RetrogeneDB ID:

retro_dnov_868

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_11598:68397..68754(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FAM213A
Ensembl ID:ENSDNOG00000001981
Aliases:None
Description:family with sequence similarity 213, member A [Source:HGNC Symbol;Acc:28651]


Retrocopy-Parental alignment summary:






>retro_dnov_868
CTCTACACGGTAGTGAAGGAGCAGGTCGGGCATGAAGTGCAGGACTCCCAGCAGTATTTTAAAGGGAAGTCTTCCTGGAT
GAAAAGGAGAAGCTCAATGGTCTCCACAGGGGGAAGATGATGCTCACGGGGAGTGTCCGTTTGGGGGTCTGGTTCAACTT
CTTCTGGCCCAGAATGGAGGCTTCTCCTGAAACCTGGAAGGCAAAGCCTTCATCATTGGGGGAGCTTTTGTGGTGGGACC
GGGAAAGCACCACATACTTCTAGAGCAGGAGAAAAAGAATTTGGAGACAAAGTAAACCTAGTTTCTTTTCTGGAAGCTGC
TAGGAAGGTGGAACCACAGACCTCCGTCTCTGAGGAG

ORF - retro_dnov_868 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.8 %
Parental protein coverage: 71.43 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalLYAVVKEQVGHEVQDFQPYFKG-EVFLDEKKEFYGPHRRKMMLLGFVRLGVWFNF-LRARNGGFSGNLEG
LY.VVKEQVGHEVQD.Q.YFKG.EVFLDEK....G.HR.KMML.G.VRLGVWFNF.L.A.NGGFS.NLEG
RetrocopyLYTVVKEQVGHEVQDSQQYFKG<EVFLDEKEKLNGLHRGKMMLTGSVRLGVWFNF<LLAQNGGFS*NLEG
ParentalEGFVLGGVFVVGPGKQGILLEHR-EKEFGDKVSLVSVLEAARKIEPQTSTSEK
..F..GG.FVVGPGK..ILLE...EKEFGDKV.LVS.LEAARK.EPQTS.SE.
RetrocopyKAFIIGGAFVVGPGKHHILLEQE<EKEFGDKVNLVSFLEAARKVEPQTSVSEE

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 .39 RPM 34 .62 RPM
SRP012922_cerebellum 0 .00 RPM 15 .67 RPM
SRP012922_heart 0 .00 RPM 7 .19 RPM
SRP012922_kidney 0 .00 RPM 104 .86 RPM
SRP012922_liver 0 .00 RPM 92 .57 RPM
SRP012922_lung 0 .76 RPM 13 .44 RPM
SRP012922_quadricep_muscle 0 .00 RPM 5 .02 RPM
SRP012922_spleen 0 .00 RPM 74 .29 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_868 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 13 parental genes, and 30 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000008131 retrocopy
Callithrix jacchus ENSCJAG000000036571 retrocopy
Dasypus novemcinctus ENSDNOG00000001981 3 retrocopies
retro_dnov_1843, retro_dnov_1901, retro_dnov_868 ,
Homo sapiens ENSG000001223782 retrocopies
Gorilla gorilla ENSGGOG000000132462 retrocopies
Microcebus murinus ENSMICG000000074852 retrocopies
Macaca mulatta ENSMMUG000000217733 retrocopies
Mus musculus ENSMUSG000000217921 retrocopy
Otolemur garnettii ENSOGAG000000136387 retrocopies
Procavia capensis ENSPCAG000000096961 retrocopy
Pongo abelii ENSPPYG000000258624 retrocopies
Pan troglodytes ENSPTRG000000026852 retrocopies
Rattus norvegicus ENSRNOG000000111401 retrocopy



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