RetrogeneDB - Retrocopy retro_mmus

						
>retro_mmus_286
ATGGCCGACAAGATGGACATGTCTTTGGACGACATCATTAAGCTGAACCGTAACCAGCGCCGGGTGAATCGAGGCGGCGG

GCCTAGGAGGAACCGGCCCGCCATCGCCCGCGGCGGCAGGAACCGGCCGGCACCGTACAGTAGACCGAAACCACTTCCGG

ACAAGTGGCAGCACGACCTATTCGACAGCGGCTGCGGGGGTGGGGAAGGCGTGGAGACCGGTGCCAAGCTGCTCGTGTCA

AACCTGGACTTCGGGGTGTCAGATGCTGACATTCAGGAACTCTTTGCTGAATTTGGAACGTTGAAAAAAGCCGCTGTGGA

CTACGATCGCTCTGGACGAAGTTTAGGGACGGCGGATGTACACTTTGAACGGAGGGCAGATGCCCTGAAGGCTATGAAGC

AGTACAAGGGCGTCCCTTTGGATGGCCGCCCTATGGACATCCAGCTTGTCACGTCACAGATCGATCCACAGCGAAGACCT

GCACAAAGCGGAAACAGAGGCGGCATGACAAGGAGCCGTGGCTCTGGAGGCTTTGGTGGCCGCGGCAGCCAGGGAAGGGG

TAGAGGCACTGGCAGGAACTCAAAGCAGCAGCAGCTTTCTGCAGAGGAGTTGGACGCACAGCTGGATGCTTACAATGCAA

GGAGGGACACCAGCTAA

ORF - retro_mmus_286 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	84.21 %
Parental protein coverage:	81.96 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalRVNRGGGPMRNRPAIARGAAGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGV
		RVNRGGGP.RNRPAIAR....GGRNRPAPYSRPK.LPDKWQHDLFDSG.GGG.GVETG.KLLVSNLDFGV
RetrocopyRVNRGGGPRRNRPAIAR----GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV
ParentalSDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQIDT
		SDADIQELFAEFGTLKKAAV.YDRSGRSLGTADVHFER.ADALKAMKQY.GVPLDGRPM.IQLVTSQID.
RetrocopySDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVTSQIDP
ParentalQRRPAQSINRGGMTRNRGSGGFGGGGTRRGTRGGSRGRGRGTGRNSKQQLSAEELDAQLDAYNARMDTS
		QRRPAQS.NRGGMTR.RGSGGFGG....RG..G..RG.GR.......QQLSAEELDAQLDAYNAR.DTS
RetrocopyQRRPAQSGNRGGMTRSRGSGGFGG----RGSQGRGRGTGR---NSKQQQLSAEELDAQLDAYNARRDTS

							

							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	1 .17 RPM	20 .42 RPM
SRP007412_cerebellum	2 .17 RPM	30 .39 RPM
SRP007412_heart	2 .09 RPM	23 .85 RPM
SRP007412_kidney	2 .14 RPM	27 .47 RPM
SRP007412_liver	2 .51 RPM	14 .94 RPM
SRP007412_testis	1 .37 RPM	41 .62 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_286 in 3 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001XVA	POLR2A	1:171503315..171504408
ENCFF001YIJ	POLR2A	1:171501115..171504392
ENCFF001YKA	POLR2A	1:171500788..171504480

EST - click to see more details

No EST(s) were mapped for retro_mmus_286 retrocopy.

TSS - click to see more details

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
TSS No.	TSS Name	no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_71908	344 libraries	407 libraries	310 libraries	11 libraries	0 libraries
TSS #2	TSS_71909	85 libraries	182 libraries	653 libraries	133 libraries	19 libraries

The graphical summary, for retro_mmus_286 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)

Display detail expression values in each library

... or ...

Directly download all expression values

Lab - click to see more details

retro_mmus_286 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_286 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005877	1 retrocopy	retro_cfam_1395,
Gorilla gorilla	ENSGGOG00000013935	1 retrocopy	retro_ggor_2523,
Macaca mulatta	ENSMMUG00000012884	1 retrocopy	retro_mmul_1679,
Mus musculus	ENSMUSG00000025134	1 retrocopy	retro_mmus_286 ,
Sarcophilus harrisii	ENSSHAG00000010459	1 retrocopy	retro_shar_332,
Tupaia belangeri	ENSTBEG00000005834	7 retrocopies	retro_tbel_237, retro_tbel_2432, retro_tbel_251, retro_tbel_2690, retro_tbel_2918, retro_tbel_3933, retro_tbel_3934,

	RetrogeneDB ID:	retro_mmus_286
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	1:171503656..171504313(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMUSG00000060244
	Aliases:	Alyref2, C130042O11Rik, REF2, Refbp2
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	Alyref
	Ensembl ID:	ENSMUSG00000025134
	Aliases:	None
	Description:	Aly/REF export factor [Source:MGI Symbol;Acc:MGI:1341044]

Parental	RVNRGGGPMRNRPAIARGAAGGGRNRPAPYSRPKQLPDKWQHDLFDSGFGGGAGVETGGKLLVSNLDFGV
	RVNRGGGP.RNRPAIAR....GGRNRPAPYSRPK.LPDKWQHDLFDSG.GGG.GVETG.KLLVSNLDFGV
Retrocopy	RVNRGGGPRRNRPAIAR----GGRNRPAPYSRPKPLPDKWQHDLFDSGCGGGEGVETGAKLLVSNLDFGV

Parental	SDADIQELFAEFGTLKKAAVHYDRSGRSLGTADVHFERKADALKAMKQYNGVPLDGRPMNIQLVTSQIDT
	SDADIQELFAEFGTLKKAAV.YDRSGRSLGTADVHFER.ADALKAMKQY.GVPLDGRPM.IQLVTSQID.
Retrocopy	SDADIQELFAEFGTLKKAAVDYDRSGRSLGTADVHFERRADALKAMKQYKGVPLDGRPMDIQLVTSQIDP

Parental	QRRPAQSINRGGMTRNRGSGGFGGGGTRRGTRGGSRGRGRGTGRNSKQQLSAEELDAQLDAYNARMDTS
	QRRPAQS.NRGGMTR.RGSGGFGG....RG..G..RG.GR.......QQLSAEELDAQLDAYNAR.DTS
Retrocopy	QRRPAQSGNRGGMTRSRGSGGFGG----RGSQGRGRGTGR---NSKQQQLSAEELDAQLDAYNARRDTS

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

RetrogeneDB ID:

retro_mmus_286