RetrogeneDB ID:

retro_itri_1552

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393537.1:1303977..1304309(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CNIH4
Ensembl ID:ENSSTOG00000027396
Aliases:None
Description:cornichon homolog 4 (Drosophila) [Source:HGNC Symbol;Acc:25013]


Retrocopy-Parental alignment summary:






>retro_itri_1552
ATGGAGGCAGTAGTGTTCATTGCCTCACTGCACAATGGTTGTGCCCTCATCTCCCTCTCAGTCTGCTTCAGAGTTATATC
ATATGATTTAGAATGTGGTTACATTAATTAGACTAGATCATGTTGCTCAGTATTAAATAAGTGGATAATTCCAGAATTGC
TTGGCCATACCAATGTCACTGTATTTTGCTTGTTTCACTGCACTGGTTTGGATTCTCTCTCCACTTACCTGTTGCTACTT
GGAATATATATTGGTTCATTATGGTGCCAATTGGAAACATGAGGGTGTTTGACTCAACAGAAATACAGTTGAAGGCAACT
GAAGTGACACAT

ORF - retro_itri_1552 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 66.96 %
Parental protein coverage: 79.14 %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMEAVVFVFSLLDCCALIFLSVYFIITLSDLECDYIN-ARSCCSKLNKWVIPELIGHTVVTV-LMLVSLHW
MEAVVF..SL...CALI.LSV.F.....DLEC.YIN..RSCCS.LNKW.IPEL.GHT.VTV...LVSLHW
RetrocopyMEAVVFIASLHNGCALISLSVCFRVISYDLECGYIN*TRSCCSVLNKWIIPELLGHTNVTV<ILLVSLHW
ParentalFIFLLNLPVATWNIYRFIMVPSGNMGVFDPTEIHNRGQLKSH
F.F.L.LPVATWNIY.FIMVP.GNM.VFD.TEI........H
RetrocopyFGFSLHLPVATWNIYWFIMVPIGNMRVFDSTEIQLKATEVTH

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_1552 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1552 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 15 parental genes, and 17 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000065441 retrocopy
Callithrix jacchus ENSCJAG000000080131 retrocopy
Cavia porcellus ENSCPOG000000073101 retrocopy
Dasypus novemcinctus ENSDNOG000000070931 retrocopy
Homo sapiens ENSG000001437711 retrocopy
Gorilla gorilla ENSGGOG000000057081 retrocopy
Myotis lucifugus ENSMLUG000000031341 retrocopy
Macaca mulatta ENSMMUG000000099361 retrocopy
Nomascus leucogenys ENSNLEG000000135491 retrocopy
Ochotona princeps ENSOPRG000000015891 retrocopy
Pongo abelii ENSPPYG000000001831 retrocopy
Pan troglodytes ENSPTRG000000020251 retrocopy
Pteropus vampyrus ENSPVAG000000140341 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000027396 2 retrocopies
retro_itri_1502, retro_itri_1552 ,
Vicugna pacos ENSVPAG000000125212 retrocopies



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