RetrogeneDB ID:

retro_itri_728

Retrocopy
location
Organism:Squirrel (Ictidomys tridecemlineatus)
Coordinates:JH393314.1:1269240..1269634(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSSTOG00000025652
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:RPS24
Ensembl ID:ENSSTOG00000013000
Aliases:None
Description:ribosomal protein S24 [Source:HGNC Symbol;Acc:10411]


Retrocopy-Parental alignment summary:






>retro_itri_728
AATGACACAGTAACTATCTGACCAGAAAGTTCATAACCAACCAACTACTTCAGAGGAAAAAAATGGTCATTGATGTTCTT
CACCCTGGGAAAGCAACAATATCTAAGATAGAAATTCCAGAAAAATCAGTCAAATGTACGAGACCACATCAGATATCATC
TTTGTGTTTGAATTCAGAACCCATCTTGGAGGTGGCAAGACAGCTGGCTTTGGCATGATTTATGATTCCTTGGCTTATAC
AAAGAAAAATGAACCCAAACATAAACTGGCAAGACATGGCCTGTATGAAAAGAAAAAGACCTCAAGAGAACAGTGTAAGG
AACGCAAGAACAGAATGAACAAAGTCAGGGGGACTGCAAAGGCAAATGTTGGTGCTGGCAAAAAGCTAGGTGAG

ORF - retro_itri_728 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.85 %
Parental protein coverage: 92.31 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNDTVTI-RTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREK-LAKMYKTTPDVIFVFGFRTHFGGGKT
NDTVTI..TRKF.TN.LLQRK.MVIDVLHPGKAT..K.EI.EK....MY.TT.D.IFVF.FRTH.GGGKT
RetrocopyNDTVTI<LTRKFITNQLLQRKKMVIDVLHPGKATISKIEIPEK<ISQMYETTSDIIFVFEFRTHLGGGKT
ParentalTGFGMIYDSLDYAKKNEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAKANVGAGKKMRE
.GFGMIYDSL.Y.KKNEPKH.LARHGLYEKKKTSR.Q.KERKNRM.KVRGTAKANVGAGKK..E
RetrocopyAGFGMIYDSLAYTKKNEPKHKLARHGLYEKKKTSREQCKERKNRMNKVRGTAKANVGAGKKLGE

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_728 retrocopy.
Ictidomys tridecemlineatus was not studied using FANTOM5 data.
retro_itri_728 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 64 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000132649 retrocopies
Dipodomys ordii ENSDORG000000001894 retrocopies
Felis catus ENSFCAG000000008493 retrocopies
Homo sapiens ENSG000001383263 retrocopies
Gadus morhua ENSGMOG000000125951 retrocopy
Loxodonta africana ENSLAFG0000002787810 retrocopies
Myotis lucifugus ENSMLUG000000241021 retrocopy
Mustela putorius furoENSMPUG000000037781 retrocopy
Mus musculus ENSMUSG0000002529013 retrocopies
Oryctolagus cuniculus ENSOCUG000000124721 retrocopy
Otolemur garnettii ENSOGAG000000110053 retrocopies
Pan troglodytes ENSPTRG0000000266610 retrocopies
Ictidomys tridecemlineatus ENSSTOG00000013000 4 retrocopies
Tarsius syrichta ENSTSYG000000067151 retrocopy



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