RetrogeneDB ID:

retro_mmus_3157

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:8:95921922..95922613(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:H2afy2
Ensembl ID:ENSMUSG00000020086
Aliases:H2afy2, macroH2A2
Description:H2A histone family, member Y2 [Source:MGI Symbol;Acc:MGI:3037658]


Retrocopy-Parental alignment summary:






>retro_mmus_3157
GGCAAGAAGGGGAGTAAGAAATCCAAGGCCACCAAGCTATGGACGTCTAAGATGTCCAAACTAACTTACAGTGATAAAGA
AAGAACATCAAATTCTACCTCAGAAGATGGGGCCAAGGAGATGGCTTTACCTATTTTCAAAGAGCCTTGTTTTGGGGCAG
AAGTTATCCCTGACCCAAAGTGACATCAGCCATATTGGCTGCACGAGGGTGGAGGGCATTGTCTACCCAACCACAGCCGA
AATCACCCTCAAAGGAGAGATAGGTAAAGCCTTTCCCAAGGCTGGAGGTAAAGAGTTCTCGGAAACAATGAAGGAACAAC
TTCACCAATCCCAAGACCCTTTGAAAATTGCCAAAGTGCCCACCAGCCAGTCCAGTGCATTCACAGCCAAATTTGTCATC
CACTGTCACATCTCCTAGTGGATCTTCCACAAATGTGAAGAACAACTGAAAGAGACCATCAACAAGTGCCCGCCCACAGC
TGAGGGCAAGAAGCTTACGTCTGTAGCCTTCCTACCTTTCCCCAGGAGCAGGAACTGGCTTCCCAAGTACATGGCAGCCT
AGGTGGCCCTCGAGACCACCTTGGTGCACTTCAATAACTTGAGCGTGTCCTTGCTGAAGAGCTAGCACTTGCAGCTATTG
GACAGCGAGAACATTGGCGTCTACATGCAGCAGATGGCCAAACTGGACACG

ORF - retro_mmus_3157 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.52 %
Parental protein coverage: 61.83 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGKKGGKKSKATKPRTSKKSKAKDSDKEGTSNSTSED-GPGDGFTILSSKSLVLGQKLSLTQSDISHIGSM
GKKG.KKSKATK..TSK.SK...SDKE.TSNSTSED.GP......L.SKSLVLGQKLSLTQSDISHIG..
RetrocopyGKKGSKKSKATKLWTSKMSKLTYSDKERTSNSTSED>GPRR-WLYLFSKSLVLGQKLSLTQSDISHIGCT
ParentalRVEGIVHPTTAEIDLKEEIGKALEKAGGKEFLETVKE-LRKSQGPLEVAEAAVSQSSGLAAKFVIHCHIP
RVEGIV.PTTAEI.LK.EIGKA..KAGGKEF.ET.KE.L..SQ.PL..A....SQSS...AKFVIHCHI.
RetrocopyRVEGIVYPTTAEITLKGEIGKAFPKAGGKEFSETMKEQLHQSQDPLKIAKVPTSQSSAFTAKFVIHCHIS
ParentalQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPKQTAAQVTLKAISAHFDDSSSSSLKNV
.W...KCEEQL.ETI..C...AE.KKL.SVAF.PFP..RN..PK..AA.V.L.....HF...S.S.LK..
Retrocopy*WIFHKCEEQLKETINKCPPTAEGKKLTSVAFLPFPRSRNWLPKYMAA*VALETTLVHFNNLSVSLLKS*
ParentalYFLLFDSESIGIYVQEMAKLDT
...L.DSE.IG.Y.Q.MAKLDT
RetrocopyHLQLLDSENIGVYMQQMAKLDT

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






RNA-Seq - click to see more details

(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 .15 RPM
SRP007412_cerebellum 0 .00 RPM 15 .50 RPM
SRP007412_heart 0 .00 RPM 6 .01 RPM
SRP007412_kidney 0 .00 RPM 4 .39 RPM
SRP007412_liver 0 .00 RPM 0 .57 RPM
SRP007412_testis 0 .00 RPM 5 .81 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_3157 was not detected

EST - click to see more details

No EST(s) were mapped for retro_mmus_3157 retrocopy.

TSS - click to see more details

No TSS is located nearby retro_mmus_3157 retrocopy 5' end.

Lab - click to see more details

retro_mmus_3157 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3157 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Mus musculus ENSMUSG00000020086 2 retrocopies
retro_mmus_1399, retro_mmus_3157 ,


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