RetrogeneDB ID:

retro_itri_373

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393286.1:24428484..24428862(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:MAGOH
Ensembl ID:ENSSTOG00000001253
Aliases:None
Description:mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]


Retrocopy-Parental alignment summary:






>retro_itri_373
ATGGAGAGTAACTTCGATCTGTGTTACTACACAGATCACAAAGGCAAGTTCAGCCACAAGTTCCTGGAGATTGAGTTTCT
GACCTGAAGGGATGGGAAATTGAATATGCCAACAAGAGCTGTGATAAAACTGATGTCATGATCAGAAAAGAGGTTTAGGT
ACATGGAAGTGCAATGACGGAACTGGGGAGTAAATTGATGATGTTGAAATTATCAACAAGGATGATGCTTCACGGCCTCT
CCTGACCCCATAGGCCAGCAGGAGCTTGAAACCATGATTGGAGATGAACACATTTCTTGCACAACATAGAAAATCAGTTC
CCTTATTGAAGTCAATTAATCCAAGGATCCAGGAGGTTTACAAGTATTTTATTATGTC

ORF - retro_itri_373 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 62.31 %
Parental protein coverage: 84.46 %
Number of stop codons detected: 4
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalMESDFYLRYYVGHKGKFGHEFLEFEFRP--DGKL-RYANNSNYKNDVMIRKEAYVHKSVMEELKRII-DD
MES.F.L.YY..HKGKF.H.FLE.EF....DGKL..YAN.S..K.DVMIRKE..VH.S.M.EL.....DD
RetrocopyMESNFDLCYYTDHKGKFSHKFLEIEFLT*RDGKL<EYANKSCDKTDVMIRKEV*VHGSAMTELGSKL<DD
ParentalSEITKEDDALWP-PPDRVGRQELEIVIGDEHISFTTSKIGSLIDVNQSKDPEGLRVFYYL
.EI...DDA..P..PD..G.QELE..IGDEHIS.TT.KI.SLI.VN.SKDP.GL.VFYY.
RetrocopyVEIINKDDASRP<SPDPIGQQELETMIGDEHISCTT*KISSLIEVN*SKDPGGLQVFYYV

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.
Ictidomys tridecemlineatus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_itri_373 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_373 was not experimentally validated.

Retrocopy orthology:
Ictidomys tridecemlineatus 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 16 parental genes, and 44 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG000000045381 retrocopy
Cavia porcellus ENSCPOG000000115111 retrocopy
Homo sapiens ENSG000001623852 retrocopies
Gorilla gorilla ENSGGOG000000075942 retrocopies
Microcebus murinus ENSMICG000000064062 retrocopies
Myotis lucifugus ENSMLUG000000024441 retrocopy
Nomascus leucogenys ENSNLEG000000179872 retrocopies
Oryctolagus cuniculus ENSOCUG000000018805 retrocopies
Otolemur garnettii ENSOGAG000000133282 retrocopies
Ochotona princeps ENSOPRG000000090201 retrocopy
Pongo abelii ENSPPYG000000013352 retrocopies
Pan troglodytes ENSPTRG000000007531 retrocopy
Rattus norvegicus ENSRNOG000000127781 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000008351 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000001253 3 retrocopies
retro_itri_373 , retro_itri_379, retro_itri_932,
Tupaia belangeri ENSTBEG0000001161117 retrocopies



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