RetrogeneDB ID:

retro_itri_1857

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH394192.1:41057..41420(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000027119
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSSTOG00000020639
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_itri_1857
TTGGCTGAGGAAAAGCTCGAGGCCTCCAAGTGTCTCCTCAAGATGCAAAACCAGCGCGGCGGCCGCACCCTCTTCCAGAA
CGTGCAGAAACCTTCTCAAGATGAGTGGGGCAACACCCTGGACGCCATGGAAGCTGCCTTGGCTCTGGAGAAGAACCTGA
ACCAAGCCATTTTGGATCTTCATGCCTTGGGTTCTACCCGCACAGACCCACATCTCTGTGACTTTCTGGAGAACCACTTC
CTTGATGAGGAGGTGAAGCTCATCAAGAAGATGGGGGACCACTTGACTAACCTCCACCGTCTGGCAGGCCCCCAGGCTGG
CCTGGGCGAGTATCTCTTCGAAAGACTCACCCTCAAGCATGAC

ORF - retro_itri_1857 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.04 %
Parental protein coverage: 69.14 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalLAEEKREASERLLKMQNQRGGRALFQDVQKPSQDEWGNTLDAMEAALALEKNLNQAILDLHALGSTRTDP
LAEEK.EAS..LLKMQNQRGGR.LFQ.VQKPSQDEWGNTLDAMEAALALEKNLNQAILDLHALGSTRTDP
RetrocopyLAEEKLEASKCLLKMQNQRGGRTLFQNVQKPSQDEWGNTLDAMEAALALEKNLNQAILDLHALGSTRTDP
ParentalHLCDFLENHFLDEEVKLIKKMGDHLTNLHRLAGPQAGLGEYLFERLTLKPD
HLCDFLENHFLDEEVKLIKKMGDHLTNLHRLAGPQAGLGEYLFERLTLK.D
RetrocopyHLCDFLENHFLDEEVKLIKKMGDHLTNLHRLAGPQAGLGEYLFERLTLKHD

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_1857 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1857 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 35 parental genes, and 531 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000001458227 retrocopies
Bos taurus ENSBTAG0000001334333 retrocopies
Canis familiaris ENSCAFG000000038611 retrocopy
Callithrix jacchus ENSCJAG0000000025013 retrocopies
Cavia porcellus ENSCPOG000000205581 retrocopy
Dasypus novemcinctus ENSDNOG000000024559 retrocopies
Dasypus novemcinctus ENSDNOG000000041265 retrocopies
Dasypus novemcinctus ENSDNOG0000000557736 retrocopies
Dasypus novemcinctus ENSDNOG000000078482 retrocopies
Dasypus novemcinctus ENSDNOG000000166838 retrocopies
Dipodomys ordii ENSDORG000000155505 retrocopies
Felis catus ENSFCAG0000000334837 retrocopies
Homo sapiens ENSG0000008708611 retrocopies
Gorilla gorilla ENSGGOG000000119999 retrocopies
Loxodonta africana ENSLAFG0000003124811 retrocopies
Microcebus murinus ENSMICG000000018617 retrocopies
Macaca mulatta ENSMMUG000000039099 retrocopies
Mustela putorius furoENSMPUG0000000330429 retrocopies
Mus musculus ENSMUSG000000507081 retrocopy
Nomascus leucogenys ENSNLEG0000000471610 retrocopies
Oryctolagus cuniculus ENSOCUG000000000146 retrocopies
Ochotona princeps ENSOPRG0000000249210 retrocopies
Procavia capensis ENSPCAG000000132276 retrocopies
Pongo abelii ENSPPYG0000001022311 retrocopies
Pan troglodytes ENSPTRG0000001126811 retrocopies
Pteropus vampyrus ENSPVAG0000000957025 retrocopies
Rattus norvegicus ENSRNOG000000208437 retrocopies
Sorex araneus ENSSARG0000001174112 retrocopies
Sus scrofa ENSSSCG0000000315333 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000145211 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000020639 7 retrocopies
Tupaia belangeri ENSTBEG0000000531113 retrocopies
Tarsius syrichta ENSTSYG0000001398856 retrocopies
Tursiops truncatus ENSTTRG0000000125266 retrocopies
Vicugna pacos ENSVPAG000000055093 retrocopies



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