RetrogeneDB ID:

retro_itri_1628

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393585.1:792205..792508(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000013481
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1628
CTAATTCATTGGCAAGATACAATTAGGGGACCTTATGACAGCCCATATCAAGGTGGTGTATTCTTTTTGACAATTCATTT
TCCTATAGACTACCTCTTCAAACCACCTAAGGTTGCATTTACAACAAGAATTTAATATCCAAATATTAACAGTAATGGCA
GCATTTGTCTTGATATTCTAGGATCACAATGGTCTCTTGCTTTAACTATTTCTAAAGTTCTTTTATCCATTTTTTCATTG
CTATGTGATCCAAATCCAGATGACCCTTTAGTGCCAGACATTGCACAGATCCATAAAACAGAC

ORF - retro_itri_1628 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.15 %
Parental protein coverage: 68.24 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALTI
..HWQ.TI.GP.DSPYQGGVFFLTIHFP.DY.FKPPKVAFTTRI..PNINSNGSICLDIL.SQWS.ALTI
RetrocopyLIHWQDTIRGPYDSPYQGGVFFLTIHFPIDYLFKPPKVAFTTRI*YPNINSNGSICLDILGSQWSLALTI
ParentalSKVLLSICSLLCDPNPDDPLVPEIARIYKTD
SKVLLSI.SLLCDPNPDDPLVP.IA.I.KTD
RetrocopySKVLLSIFSLLCDPNPDDPLVPDIAQIHKTD

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_1628 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1628 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 30 parental genes, and 101 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000041616 retrocopies
Canis familiaris ENSCAFG000000310415 retrocopies
Ciona intestinalis ENSCING000000187112 retrocopies
Callithrix jacchus ENSCJAG000000154923 retrocopies
Ciona savignyi ENSCSAVG000000061361 retrocopy
Equus caballus ENSECAG000000206781 retrocopy
Erinaceus europaeus ENSEEUG000000146583 retrocopies
Echinops telfairi ENSETEG000000012913 retrocopies
Felis catus ENSFCAG000000249182 retrocopies
Gorilla gorilla ENSGGOG000000013682 retrocopies
Gorilla gorilla ENSGGOG000000108321 retrocopy
Loxodonta africana ENSLAFG000000068782 retrocopies
Macaca mulatta ENSMMUG000000206663 retrocopies
Monodelphis domestica ENSMODG000000117832 retrocopies
Mus musculus ENSMUSG0000007857811 retrocopies
Mus musculus ENSMUSG000000918963 retrocopies
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
Ochotona princeps ENSOPRG000000116959 retrocopies
Pongo abelii ENSPPYG000000149671 retrocopy
Pongo abelii ENSPPYG000000158446 retrocopies
Pan troglodytes ENSPTRG000000173033 retrocopies
Pteropus vampyrus ENSPVAG000000154381 retrocopy
Rattus norvegicus ENSRNOG000000137419 retrocopies
Sus scrofa ENSSSCG000000243061 retrocopy
Sus scrofa ENSSSCG000000298224 retrocopies
Ictidomys tridecemlineatus ENSSTOG00000013481 6 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000162932 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000257992 retrocopies
Tupaia belangeri ENSTBEG000000002705 retrocopies
Tarsius syrichta ENSTSYG000000054591 retrocopy



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