RetrogeneDB ID:

retro_dnov_2332

Retrocopy
location
Organism:Armadillo (Dasypus novemcinctus)
Coordinates:scaffold_65008:2640..2990(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GABARAPL2
Ensembl ID:ENSDNOG00000002240
Aliases:None
Description:GABA(A) receptor-associated protein-like 2 [Source:HGNC Symbol;Acc:13291]


Retrocopy-Parental alignment summary:






>retro_dnov_2332
CTGAAGTGGATGTGCACGGAGGACCATCGGTGGAATAAGGCTGCGTGGAATCCGCTAAGATCGGAGCAACAATATCCCGA
CCAGGTTCCGGTGATTGTGGAAAAAGTCTCAGGCTCTCAGCTTGTTCACATTGACAAGCGAAAGTACGTGGTTCCATCTG
ATATCACTGTGGCTCAATTCATGTGGATCATCAGGAAAAGGACCCAGCTTCCTTCTGAAAAGGCAGTCTTCCTGTTTGTG
GATAGGACAGTCCCACAGTCCAGCCTAACCGTGGGACAGCTCTATGAGAAGGAAAAGGATGAAGATGGATTCTCGTATGT
GGCCTACAGCAGGAGAACACTTTTGGCGTC

ORF - retro_dnov_2332 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 82.5 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMKWMFKEDH-SLEHRCVESAKIRA-KYPDRVPVIVEKVSGSQIVDIDKRKYLVPSDITVAQFMWIIRKRI
.KWM..EDH.S.E..CVESAKI.A..YPD.VPVIVEKVSGSQ.V.IDKRKY.VPSDITVAQFMWIIRKR.
RetrocopyLKWMCTEDH<SVE*GCVESAKIGA>QYPDQVPVIVEKVSGSQLVHIDKRKYVVPSDITVAQFMWIIRKRT
ParentalQLPSEKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYS-GENTFGV
QLPSEKA.FLFVD.TVPQSSLT.GQLYEKEKDEDGF.YVAYS..ENTFGV
RetrocopyQLPSEKAVFLFVDRTVPQSSLTVGQLYEKEKDEDGFSYVAYS<QENTFGV

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 35 .39 RPM
SRP012922_cerebellum 0 .00 RPM 99 .80 RPM
SRP012922_heart 0 .00 RPM 48 .96 RPM
SRP012922_kidney 0 .00 RPM 65 .98 RPM
SRP012922_liver 0 .00 RPM 27 .25 RPM
SRP012922_lung 0 .00 RPM 73 .00 RPM
SRP012922_quadricep_muscle 0 .00 RPM 90 .18 RPM
SRP012922_spleen 0 .00 RPM 100 .15 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_2332 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 36 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000054532 retrocopies
Canis familiaris ENSCAFG000000314551 retrocopy
Callithrix jacchus ENSCJAG000000142531 retrocopy
Dasypus novemcinctus ENSDNOG00000002240 2 retrocopies
retro_dnov_1755, retro_dnov_2332 ,
Dasypus novemcinctus ENSDNOG000000102287 retrocopies
Erinaceus europaeus ENSEEUG000000111341 retrocopy
Homo sapiens ENSG000000347131 retrocopy
Gorilla gorilla ENSGGOG000000122992 retrocopies
Loxodonta africana ENSLAFG000000170652 retrocopies
Microcebus murinus ENSMICG000000119811 retrocopy
Myotis lucifugus ENSMLUG000000151121 retrocopy
Macaca mulatta ENSMMUG000000057592 retrocopies
Mustela putorius furoENSMPUG000000098941 retrocopy
Mus musculus ENSMUSG000000319505 retrocopies
Nomascus leucogenys ENSNLEG000000130482 retrocopies
Pongo abelii ENSPPYG000000075652 retrocopies
Pan troglodytes ENSPTRG000000083622 retrocopies
Rattus norvegicus ENSRNOG000000194251 retrocopy



Copyright © RetrogeneDB 2014-2017