RetrogeneDB ID:

retro_mmus_2633

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:5:22528323..22528689(-)
Located in intron of:ENSMUSG00000029012
Retrocopy
information
Ensembl ID:ENSMUSG00000084235
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Rpl22l1
Ensembl ID:ENSMUSG00000039221
Aliases:Rpl22l1, 3110001N18Rik, AU041196
Description:ribosomal protein L22 like 1 [Source:MGI Symbol;Acc:MGI:1915278]


Retrocopy-Parental alignment summary:






>retro_mmus_2633
ATGGCGCCGCAGAAAGACAAGAAGCCTAAGAAGTCCACCTGGAGGTTTCATTTGGACCTTACTCATCCAGTAGAAGATGG
AATTTTTGACTCTGGAAATTTTGAACAGTTTCTACGGGAGAAGGTTAAAGTCAATGGGAAAACTGGAAATCTTGGCAATG
TTGTTCACATTGAACGCCTGAAGAATAAAATCACAGTTGTTTCTGAGAAACAGTTCTCCAAAAGGTATTTGAAATATCTT
ACCAAGAAATACCTTAAGAAGAATAATCTCCGTGATTGGCTACGTGTGGTCGCATCTGACAAGGAGACTTACGAACTTCG
TTATTTCCAGATTAGTCAAGATGAAGATGGTTCAGAGCCTGAGGAC

ORF - retro_mmus_2633 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.18 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK
MAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK
RetrocopyMAPQKDKKPKKSTWRFHLDLTHPVEDGIFDSGNFEQFLREKVKVNGKTGNLGNVVHIERLKNKITVVSEK
ParentalQFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSESED
QFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSE.ED
RetrocopyQFSKRYLKYLTKKYLKKNNLRDWLRVVASDKETYELRYFQISQDEDGSEPED

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .12 RPM 17 .36 RPM
SRP007412_cerebellum 0 .04 RPM 5 .17 RPM
SRP007412_heart 0 .12 RPM 5 .35 RPM
SRP007412_kidney 0 .12 RPM 6 .78 RPM
SRP007412_liver 0 .03 RPM 7 .46 RPM
SRP007412_testis 0 .05 RPM 7 .27 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2633 was not detected
No EST(s) were mapped for retro_mmus_2633 retrocopy.


TSS No. TSS Name TSS expression level (Expr) in TPM range:
no expression 0 < Expr ≤ 1 1 < Expr ≤ 5 5 < Expr ≤ 10 Expr > 10
TSS #1 TSS_11267514 libraries3 libraries23 libraries86 libraries946 libraries

The graphical summary, for retro_mmus_2633 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

retro_mmus_2633 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2633 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 28 parental genes, and 86 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000047301 retrocopy
Canis familiaris ENSCAFG000000149552 retrocopies
Callithrix jacchus ENSCJAG000000024271 retrocopy
Cavia porcellus ENSCPOG000000092151 retrocopy
Equus caballus ENSECAG000000188941 retrocopy
Erinaceus europaeus ENSEEUG000000119415 retrocopies
Echinops telfairi ENSETEG000000106589 retrocopies
Homo sapiens ENSG000001635841 retrocopy
Gorilla gorilla ENSGGOG000000017341 retrocopy
Gadus morhua ENSGMOG000000040771 retrocopy
Loxodonta africana ENSLAFG000000132202 retrocopies
Macropus eugenii ENSMEUG000000094841 retrocopy
Myotis lucifugus ENSMLUG000000230522 retrocopies
Myotis lucifugus ENSMLUG000000276838 retrocopies
Macaca mulatta ENSMMUG000000228812 retrocopies
Mus musculus ENSMUSG000000289365 retrocopies
Mus musculus ENSMUSG00000039221 4 retrocopies
Nomascus leucogenys ENSNLEG000000052872 retrocopies
Oryctolagus cuniculus ENSOCUG000000149622 retrocopies
Otolemur garnettii ENSOGAG000000126422 retrocopies
Procavia capensis ENSPCAG000000087041 retrocopy
Pongo abelii ENSPPYG000000259001 retrocopy
Pteropus vampyrus ENSPVAG000000115241 retrocopy
Rattus norvegicus ENSRNOG000000118172 retrocopies
Sus scrofa ENSSSCG000000274415 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000229723 retrocopies
Tupaia belangeri ENSTBEG0000000035717 retrocopies
Tursiops truncatus ENSTTRG000000070353 retrocopies



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