RetrogeneDB - Retrocopy retro_mmus

						
>retro_mmus_97
ATGGCAGAGGCTCCAAAAGCGGTTTTGGGGCCGTTGGTAGGGGCAGTGGACCAAGGTACCAGCTCAACACGTTTTTTGGT

TTTCAATCCCCAAACAGCTGAATTACTTTGTCATCATCAAGTGGAAATAGCCCAGGAGTTCCCAAAAGAAGGATGGGTAG

AGCAAGACCCAAAGGCAATCCTGCAGTCTGTGTACGAGTGTATAGAGAAAGCATGTGAGAAACTCGGACAGCAGAGCATT

GATATTTCCAACATAAAAGCTATCGGTGTCACCAACCAGCGGGAAACTACGATAGTCTGGGACAAGTTCACTGGAGAACC

TCTCTACAATGCTGTGGTGTGGCTTGACCTAAGGACCCAGTCTACTGTGGAGAATCTCAGCAAAAGTATTTCAGTAAGCA

ATAACTTTGTCAAGAACAAGACAGGCCTTCCAATCAGCACTTATTTTAGTGCCGTGAAACTTCACTGGCTCATTGAAAAT

GTGAGAAAAGTGCAAAAGGCTATTGAAGATGGCAGAGCTATTTTTGGGACGGTTGATTCGTGGCTTATCTGGTGTATGAC

TGGAGGTATCAACGGAGGTGTCCACTGTACAGATGTAAGTAATGCCAGCAGGACCATGCTTTTCAACATTCACTCTTTGC

AATGGGATGAAGAGCTCTGCGACTTTTTTGGAATTCCAATGACCATCCTTCCCCGAATCCGGAGTTCTTCTGAGATCTAT

GGCCTAGTGAAAAGTGGCGTGTTGGAAGGTGTGCCAATATCTGGATGTCTGGGAGACCAGTCTGCTGCTTTGGTGGGACA

ACTGTGTCTTCAGGACGGACAAGCTAAAAGCACATATGGAACAGGCTGTTTCTTACTATGTAACACAGGCCAGAAGTGTG

TAAACTCTGAACATGGCCTTCTGACCACAGTGGCTTACCAGCTTGGCAGACAGGAGCCTGTCTATTATGCCCTGGAAGGT

TCCGTAGCCATAGCCGGTGCTGTTGTTAGCTGGATAAAAAACAATCTTCAAATTATTCAGTCTTCATCGGAAATTGAAAA

ACTTGCTGAAGTAGCAGGGACTTCTTATGGTTGTTACTTCGTCCCAGCCTTTTCAGGCTTATACGCTCCATATTGGGACC

CAAGTGCGAGAGGGATCATCTGCGGGCTCACCCAGTTCACCAATAAGTTCCATATTGCCTTTGCTGCGTTAGAAGCTGTT

TGCTTCCAAACGCGGGAGATTTTGGATGCCATGAACAGTGATTGTGGAATCCCGCTGACGCATTTGCAGGTAGATGGAGG

AATGACCGCAAACAGAGTTCTCATGCAACTGCAGGCGGACATTCTGTGTATTCCGGTGATGAAACCTTTCATGCCAGAAA

CAACTGCACTGGGAGTCGCAATGGCAGCGGGAGCGGCAGAAGGAGTTAGCGTGTGGAGTCTGGATCCTAAGGATTTGTCA

AGTGTCCAGATGGAGAAGTTTGAACCCCAGATCAATGTCGAGGAAAGTGAAGGTCGTTACGCCACATGGAAGAAAGCTGT

GCTGAAGTCAATGGGTTGGGTTTTGACTCAGTCTCCTGATGGTCGCGACCCTAGTATTTTCAGCAGCCTGACGCTGGGCT

TTTATGTAGTGAGTAGTATGGTGATATTAATTGGAGCAAGGTACATGTAA

ORF - retro_mmus_97 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.88 %
Parental protein coverage:	99.28 %
Number of stop codons detected:	0
Number of frameshifts detected	0

Retrocopy - Parental Gene Alignment:

									ParentalMAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
		MA.A.KAVLGPLVGAVDQGTSSTRFLVFN..TAELL.HHQVEI.QEFP.EGWVEQDPK.ILQSVYECIEK
RetrocopyMAEAPKAVLGPLVGAVDQGTSSTRFLVFNPQTAELLCHHQVEIAQEFPKEGWVEQDPKAILQSVYECIEK
ParentalTCEKLGQLNIDISNIKAIGVSNQRETTVVWDKVTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
		.CEKLGQ..IDISNIKAIGV.NQRETT.VWDK.TGEPLYNAVVWLDLRTQSTVENLSK.I...NNFVK.K
RetrocopyACEKLGQQSIDISNIKAIGVTNQRETTIVWDKFTGEPLYNAVVWLDLRTQSTVENLSKSISVSNNFVKNK
ParentalTGLPLSTYFSAVKLRWLLDNVKKVQEAVEENRALFGTIDSWLIWSLTGGIHGGVHCTDVTNASRTMLFNI
		TGLP.STYFSAVKL.WL..NV.KVQ.A.E..RA.FGT.DSWLIW..TGGI.GGVHCTDV.NASRTMLFNI
RetrocopyTGLPISTYFSAVKLHWLIENVRKVQKAIEDGRAIFGTVDSWLIWCMTGGINGGVHCTDVSNASRTMLFNI
ParentalHSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
		HSL.WD.ELC.FFGIPM.ILP..RSSSEIYGL.K.G.LEGVPISGCLGDQSAALVGQ.C.QDGQAK.TYG
RetrocopyHSLQWDEELCDFFGIPMTILPRIRSSSEIYGLVKSGVLEGVPISGCLGDQSAALVGQLCLQDGQAKSTYG
ParentalTGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
		TGCFLLCNTG.KCV.SEHGLLTTVAY.LGR..PVYYALEGSVAIAGAV..W...NL.II.SS.EIEKLA.
RetrocopyTGCFLLCNTGQKCVNSEHGLLTTVAYQLGRQEPVYYALEGSVAIAGAVVSWIKNNLQIIQSSSEIEKLAE
ParentalEVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
		..GTSYGCYFVPAFSGLYAPYW.PSARGIICGLTQFTNK.HIAFAALEAVCFQTREILDAMN.DCGIPL.
RetrocopyVAGTSYGCYFVPAFSGLYAPYWDPSARGIICGLTQFTNKFHIAFAALEAVCFQTREILDAMNSDCGIPLT
ParentalHLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
		HLQVDGGMT.N..LMQLQADIL.IPV.KP.MPETTALG.AMAAGAAEGV.VWSL.P.DLS.V.ME.FEPQ
RetrocopyHLQVDGGMTANRVLMQLQADILCIPVMKPFMPETTALGVAMAAGAAEGVSVWSLDPKDLSSVQMEKFEPQ
ParentalINAEESEIRYSTWKKAVMKSIGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYI
		IN.EESE.RY.TWKKAV.KS.GWV.TQSP...DPSIF.SL.LGF..VSSMV.LIGARY.
RetrocopyINVEESEGRYATWKKAVLKSMGWVLTQSPDGRDPSIFSSLTLGFYVVSSMVILIGARYM

							

							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 .12 RPM	18 .83 RPM
SRP007412_cerebellum	0 .00 RPM	15 .68 RPM
SRP007412_heart	0 .00 RPM	23 .60 RPM
SRP007412_kidney	0 .00 RPM	331 .61 RPM
SRP007412_liver	0 .05 RPM	75 .92 RPM
SRP007412_testis	412 .29 RPM	1 .56 RPM

ChIP-Seq - click to see more details

RNA Polymerase II actvity near the 5' end of retro_mmus_97 was not detected

EST - click to see more details

19 EST(s) were mapped to retro_mmus_97 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA063880	52693720	52694216	98	485	9	473
AA064451	52693715	52693838	99.2	122	1	121
AA065397	52693724	52693826	99.1	101	1	100
AA107211	52693727	52694319	99.2	585	5	579
AA107620	52693734	52694217	97.5	468	9	457
AA492930	52694279	52694398	97.5	116	3	113
AI647419	52694339	52694672	99.4	329	2	326
BB572574	52693689	52693965	96.8	267	9	258
BB614799	52693706	52694352	98.5	633	9	621
BF013306	52693858	52694191	100	333	0	333
BF149591	52693736	52694318	99.2	572	4	565
BF149654	52693766	52694281	100	515	0	515
BG100740	52694785	52695079	100	292	0	290
BG101398	52693964	52694342	98.2	371	7	364
BU962784	52693689	52694460	98.9	770	0	766
BY094838	52693690	52694081	99.3	388	3	385
BY353966	52694111	52694370	97.7	252	4	244
CA463392	52693875	52694517	100	635	0	628
CF105239	52693714	52694290	99.7	574	2	572

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_59780	1066 libraries	2 libraries	0 libraries	2 libraries	2 libraries
TSS #2	TSS_59781	1061 libraries	5 libraries	0 libraries	0 libraries	6 libraries

The graphical summary, for retro_mmus_97 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_97 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmus_97 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Rattus norvegicus	retro_rnor_114

Parental genes homology:

Parental genes homology involve 14 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007633	3 retrocopies	retro_cjac_125, retro_cjac_3161, retro_cjac_4035,
Cavia porcellus	ENSCPOG00000003261	2 retrocopies	retro_cpor_11, retro_cpor_20,
Echinops telfairi	ENSETEG00000008279	2 retrocopies	retro_etel_2000, retro_etel_247,
Felis catus	ENSFCAG00000004264	1 retrocopy	retro_fcat_140,
Homo sapiens	ENSG00000198814	4 retrocopies	retro_hsap_3087, retro_hsap_3120, retro_hsap_4885, retro_hsap_70,
Loxodonta africana	ENSLAFG00000007632	1 retrocopy	retro_lafr_30,
Monodelphis domestica	ENSMODG00000002417	1 retrocopy	retro_mdom_234,
Mus musculus	ENSMUSG00000025059	2 retrocopies	retro_mmus_119, retro_mmus_97 ,
Nomascus leucogenys	ENSNLEG00000010102	2 retrocopies	retro_nleu_1650, retro_nleu_771,
Oryctolagus cuniculus	ENSOCUG00000013023	2 retrocopies	retro_ocun_2, retro_ocun_81,
Rattus norvegicus	ENSRNOG00000034116	2 retrocopies	retro_rnor_114, retro_rnor_34,
Sarcophilus harrisii	ENSSHAG00000006470	1 retrocopy	retro_shar_35,
Ictidomys tridecemlineatus	ENSSTOG00000008732	1 retrocopy	retro_itri_1436,
Tarsius syrichta	ENSTSYG00000008249	1 retrocopy	retro_tsyr_29,

	RetrogeneDB ID:	retro_mmus_97
Retrocopy location	Organism:	*Mouse (Mus musculus)*
	Coordinates:	18:52693721..52695371(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	ENSMUSG00000053624
	Aliases:	Gykl1, AI449806, Gk-rs1
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	Gyk
	Ensembl ID:	ENSMUSG00000025059
	Aliases:	Gyk, D930012N15Rik, GK
	Description:	glycerol kinase [Source:MGI Symbol;Acc:MGI:106594]

Parental	MAAAKKAVLGPLVGAVDQGTSSTRFLVFNSKTAELLSHHQVEIKQEFPREGWVEQDPKEILQSVYECIEK
	MA.A.KAVLGPLVGAVDQGTSSTRFLVFN..TAELL.HHQVEI.QEFP.EGWVEQDPK.ILQSVYECIEK
Retrocopy	MAEAPKAVLGPLVGAVDQGTSSTRFLVFNPQTAELLCHHQVEIAQEFPKEGWVEQDPKAILQSVYECIEK

Parental	TCEKLGQLNIDISNIKAIGVSNQRETTVVWDKVTGEPLYNAVVWLDLRTQSTVENLSKRIPGNNNFVKSK
	.CEKLGQ..IDISNIKAIGV.NQRETT.VWDK.TGEPLYNAVVWLDLRTQSTVENLSK.I...NNFVK.K
Retrocopy	ACEKLGQQSIDISNIKAIGVTNQRETTIVWDKFTGEPLYNAVVWLDLRTQSTVENLSKSISVSNNFVKNK

Parental	TGLPLSTYFSAVKLRWLLDNVKKVQEAVEENRALFGTIDSWLIWSLTGGIHGGVHCTDVTNASRTMLFNI
	TGLP.STYFSAVKL.WL..NV.KVQ.A.E..RA.FGT.DSWLIW..TGGI.GGVHCTDV.NASRTMLFNI
Retrocopy	TGLPISTYFSAVKLHWLIENVRKVQKAIEDGRAIFGTVDSWLIWCMTGGINGGVHCTDVSNASRTMLFNI

Parental	HSLEWDKELCEFFGIPMEILPNVRSSSEIYGLMKAGALEGVPISGCLGDQSAALVGQMCFQDGQAKNTYG
	HSL.WD.ELC.FFGIPM.ILP..RSSSEIYGL.K.G.LEGVPISGCLGDQSAALVGQ.C.QDGQAK.TYG
Retrocopy	HSLQWDEELCDFFGIPMTILPRIRSSSEIYGLVKSGVLEGVPISGCLGDQSAALVGQLCLQDGQAKSTYG

Parental	TGCFLLCNTGHKCVFSEHGLLTTVAYKLGRDKPVYYALEGSVAIAGAVIRWLRDNLGIIKSSEEIEKLAK
	TGCFLLCNTG.KCV.SEHGLLTTVAY.LGR..PVYYALEGSVAIAGAV..W...NL.II.SS.EIEKLA.
Retrocopy	TGCFLLCNTGQKCVNSEHGLLTTVAYQLGRQEPVYYALEGSVAIAGAVVSWIKNNLQIIQSSSEIEKLAE

Parental	EVGTSYGCYFVPAFSGLYAPYWEPSARGIICGLTQFTNKCHIAFAALEAVCFQTREILDAMNRDCGIPLS
	..GTSYGCYFVPAFSGLYAPYW.PSARGIICGLTQFTNK.HIAFAALEAVCFQTREILDAMN.DCGIPL.
Retrocopy	VAGTSYGCYFVPAFSGLYAPYWDPSARGIICGLTQFTNKFHIAFAALEAVCFQTREILDAMNSDCGIPLT

Parental	HLQVDGGMTSNKILMQLQADILYIPVVKPSMPETTALGAAMAAGAAEGVGVWSLEPEDLSAVTMERFEPQ
	HLQVDGGMT.N..LMQLQADIL.IPV.KP.MPETTALG.AMAAGAAEGV.VWSL.P.DLS.V.ME.FEPQ
Retrocopy	HLQVDGGMTANRVLMQLQADILCIPVMKPFMPETTALGVAMAAGAAEGVSVWSLDPKDLSSVQMEKFEPQ

Parental	INAEESEIRYSTWKKAVMKSIGWVTTQSPESGDPSIFCSLPLGFFIVSSMVMLIGARYI
	IN.EESE.RY.TWKKAV.KS.GWV.TQSP...DPSIF.SL.LGF..VSSMV.LIGARY.
Retrocopy	INVEESEGRYATWKKAVLKSMGWVLTQSPDGRDPSIFSSLTLGFYVVSSMVILIGARYM

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

RetrogeneDB ID:

retro_mmus_97