACAAAAACACATGTCAGCGGAGCCTATGGTGGTT
CCATGTGTGCTAAATGTGTCCGTGACAGGATGAAGTGTGCTTTCCTGACTGAGGAGCAGAAAATCATTGTGAAAGTGTTG
AAAGCACAAGCACAGAGTTAGAAAGCTAAA

ORF - retro_dnov_252 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 84.75 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMVQRLTYRRRLSYNTASNKTRLSRTPGNRIVYLYTKK-VGKAPKSACGVCPGRLRGVRAVRPKVLMRLSK
MVQRLTYRRRLSY.TASN..RLSRTP.NRIVYLYTKK.VGK.PKS.CGVC.GRLRG.RAVR.KVLM.LSK
RetrocopyMVQRLTYRRRLSYSTASNTSRLSRTPANRIVYLYTKK<VGKTPKSTCGVCLGRLRGLRAVRLKVLMKLSK
ParentalTKKHVSRAYGGSMCAKCVRDRIKRAFLIEEQKIVVKVLKAQAQSQKAK
TK.HVS.AYGGSMCAKCVRDR.K.AFL.EEQKI.VKVLKAQAQS.KAK
RetrocopyTKTHVSGAYGGSMCAKCVRDRMKCAFLTEEQKIIVKVLKAQAQS*KAK

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 .19 RPM 104 .23 RPM
SRP012922_cerebellum 0 .00 RPM 55 .81 RPM
SRP012922_heart 0 .00 RPM 69 .38 RPM
SRP012922_kidney 0 .00 RPM 133 .06 RPM
SRP012922_liver 0 .00 RPM 60 .84 RPM
SRP012922_lung 0 .00 RPM 161 .28 RPM
SRP012922_quadricep_muscle 0 .00 RPM 78 .41 RPM
SRP012922_spleen 0 .11 RPM 168 .03 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_252 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 36 parental genes, and 473 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000175820 retrocopies
Bos taurus ENSBTAG0000001422613 retrocopies
Callithrix jacchus ENSCJAG000000159934 retrocopies
Cavia porcellus ENSCPOG000000008026 retrocopies
Dasypus novemcinctus ENSDNOG00000011179 26 retrocopies
Equus caballus ENSECAG000000197191 retrocopy
Erinaceus europaeus ENSEEUG000000103905 retrocopies
Felis catus ENSFCAG0000001550216 retrocopies
Homo sapiens ENSG0000010947533 retrocopies
Gorilla gorilla ENSGGOG0000000765032 retrocopies
Gadus morhua ENSGMOG000000099821 retrocopy
Loxodonta africana ENSLAFG000000326156 retrocopies
Macropus eugenii ENSMEUG000000093613 retrocopies
Microcebus murinus ENSMICG0000000218032 retrocopies
Myotis lucifugus ENSMLUG000000004644 retrocopies
Macaca mulatta ENSMMUG000000119011 retrocopy
Monodelphis domestica ENSMODG000000206013 retrocopies
Mustela putorius furoENSMPUG0000000887317 retrocopies
Mus musculus ENSMUSG0000006200626 retrocopies
Nomascus leucogenys ENSNLEG0000001293420 retrocopies
Otolemur garnettii ENSOGAG000000067741 retrocopy
Pongo abelii ENSPPYG0000001498818 retrocopies
Pelodiscus sinensis ENSPSIG000000032951 retrocopy
Pan troglodytes ENSPTRG0000001635331 retrocopies
Pteropus vampyrus ENSPVAG000000059149 retrocopies
Rattus norvegicus ENSRNOG0000001638736 retrocopies
Sorex araneus ENSSARG000000001778 retrocopies
Sarcophilus harrisii ENSSHAG000000013571 retrocopy
Sarcophilus harrisii ENSSHAG000000020523 retrocopies
Sus scrofa ENSSSCG000000091468 retrocopies
Ictidomys tridecemlineatus ENSSTOG0000002596414 retrocopies
Tupaia belangeri ENSTBEG0000000357424 retrocopies
Tarsius syrichta ENSTSYG0000000178134 retrocopies
Tursiops truncatus ENSTTRG000000034436 retrocopies
Vicugna pacos ENSVPAG000000059539 retrocopies
Xenopus tropicalis ENSXETG000000210951 retrocopy



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