RetrogeneDB ID:

retro_dnov_1230

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_16687:9922..10247(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SUB1
Ensembl ID:ENSDNOG00000007611
Aliases:None
Description:SUB1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:19985]


Retrocopy-Parental alignment summary:






>retro_dnov_1230
ATTCCTAAATCGAAGGAACTTGTTTCTTCAAGCTCATCTGGCAGTGATTCTAATGGTGAAGTTTACAAAGAGTTAAAGAA
GAAAAAGCAAGTTACTCCAGAACATCCCACAAAGAAGCGAAAGACTGGTGAAAACTCATTAGCCCTGACATCTTCCAAGC
AGAGCAGCAACATGCTTCAGGTTGTAAAAATGACATAGATCAGTGCTCAGGATTTTAAAGGGAAAGTCCTAATTGATATT
AGAGAAAATTCGATAGATCCAGAAGGTGAAATGAAACCAGGAAGAAAATTATATCTCTTGAAATCCCGAGCAGTGGAGCC
AGGTG

ORF - retro_dnov_1230 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.63 %
Parental protein coverage: 88.98 %
Number of stop codons detected: 2
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMPKSKELVSSSSSGSDSDSEVDKKLKRKKQIPPEKPVKKQKTGETSRALSSSKQSSSSRDDNMFQIGKMR
.PKSKELVSSSSSG..SDS........KK............T........S....SS....NM.Q..KM.
RetrocopyIPKSKELVSSSSSG--SDSNGEVYKELKKK---KQVTPEHPTKKRKTGENSLALTSSKQSSNMLQVVKMT
ParentalYVSVRDFKGKVLIDIREYWMDPEGEMKPGRK-GISLNPEQWSQL
..S..DFKGKVLIDIRE...DPEGEMKPGRK..IS.NPEQWSQ.
Retrocopy*ISAQDFKGKVLIDIRENSIDPEGEMKPGRK>YIS*NPEQWSQV

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 82 .65 RPM
SRP012922_cerebellum 0 .00 RPM 62 .82 RPM
SRP012922_heart 0 .00 RPM 75 .18 RPM
SRP012922_kidney 0 .00 RPM 115 .27 RPM
SRP012922_liver 0 .00 RPM 51 .24 RPM
SRP012922_lung 0 .00 RPM 114 .70 RPM
SRP012922_quadricep_muscle 0 .00 RPM 49 .85 RPM
SRP012922_spleen 0 .00 RPM 203 .97 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_1230 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 77 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000188795 retrocopies
Callithrix jacchus ENSCJAG000000187182 retrocopies
Cavia porcellus ENSCPOG000000055844 retrocopies
Dasypus novemcinctus ENSDNOG00000007611 5 retrocopies
Dipodomys ordii ENSDORG000000139162 retrocopies
Homo sapiens ENSG000001133872 retrocopies
Gorilla gorilla ENSGGOG000000270333 retrocopies
Loxodonta africana ENSLAFG000000110061 retrocopy
Macropus eugenii ENSMEUG000000077704 retrocopies
Microcebus murinus ENSMICG000000145352 retrocopies
Myotis lucifugus ENSMLUG000000136856 retrocopies
Macaca mulatta ENSMMUG000000114702 retrocopies
Monodelphis domestica ENSMODG000000204103 retrocopies
Mustela putorius furoENSMPUG000000151852 retrocopies
Mus musculus ENSMUSG000000222054 retrocopies
Oryctolagus cuniculus ENSOCUG000000062625 retrocopies
Otolemur garnettii ENSOGAG000000090126 retrocopies
Pongo abelii ENSPPYG000000153792 retrocopies
Rattus norvegicus ENSRNOG0000005056312 retrocopies
Sarcophilus harrisii ENSSHAG000000149861 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000193642 retrocopies
Tarsius syrichta ENSTSYG000000140692 retrocopies



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