RetrogeneDB ID:

retro_mmus_2785

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:6:122456903..122457371(+)
Located in intron of:ENSMUSG00000040649
Retrocopy
information
Ensembl ID:ENSMUSG00000055093
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Rps27a
Ensembl ID:ENSMUSG00000020460
Aliases:Rps27a, 0610006J14Rik, Uba52, Ubb, Ubc
Description:ribosomal protein S27A [Source:MGI Symbol;Acc:MGI:1925544]


Retrocopy-Parental alignment summary:






>retro_mmus_2785
ATGCAGATCTTTGTGAAGACCCTTACGGGGAAAACCATCACGCTCGAGGTTGAACCCTCGGACACTATAGGAAATGTAAA
GGCCAAGATCCAGGATAAGGAAGGAATTCCTCCTGATCAGCAGAGGCTGATCTTTGCTGGTAAGCAGCTGGAAGATGGCC
GGACTTTGTCTGACTACAACATTCAAAAGGAGTCCACCCTTCATCTGGTGTTGAGACTTCGGGGTGGTGCTAAGAAAAGG
AAGAAGAAGTCTTACACCACTCCCAAGAAGAACAAGCATAAGAGGAAGAAGGTTAAGTTGGCTGTGCTGAAATACTATAA
GGTGGATGAAAATGGCAAAATTAGCCGACTTCGTCGAGAGTGTCCTTCTGATGAATGTGGTGCTGGAGTTTTCATGGGAA
GCCACTTTGACAGGCATTACTGTGGCAAGTGTTGTCTGACTTACTGCTTCAACAAACCAGAAGACAAG

ORF - retro_mmus_2785 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 99.36 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
MQIFVKTLTGKTITLEVEPSDTI.NVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
RetrocopyMQIFVKTLTGKTITLEVEPSDTIGNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLV
ParentalLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMGSHFDRHY
LRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMGSHFDRHY
RetrocopyLRLRGGAKKRKKKSYTTPKKNKHKRKKVKLAVLKYYKVDENGKISRLRRECPSDECGAGVFMGSHFDRHY
ParentalCGKCCLTYCFNKPEDK
CGKCCLTYCFNKPEDK
RetrocopyCGKCCLTYCFNKPEDK

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 .07 RPM 54 .37 RPM
SRP007412_cerebellum 0 .00 RPM 28 .27 RPM
SRP007412_heart 0 .00 RPM 37 .01 RPM
SRP007412_kidney 0 .02 RPM 40 .75 RPM
SRP007412_liver 0 .03 RPM 49 .78 RPM
SRP007412_testis 0 .00 RPM 26 .89 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_2785 was not detected
No EST(s) were mapped for retro_mmus_2785 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_118068156 libraries255 libraries602 libraries53 libraries6 libraries

The graphical summary, for retro_mmus_2785 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_2785 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_2785 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 15 parental genes, and 88 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000040175 retrocopies
Canis familiaris ENSCAFG000000234713 retrocopies
Callithrix jacchus ENSCJAG000000100525 retrocopies
Loxodonta africana ENSLAFG000000231332 retrocopies
Macropus eugenii ENSMEUG0000000891713 retrocopies
Myotis lucifugus ENSMLUG0000001706410 retrocopies
Myotis lucifugus ENSMLUG000000294491 retrocopy
Macaca mulatta ENSMMUG000000155638 retrocopies
Monodelphis domestica ENSMODG000000018193 retrocopies
Mus musculus ENSMUSG00000020460 19 retrocopies
Oryctolagus cuniculus ENSOCUG0000000361310 retrocopies
Pongo abelii ENSPPYG000000258711 retrocopy
Pan troglodytes ENSPTRG000000119281 retrocopy
Rattus norvegicus ENSRNOG000000044262 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000095665 retrocopies



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