RetrogeneDB ID:

retro_itri_1121

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393380.1:5414904..5415269(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS18
Ensembl ID:ENSSTOG00000002417
Aliases:None
Description:ribosomal protein S18 [Source:HGNC Symbol;Acc:10401]


Retrocopy-Parental alignment summary:






>retro_itri_1121
TCTGTCATTAAGGGCGTGGAACGAAGATATGCTCATATGGTGTTGAGGAAAACAGACACTGACCTCACCAAGAGGCTGGA
GAATTCATTGTTGGTGAGGTTGAACGTGTGATCACTATTATGTATAATCCATGACAGTACAAAATCCTAGACTGGTTCTT
GAACAGACAGAAGGTTGTAAAGAATGGAAAATTCAACCAGGTTCTGGCCAATGGTCTCGATAGTAAGCCCCAGCAGGACT
TGGAGCAACTGAGGAAGATTAGGACCCATAGGGGGCTATGCCAATTTTGGGACTTTGTATCCAAGGCCAGCAGACTAACA
CAACTGGTCACATGGCCGACACCGTAGGTTGTGTCCAAGAAGAAG

ORF - retro_itri_1121 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 69.6 %
Parental protein coverage: 80.79 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalTAIKGVGRRYAHVVLRKADIDLTKR-AGELTEDEVERVITIMQNPRQYKIPDWFLNRQKDVKDGKYSQVL
..IKGV.RRYAH.VLRK.D.DLTKR.AGE....EVERVITIM.NP.QYKI.DWFLNRQK.VK.GK..QVL
RetrocopySVIKGVERRYAHMVLRKTDTDLTKR<AGEFIVGEVERVITIMYNP*QYKILDWFLNRQKVVKNGKFNQVL
ParentalANGLDNKLREDLERLKKIRAHRGLRHFW-GLRVRGQHTKTTGRRGRTVG-VSKKK
ANGLD.K...DLE.L.KIR.HRGL..FW.GL...GQ.T.TTG....TVG.VSKKK
RetrocopyANGLDSKPQQDLEQLRKIRTHRGLCQFW<GLCIQGQQTNTTGHMADTVG>VSKKK

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_1121 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_1121 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 65 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000029181 retrocopy
Ailuropoda melanoleuca ENSAMEG000000016232 retrocopies
Cavia porcellus ENSCPOG000000196754 retrocopies
Felis catus ENSFCAG000000040137 retrocopies
Gorilla gorilla ENSGGOG000000065715 retrocopies
Loxodonta africana ENSLAFG000000321731 retrocopy
Myotis lucifugus ENSMLUG000000073602 retrocopies
Macaca mulatta ENSMMUG000000038671 retrocopy
Mustela putorius furoENSMPUG000000023066 retrocopies
Oryctolagus cuniculus ENSOCUG000000105461 retrocopy
Pongo abelii ENSPPYG0000002595314 retrocopies
Pan troglodytes ENSPTRG000000180391 retrocopy
Rattus norvegicus ENSRNOG000000285054 retrocopies
Sarcophilus harrisii ENSSHAG000000068572 retrocopies
Sarcophilus harrisii ENSSHAG000000086581 retrocopy
Ictidomys tridecemlineatus ENSSTOG00000002417 13 retrocopies



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