RetrogeneDB ID:

retro_mmus_3425

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:20339299..20339708(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000087415
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:H3f3a
Ensembl ID:ENSMUSG00000060743
Aliases:H3f3a, H3.3A
Description:H3 histone, family 3A [Source:MGI Symbol;Acc:MGI:1097686]


Retrocopy-Parental alignment summary:






>retro_mmus_3425
ATGGCTCTTACAAAGCAGACTGCACACAAATCCAACGGTGGTAAAGCATCCAGGAAAGAACTGCCTACAAAAGCCGCTCG
CAAAAGGGCATCCTCTACTGGAGGGGTGAAGAAACCTCATCGTTACGGGCCTGGTACTGTAGCACTCCATGAAATCAGAA
GCTATCAGAAGTCCACTGAACTTCTGATTAGCAAGCTCCCCTTTCAGCATCTGGTGCAAGAAATTGTTCAGGACTTCAAA
ACAGATCTGCGCTTCCAGAGTGCAGCTATTGGTGCTTTGTGGAAGGCAAGTGAGGCCTATCTGGTTGGCCTTTTTGAAGA
TACCAACCTGTGTGCTATCCATGCCAAATGTGTAACAATTACGCCAAAAAAATTTCCAGCTAACACGCTGCATATGTGGA
GAACATTCT

ORF - retro_mmus_3425 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.29 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMARTKQTARKSTGGKAPRKQLATKAARKSAPSTGGVKKPHRYRPGTVALREIRRYQKSTELLIRKLPFQR
MA.TKQTA.KS.GGKA.RK.L.TKAARK.A.STGGVKKPHRY.PGTVAL.EIR.YQKSTELLI.KLPFQ.
RetrocopyMALTKQTAHKSNGGKASRKELPTKAARKRASSTGGVKKPHRYGPGTVALHEIRSYQKSTELLISKLPFQH
ParentalLVREIAQDFKTDLRFQSAAIGALQEASEAYLVGLFEDTNLCAIHAKRVTIMP-KDIQLARRIRGERA
LV.EI.QDFKTDLRFQSAAIGAL..ASEAYLVGLFEDTNLCAIHAK.VTI.P.K..QL.R.I.GE..
RetrocopyLVQEIVQDFKTDLRFQSAAIGALWKASEAYLVGLFEDTNLCAIHAKCVTITP>KNFQLTRCICGEHS

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 .00 RPM 12 .50 RPM
SRP007412_cerebellum 0 .00 RPM 12 .64 RPM
SRP007412_heart 0 .00 RPM 12 .70 RPM
SRP007412_kidney 0 .00 RPM 15 .34 RPM
SRP007412_liver 0 .00 RPM 8 .74 RPM
SRP007412_testis 0 .00 RPM 30 .87 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_3425 was not detected
No EST(s) were mapped for retro_mmus_3425 retrocopy.
No TSS is located nearby retro_mmus_3425 retrocopy 5' end.
retro_mmus_3425 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3425 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 95 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000097653 retrocopies
Choloepus hoffmanni ENSCHOG0000000966110 retrocopies
Cavia porcellus ENSCPOG000000047077 retrocopies
Loxodonta africana ENSLAFG000000216244 retrocopies
Myotis lucifugus ENSMLUG0000001544710 retrocopies
Mus musculus ENSMUSG0000001655918 retrocopies
Mus musculus ENSMUSG00000060743 19 retrocopies
Oryctolagus cuniculus ENSOCUG000000246442 retrocopies
Pongo abelii ENSPPYG000000086361 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000242268 retrocopies
Tupaia belangeri ENSTBEG0000000617713 retrocopies



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