RetrogeneDB ID:

retro_mmus_908

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:116597244..116597560(+)
Located in intron of:ENSMUSG00000056553
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Atpif1
Ensembl ID:ENSMUSG00000054428
Aliases:Atpif1, Atpi, If1
Description:ATPase inhibitory factor 1 [Source:MGI Symbol;Acc:MGI:1196457]


Retrocopy-Parental alignment summary:






>retro_mmus_908
CTCACAGGCTCGGCATTGGCGGTTCGGGCTCGGCTCGGCGTCTGGGGTATGAGGGCCCTGCAAACCCGAGGCTTCGTCTC
GGACTTGATGGAGAGCATGGATACGGGCGCTGGCTAAATCCGAGAAGCTGGTAGAGCCTTCGGAAAACGAGAAAAGGCTG
AAGAGGATCGGTACTTCCGAGAGAAGGCTAGAGAACAGCTGGCTGCCCTGAAAAAAACACCATGAAAATGAGGTTGACCA
CCATTCGAAGGAGATAGAGCGTCTGCAGAAGCAAATTGAATGCCGTGAGAAGATTAAACACCTAAAGTGTGGTCAT

ORF - retro_mmus_908 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.57 %
Parental protein coverage: 100. %
Number of stop codons detected: 1
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMAGSALAVRARFGVWGMKVLQTRGFVSDSSDSMDTGAGSIREAGGAFGKREKAEEDRYFREKTKEQLAAL
..GSALAVRAR.GVWGM..LQTRGFVSD...SMDTGAG.IREAG.AFGKREKAEEDRYFREK..EQLAAL
RetrocopyLTGSALAVRARLGVWGMRALQTRGFVSDLMESMDTGAG*IREAGRAFGKREKAEEDRYFREKAREQLAAL
Parental-RKHHEDEIDHHSKEIERLQKQIERHKKKIQQLKNNH
..KHHE.E.DHHSKEIERLQKQIE....KI..LK..H
Retrocopy>KKHHENEVDHHSKEIERLQKQIE-CREKIKHLKCGH

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 .21 RPM 52 .59 RPM
SRP007412_cerebellum 0 .00 RPM 39 .90 RPM
SRP007412_heart 0 .00 RPM 36 .58 RPM
SRP007412_kidney 0 .06 RPM 77 .60 RPM
SRP007412_liver 0 .00 RPM 7 .54 RPM
SRP007412_testis 0 .00 RPM 58 .23 RPM
RNA Polymerase II actvity may be related with retro_mmus_908 in 1 libraries
ENCODE library ID Target ChIP-Seq Peak coordinates
ENCFF001YIJ POLR2A 12:116596916..116598851
No EST(s) were mapped for retro_mmus_908 retrocopy.
No TSS is located nearby retro_mmus_908 retrocopy 5' end.
retro_mmus_908 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_908 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000324582 retrocopies
Callithrix jacchus ENSCJAG000000095811 retrocopy
Dasypus novemcinctus ENSDNOG000000154601 retrocopy
Myotis lucifugus ENSMLUG000000001701 retrocopy
Mustela putorius furoENSMPUG000000155361 retrocopy
Mus musculus ENSMUSG00000054428 2 retrocopies
retro_mmus_2516, retro_mmus_908 ,
Otolemur garnettii ENSOGAG000000103372 retrocopies
Pteropus vampyrus ENSPVAG000000176151 retrocopy
Rattus norvegicus ENSRNOG000000133001 retrocopy
Sorex araneus ENSSARG000000108601 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000207661 retrocopy



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