RetrogeneDB ID:

retro_dnov_2317

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_63406:3566..3850(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FXN
Ensembl ID:ENSDNOG00000024066
Aliases:None
Description:frataxin [Source:HGNC Symbol;Acc:3951]


Retrocopy-Parental alignment summary:






>retro_dnov_2317
TCTCTAGATGAGACCACCTACGAAAGACTGTTCAGAGGAAGCTCTGGACTCCGTAGCAGAGTTTTTGAAAACCTTGCAGA
TAAATCTTACACATATGAGGATTATGATGTCTTATCTATGAGTGGTGTTTTATCAATTAAACTGGATGGAGATCTGGAAA
CCAACATGGTCAACAAACAGACCCCAATCAAACAAATCTGGTTATCTTCTCTATCCTGAGGATCAGAGTGTTAAGACTGG
ACTGGAAAAAAACGGTGTACTCCCAAAATGGTGCACCCCTCCAC

ORF - retro_dnov_2317 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.31 %
Parental protein coverage: 61.69 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalSLDETTYERL-AEETLDSLAEF-FEDLADKSCTFEDYDVSFGSGVLTIKLGGNLGTYVINKQTPNRQIWL
SLDETTYERL..EE.LDS.AEF.FE.LADKS.T.EDYDV...SGVL.IKL.G.L.T...NKQTP..QIWL
RetrocopySLDETTYERL>SEEALDSVAEF<FENLADKSYTYEDYDVLSMSGVLSIKLDGDLETNMVNKQTPIKQIWL
ParentalSSPSXXXXXYDWTG-KNWVYSHDGVSLH
SS.S......DWTG.K..VYS..G..LH
RetrocopySSLS*GSEC*DWTG<KKTVYSQNGAPLH

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 2 .14 RPM
SRP012922_cerebellum 0 .00 RPM 4 .81 RPM
SRP012922_heart 0 .46 RPM 4 .64 RPM
SRP012922_kidney 0 .00 RPM 4 .65 RPM
SRP012922_liver 0 .00 RPM 1 .55 RPM
SRP012922_lung 0 .00 RPM 5 .04 RPM
SRP012922_quadricep_muscle 0 .00 RPM 3 .46 RPM
SRP012922_spleen 0 .00 RPM 6 .75 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_2317 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 29 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000069151 retrocopy
Choloepus hoffmanni ENSCHOG000000051072 retrocopies
Callithrix jacchus ENSCJAG000000016954 retrocopies
Dasypus novemcinctus ENSDNOG00000024066 3 retrocopies
retro_dnov_2204, retro_dnov_2317 , retro_dnov_307,
Equus caballus ENSECAG000000191741 retrocopy
Homo sapiens ENSG000001650602 retrocopies
Gorilla gorilla ENSGGOG000000076363 retrocopies
Macaca mulatta ENSMMUG000000003572 retrocopies
Mustela putorius furoENSMPUG000000096192 retrocopies
Mus musculus ENSMUSG000000593632 retrocopies
Otolemur garnettii ENSOGAG000000311052 retrocopies
Rattus norvegicus ENSRNOG000000152131 retrocopy
Tursiops truncatus ENSTTRG000000103364 retrocopies



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