RetrogeneDB ID: retro_mmus_1399

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:62218366..62219332(-)
• Located in intron of: ENSMUSG00000097039

Retrocopy information

• Ensembl ID: ENSMUSG00000056590
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: H2afy2
• Ensembl ID: ENSMUSG00000020086
• Aliases: H2afy2, macroH2A2
• Description: H2A histone family, member Y2 [Source:MGI Symbol;Acc:MGI:3037658]

Sequence

>retro_mmus_1399
ATGTCAGGCCGGAGCGGGAAGAAGAAAATGTCCAAGCTGTCCCAGTCAGCCAAGGCCGGAGTCATCTTTCCAGTAGGCCG
GTTGATGCGCTACCTGAAAAAGGGAACCTTCAAGTACAGGATCAGCGTAGGTGCTCAGGTCTACATGGCTGCGGTCACTG
AGTACCTAGCAGCGGAAATCCTGGAGTTGGCCAGGAACGCTGCGAGGGACAACAAGAAGGCCCGGATAGCCCCCAGACAC
ATCCTGCTGGCCGTTGCCAACGACCAGGAACTCAACCAGCTACTGAAAGGAGTGACTATCGCCAGTGGGGGTGTCCTGCC
GAGAATTCTCCACGAACTGCTGGCCAAGAAGAGGGACCAAAGGCAAGTCAGAGACAATCCTCTCCCACCCCCAGAGAAAA
GAGGAAGGAAGGCCACATCAGGCAAGAAGGGGGCTAAGAAATCCAAGGCCACCAAGCCAGGGACGTCGAAGAAGTCTAAA
GCAAAGGACAGCAATAAAGAAGGAACATCAAATTCCACCTCGGAGGATGTGCCGGGGGATGGCTTCACCATCTTGTCTTC
GAAGAGCCACGTTCTGGGGCAGAAGCTATCCCTGACCCAGAGTGACATCAGCCATATTGGCTCCATGAGGGTGGAGGGCA
TCGTCCATCCAACCACAGCTGAGATCGACCTCAAGGAAGAGATAGGGAAAGCCTTGGAAAAGGCTGGGGGTAAAGAGTTC
TTGGAAACAGTAAAGGAGCTTCGCAAGTCCCAAGGCCCTTTAGAAATCGCTGAAGCTGCCGTCAGCCAATCCAGTGGACT
CGCAGCCAAATTTGTCATCCACTGTCACATCCCCCGGTGGGGCTCTGACAAATGTGAAGAACAGCTGGAAGAGACCATCA
AAAACTGCCTGTCTGCAGCTGAGGATAAGAAGCTTAAATCCGTCGCCTTCCCACCGTTCCCCAGTGGCAGAAACTGCTTC
CCCAGG

Alignment

ORF - retro_mmus_1399 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.56 %
• Parental protein coverage: 86.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MSGRSGKKKMSKLSRSARAGVIFPVGRLMRYLKKGTFKYRISVGAPVYMAAVIEYLAAEILELAGNAARD
          MSGRSGKKKMSKLS.SA.AGVIFPVGRLMRYLKKGTFKYRISVGA.VYMAAV.EYLAAEILELA.NAARD
Retrocopy MSGRSGKKKMSKLSQSAKAGVIFPVGRLMRYLKKGTFKYRISVGAQVYMAAVTEYLAAEILELARNAARD

Parental  NKKARIAPRHILLAVANDEELNQLLKGVTIASGGVLPRIHPELLAKKR-GTK-GKSETILS-PPPEKRGR
          NKKARIAPRHILLAVAND.ELNQLLKGVTIASGGVLPRI..ELLAKKR.G.K.GKSETILS.PPPEKRGR
Retrocopy NKKARIAPRHILLAVANDQELNQLLKGVTIASGGVLPRILHELLAKKR<GPK<GKSETILS<PPPEKRGR

Parental  KAASGKKGGKKSKATKPRTSKKSKAKDSDKEGTSNSTSEDGPGDGFTILSSKSLVLGQKLSLTQSDISHI
          KA.SGKKG.KKSKATKP.TSKKSKAKDS.KEGTSNSTSED.PGDGFTILSSKS.VLGQKLSLTQSDISHI
Retrocopy KATSGKKGAKKSKATKPGTSKKSKAKDSNKEGTSNSTSEDVPGDGFTILSSKSHVLGQKLSLTQSDISHI

Parental  GSMRVEGIVHPTTAEIDLKEEIGKALEKAGGKEFLETVKELRKSQGPLEVAEAAVSQSSGLAAKFVIHCH
          GSMRVEGIVHPTTAEIDLKEEIGKALEKAGGKEFLETVKELRKSQGPLE.AEAAVSQSSGLAAKFVIHCH
Retrocopy GSMRVEGIVHPTTAEIDLKEEIGKALEKAGGKEFLETVKELRKSQGPLEIAEAAVSQSSGLAAKFVIHCH

Parental  IPQWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPK
          IP.WGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFP.
Retrocopy IPRWGSDKCEEQLEETIKNCLSAAEDKKLKSVAFPPFPSGRNCFPR

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0.07 RPM	12.15 RPM
SRP007412_cerebellum	0.09 RPM	15.50 RPM
SRP007412_heart	0.06 RPM	6.01 RPM
SRP007412_kidney	0.08 RPM	4.39 RPM
SRP007412_liver	0.00 RPM	0.57 RPM
SRP007412_testis	10.29 RPM	5.81 RPM

ChIP-Seq

RNA Polymerase II actvity may be related with retro_mmus_1399 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YIJ	POLR2A	15:62218584..62225502
ENCFF001YJZ	POLR2A	15:62213268..62225254
ENCFF001YKA	POLR2A	15:62212292..62226288

EST

No EST(s) were mapped for retro_mmus_1399 retrocopy.

TSS

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_40779	1065 libraries	3 libraries	2 libraries	2 libraries	0 libraries

The graphical summary, for retro_mmus_1399 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)

Lab

retro_mmus_1399 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1399 has 0 orthologous retrocopies within eutheria group .

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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,