RetrogeneDB - Retrocopy retro_mmus

						
>retro_mmus_234
ATGCAGAGCATCAAGTGTGTGGTGGTGGGCGATGGGGCCGTAGGCAAGACGTGCCTTCTCATCTGCTATACAACTAACGC

CTTCCCCAAGGAATACATCCCCACTGTGTTTGACAATTACAGCGCCCAGAGTGCGGTTGATGGGCGCACCGTGAACCTAA

ACCTGTGGGACACTGCGGGCCAGGAGGAATATGACCGCCTCCGCACCCTTTCCTACCCTCAGACCAACGTCTTCGTCATC

TGTTTCTCCATTGCCAGTCCACCCTCCTATGAGAACGTGAGGCACAAATGGCACCCAGAGGTTTGTCACCACTGCCCTGA

CGTGCCTATCCTCCTGGTGGGTACCAAGAAGGACCTGAGAGCCCAGCCTGATACCCTACGGCGCCTCAAGGAGCAGGGTC

AAGCGCCCATCACTCCACAGCAGGGCCAGGCACTGGCCAAGCAGATCCATGCTGTGCGCTACCTCGAGTGCTCAGCACTG

CAACAAGACGGCGTCAAGGAGGTGTTTGCGGAGGCTGTCCGGGCGGTGCTTAACCCAACACCGATAAAGCGTGGGCGGTC

CTGCATCCTCTTGTGA

ORF - retro_mmus_234 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	71.88 %
Parental protein coverage:	100. %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
		MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VDG..VNL.LWDTAGQE.YDRLR.L
RetrocopyMQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL
ParentalSYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYP
		SYPQT.VF.ICFS..SP.S.ENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE....PIT..
RetrocopySYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ
ParentalQGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
		QG.A.AK.I.AV.YLECSAL.Q.G.K.VF.EA.RAVL.P.P..KR.R.C.LL
RetrocopyQGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPI-KRGRSCILL

							

							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	11 .73 RPM	233 .30 RPM
SRP007412_cerebellum	12 .90 RPM	180 .20 RPM
SRP007412_heart	8 .93 RPM	117 .67 RPM
SRP007412_kidney	8 .39 RPM	141 .31 RPM
SRP007412_liver	9 .67 RPM	97 .08 RPM
SRP007412_testis	2 .97 RPM	23 .88 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity may be related with retro_mmus_234 in 1 libraries

ENCODE library ID	Target	ChIP-Seq Peak coordinates
ENCFF001YKA	POLR2A	7:102236182..102251463

EST - click to see more details

No EST(s) were mapped for retro_mmus_234 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_127187	436 libraries	409 libraries	202 libraries	24 libraries	1 library
TSS #2	TSS_127188	377 libraries	456 libraries	205 libraries	34 libraries	0 libraries

The graphical summary, for retro_mmus_234 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_234 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_234 has 6 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_28
Gorilla gorilla	retro_ggor_188
Pongo abelii	retro_pabe_21
Macaca mulatta	retro_mmul_210
Rattus norvegicus	retro_rnor_230
Oryctolagus cuniculus	retro_ocun_43

Parental genes homology:

Parental genes homology involve 10 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000136238	6 retrocopies	retro_hsap_1256, retro_hsap_1925, retro_hsap_28, retro_hsap_3036, retro_hsap_3072, retro_hsap_4910,
Gorilla gorilla	ENSGGOG00000026733	2 retrocopies	retro_ggor_2110, retro_ggor_217,
Mus musculus	ENSMUSG00000001847	2 retrocopies	retro_mmus_1372, retro_mmus_234 ,
Mus musculus	ENSMUSG00000006699	3 retrocopies	retro_mmus_2816, retro_mmus_2995, retro_mmus_3170,
Pan troglodytes	ENSPTRG00000018910	4 retrocopies	retro_ptro_1288, retro_ptro_3044, retro_ptro_3274, retro_ptro_36,
Rattus norvegicus	ENSRNOG00000001068	1 retrocopy	retro_rnor_230,
Ictidomys tridecemlineatus	ENSSTOG00000006784	1 retrocopy	retro_itri_1503,
Tupaia belangeri	ENSTBEG00000007272	4 retrocopies	retro_tbel_1796, retro_tbel_2564, retro_tbel_4296, retro_tbel_9,
Tarsius syrichta	ENSTSYG00000001618	2 retrocopies	retro_tsyr_2027, retro_tsyr_2068,
Xenopus tropicalis	ENSXETG00000027593	1 retrocopy	retro_xtro_1,

	RetrogeneDB ID:	retro_mmus_234
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	7:102239668..102240244(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMUSG00000073982
	Aliases:	Rhog, 2810426G09Rik, Arhg, Sid10750
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	Rac1
	Ensembl ID:	ENSMUSG00000001847
	Aliases:	Rac1, AL023026, D5Ertd559e
	Description:	RAS-related C3 botulinum substrate 1 [Source:MGI Symbol;Acc:MGI:97845]

Parental	MQAIKCVVVGDGAVGKTCLLISYTTNAFPGEYIPTVFDNYSANVMVDGKPVNLGLWDTAGQEDYDRLRPL
	MQ.IKCVVVGDGAVGKTCLLI.YTTNAFP.EYIPTVFDNYSA...VDG..VNL.LWDTAGQE.YDRLR.L
Retrocopy	MQSIKCVVVGDGAVGKTCLLICYTTNAFPKEYIPTVFDNYSAQSAVDGRTVNLNLWDTAGQEEYDRLRTL

Parental	SYPQTDVFLICFSLVSPASFENVRAKWYPEVRHHCPNTPIILVGTKLDLRDDKDTIEKLKEKKLTPITYP
	SYPQT.VF.ICFS..SP.S.ENVR.KW.PEV.HHCP..PI.LVGTK.DLR...DT...LKE....PIT..
Retrocopy	SYPQTNVFVICFSIASPPSYENVRHKWHPEVCHHCPDVPILLVGTKKDLRAQPDTLRRLKEQGQAPITPQ

Parental	QGLAMAKEIGAVKYLECSALTQRGLKTVFDEAIRAVLCPPPVKKRKRKCLLL
	QG.A.AK.I.AV.YLECSAL.Q.G.K.VF.EA.RAVL.P.P..KR.R.C.LL
Retrocopy	QGQALAKQIHAVRYLECSALQQDGVKEVFAEAVRAVLNPTPI-KRGRSCILL

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

RetrogeneDB ID:

retro_mmus_234