RetrogeneDB ID:

retro_dnov_854

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_114504:3159..3486(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HINT2
Ensembl ID:ENSDNOG00000009083
Aliases:None
Description:histidine triad nucleotide binding protein 2 [Source:HGNC Symbol;Acc:18344]


Retrocopy-Parental alignment summary:






>retro_dnov_854
CTCTTCGGGAAGATTATCTGCAAGGAAATCCCCACCAAAATCATTTTTGAAGATAACTAGTGTCTTGCTTTCCAGGACAT
TTCCCCTCAAACACCAACACATTTTCTGGTGATTCCTAAGAAACATGTTTGTCAGATTTCTATAGAAGAAGAGAGTGATG
AAAGGCTACTTGGACATTTAATGATTGTTGTCAAGAAATGTGCTGCTGACCTGGGCCTAAAGAGGGGTTTTTGAATGGTG
GTGAATGAAGGTTCAGATGGAGGGCAGTCTGTCCACCGCGTTCATCTCCATGTTCTTGAAGGTCGGCAGATGAGTTGGCC
TTCTGGT

ORF - retro_dnov_854 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 51.38 %
Parental protein coverage: 80.15 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalIFSRILDRSLPADILYEDQQCLVFRDVAPQAPVHFLVIPKKPIPRISQAEEEDEQLLGHLLLVAKKAAKA
.F..I.....P..I..ED..CL.F.D..PQ.P.HFLVIPKK....IS..EE.DE.LLGHL..V.KK.A..
RetrocopyLFGKIICKEIPTKIIFEDN*CLAFQDISPQTPTHFLVIPKKHVCQISIEEESDERLLGHLMIVVKKCAAD
ParentalEGLGDGYRLVINDGKLGAQSVYHLHIHVLGGRQLQWPPG
.GL..G...V.N.G..G.QSV...H.HVL.GRQ..WP.G
RetrocopyLGLKRGF*MVVNEGSDGGQSVHRVHLHVLEGRQMSWPSG

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 .58 RPM 29 .75 RPM
SRP012922_cerebellum 1 .24 RPM 21 .58 RPM
SRP012922_heart 0 .46 RPM 30 .63 RPM
SRP012922_kidney 2 .19 RPM 134 .71 RPM
SRP012922_liver 0 .31 RPM 74 .93 RPM
SRP012922_lung 2 .14 RPM 50 .09 RPM
SRP012922_quadricep_muscle 0 .35 RPM 11 .60 RPM
SRP012922_spleen 1 .95 RPM 33 .31 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_854 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 18 parental genes, and 25 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000114441 retrocopy
Callithrix jacchus ENSCJAG000000100681 retrocopy
Cavia porcellus ENSCPOG000000004191 retrocopy
Dasypus novemcinctus ENSDNOG00000009083 2 retrocopies
retro_dnov_201, retro_dnov_854 ,
Echinops telfairi ENSETEG000000179291 retrocopy
Homo sapiens ENSG000001371331 retrocopy
Gorilla gorilla ENSGGOG000000112651 retrocopy
Loxodonta africana ENSLAFG000000150221 retrocopy
Macaca mulatta ENSMMUG000000163371 retrocopy
Nomascus leucogenys ENSNLEG000000269141 retrocopy
Oryctolagus cuniculus ENSOCUG000000272061 retrocopy
Otolemur garnettii ENSOGAG000000118301 retrocopy
Pongo abelii ENSPPYG000000190821 retrocopy
Pan troglodytes ENSPTRG000000209231 retrocopy
Pteropus vampyrus ENSPVAG000000030281 retrocopy
Tupaia belangeri ENSTBEG000000130201 retrocopy
Tarsius syrichta ENSTSYG000000027007 retrocopies
Tursiops truncatus ENSTTRG000000119321 retrocopy



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