RetrogeneDB ID:

retro_itri_649

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393309.1:409226..409528(+)
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:ENSSTOG00000024226
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_649
CCCCAAACAGCTGGCCACCAAGCTGCCAAGAAAAGCGCTCCCTCTACCTGCAGGGTGAAGAAACCTCATCGCTACAGGCC
CGGGACTGAGCTTCTCATCTGGAAATTGCCTTTCCAGAGATTGGTGAGAGAGATCGCCCAGGATTTCAAAACCAACTTGA
GGTTTCACAGGCAGCCATTGGTGCCCTTCAGGAGGCTAGTGAAGCGTACCTGGTGGGTTTATTTGAAAATACTAATCTGT
GTGCCATCCACGCTAAGAGAGTCACCATCATGCCCAAAGACATCCAGTTGGCTCCCCAGATT

ORF - retro_itri_649 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.57 %
Parental protein coverage: 74.26 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQRLVREIAQDFKTDLRFQ-SAAIGALQEASEA
P.T.G........P.T.......RY...TELLI.KLPFQRLVREIAQDFKT.LRF...AAIGALQEASEA
RetrocopyPQTAGHQAAKKSAPSTCRVKKPHRYRPGTELLIWKLPFQRLVREIAQDFKTNLRFH<QAAIGALQEASEA
ParentalYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRI
YLVGLFE.TNLCAIHAKRVTIMPKDIQLA..I
RetrocopyYLVGLFENTNLCAIHAKRVTIMPKDIQLAPQI

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_649 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_649 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 14 parental genes, and 96 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097653 retrocopies
Choloepus hoffmanni ENSCHOG0000000966110 retrocopies
Cavia porcellus ENSCPOG000000047077 retrocopies
Gorilla gorilla ENSGGOG000000229287 retrocopies
Loxodonta africana ENSLAFG000000216244 retrocopies
Myotis lucifugus ENSMLUG0000001544710 retrocopies
Mus musculus ENSMUSG0000006074319 retrocopies
Oryctolagus cuniculus ENSOCUG000000246442 retrocopies
Oreochromis niloticus ENSONIG000000199755 retrocopies
Ochotona princeps ENSOPRG000000159522 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000024226 8 retrocopies
Tupaia belangeri ENSTBEG0000000617713 retrocopies
Vicugna pacos ENSVPAG000000115315 retrocopies



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