RetrogeneDB - Retrocopy retro_mmul

						
>retro_mmul_1729
CTCAGATACCAACACACTGGTGCCGTCCTGGACTGAGCCTTCTACAATCCAGCGCAGGCCTGGAGAGGAGGACTAGATCA

TCAATTGAAAATGCATTATTTGAACACTGATCAAGAAAATCTTGTTGGGACCCATGATGTCCCCATCAGATGTGTCGAAT

ACTGTCCAGAAGTGAATGTGGTGGTTACTGGAAGTTGGGATCAGACAGTTAAATTGTGGGATCCCAGAAATCGTGGTAAC

GCCAGGACCTTCTCTCAGCCTAAAAAGGCATATACCTTCTCAGTGTCTGGAGACCGGCTGACTGTGAGAACACTGGGCCT

CAGAGTGTTGGTGTGGGGCTTATGGAACATGGGTTATGTGCAGCAGAGCAGGGAGTCCAGCCTGAAATACCAGACTTGCT

GCATACAAGCATCTCCAAACAAGCAGGGTTATGTATTAAGCTCTATTGAAGGCAGAGTGGCAGTTGAATACTTGGCCCAA

GCCCTGAGGTACAGAGGAAATATGCCTTCAAATGTCACAGACTAAAAGAAAATAATATTGAGCAGGTTTACCCAGTTAAT

GCCATTTCTTTCCAGAATATCCGTAATACATTTGCCATAGGTGGTTCTGATGGCTTTGTAAATACTTGGAATCCATTTAA

CAAAAAGCAACTGTGCCAGTTGCATCGGTACGCCATGAGCATCACATCACTTGCCTTCAGTAATGATAGGACTATGCTTG

CAATAGCATCATCATATATTATAAAATGGATGACACGGAACATCCTGAAGATGGTATCTTCATTCACCCAGTGACAGATG

CAGAAACGAAACCCAAG

ORF - retro_mmul_1729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.61 %
Parental protein coverage:	83.54 %
Number of stop codons detected:	1
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalLKYQHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTV
		L.YQHTGAVLD.AFY.P..AW.GGLDHQLKMH.LNTDQENLVGTHD.PIRCVEYCPEVNV.VTGSWDQTV
RetrocopyLRYQHTGAVLD*AFYNPAQAWRGGLDHQLKMHYLNTDQENLVGTHDVPIRCVEYCPEVNVVVTGSWDQTV
ParentalKLWDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAGRRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPN
		KLWDPR...NA.TFSQP.K.YT.SVSGDRL.V.T.G.RVLVW.L.NMGYVQQ.RESSLKYQT.CI.A.PN
RetrocopyKLWDPRNRGNARTFSQPKKAYTFSVSGDRLTVRTLGLRVLVWGLWNMGYVQQSRESSLKYQTCCIQASPN
ParentalKQGYVLSSIEGRVAVEYL-DPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVN
		KQGYVLSSIEGRVAVEYL..PSPEVQ..KYAFKCHRLKENNIEQ.YPVNAISF.NI.NTFA.GGSDGFVN
RetrocopyKQGYVLSSIEGRVAVEYL<GPSPEVQ-RKYAFKCHRLKENNIEQVYPVNAISFQNIRNTFAIGGSDGFVN
ParentalIWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM-YEMDDTEHPEDGIFIRQVTDAETKPK
		.W.PFNKK.LCQ.HRY..SI.SLAFSND.T.LAIASSY..Y.MDDTEHPEDGIFI..VTDAETKPK
RetrocopyTWNPFNKKQLCQLHRYAMSITSLAFSNDRTMLAIASSYI<YKMDDTEHPEDGIFIHPVTDAETKPK

							

							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	16 .02 RPM
SRP007412_brain_prefrontal_cortex	0 .00 RPM	17 .53 RPM
SRP007412_cerebellum	0 .00 RPM	22 .79 RPM
SRP007412_heart	0 .00 RPM	14 .37 RPM
SRP007412_kidney	0 .00 RPM	17 .84 RPM
SRP007412_liver	0 .00 RPM	12 .98 RPM
SRP007412_testis	0 .00 RPM	65 .10 RPM

ChIP-Seq - click to see more details

Macaca mulatta was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mmul_1729 retrocopy.

TSS - click to see more details

Macaca mulatta was not studied using FANTOM5 data.

Lab - click to see more details

retro_mmul_1729 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_mmul_1729 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 15 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012700	1 retrocopy	retro_cfam_399,
Choloepus hoffmanni	ENSCHOG00000010213	1 retrocopy	retro_chof_1339,
Callithrix jacchus	ENSCJAG00000001066	1 retrocopy	retro_cjac_3085,
Cavia porcellus	ENSCPOG00000011957	1 retrocopy	retro_cpor_997,
Homo sapiens	ENSG00000154473	1 retrocopy	retro_hsap_3887,
Gorilla gorilla	ENSGGOG00000023971	1 retrocopy	retro_ggor_2614,
Myotis lucifugus	ENSMLUG00000017732	1 retrocopy	retro_mluc_627,
Macaca mulatta	ENSMMUG00000003092	1 retrocopy	retro_mmul_1729 ,
Nomascus leucogenys	ENSNLEG00000027075	1 retrocopy	retro_nleu_1887,
Procavia capensis	ENSPCAG00000007736	1 retrocopy	retro_pcap_412,
Pongo abelii	ENSPPYG00000002731	1 retrocopy	retro_pabe_3168,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358,
Ictidomys tridecemlineatus	ENSSTOG00000021785	1 retrocopy	retro_itri_1095,
Tarsius syrichta	ENSTSYG00000013444	2 retrocopies	retro_tsyr_1652, retro_tsyr_732,
Tursiops truncatus	ENSTTRG00000016194	1 retrocopy	retro_ttru_1136,

	RetrogeneDB ID:	retro_mmul_1729
Retrocopy location	Organism:	*Rhesus macaque (Macaca mulatta)*
	Coordinates:	3:146412309..146413126(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	MMU.1219
	Ensembl ID:	ENSMMUG00000003092
	Aliases:	None
	Description:	mitotic checkpoint protein BUB3 [Source:RefSeq peptide;Acc:NP_001253182]

Parental	LKYQHTGAVLDCAFYDPTHAWSGGLDHQLKMHDLNTDQENLVGTHDAPIRCVEYCPEVNVMVTGSWDQTV
	L.YQHTGAVLD.AFY.P..AW.GGLDHQLKMH.LNTDQENLVGTHD.PIRCVEYCPEVNV.VTGSWDQTV
Retrocopy	LRYQHTGAVLD*AFYNPAQAWRGGLDHQLKMHYLNTDQENLVGTHDVPIRCVEYCPEVNVVVTGSWDQTV

Parental	KLWDPRTPCNAGTFSQPEKVYTLSVSGDRLIVGTAGRRVLVWDLRNMGYVQQRRESSLKYQTRCIRAFPN
	KLWDPR...NA.TFSQP.K.YT.SVSGDRL.V.T.G.RVLVW.L.NMGYVQQ.RESSLKYQT.CI.A.PN
Retrocopy	KLWDPRNRGNARTFSQPKKAYTFSVSGDRLTVRTLGLRVLVWGLWNMGYVQQSRESSLKYQTCCIQASPN

Parental	KQGYVLSSIEGRVAVEYL-DPSPEVQKKKYAFKCHRLKENNIEQIYPVNAISFHNIHNTFATGGSDGFVN
	KQGYVLSSIEGRVAVEYL..PSPEVQ..KYAFKCHRLKENNIEQ.YPVNAISF.NI.NTFA.GGSDGFVN
Retrocopy	KQGYVLSSIEGRVAVEYL<GPSPEVQ-RKYAFKCHRLKENNIEQVYPVNAISFQNIRNTFAIGGSDGFVN

Parental	IWDPFNKKRLCQFHRYPTSIASLAFSNDGTTLAIASSYM-YEMDDTEHPEDGIFIRQVTDAETKPK
	.W.PFNKK.LCQ.HRY..SI.SLAFSND.T.LAIASSY..Y.MDDTEHPEDGIFI..VTDAETKPK
Retrocopy	TWNPFNKKQLCQLHRYAMSITSLAFSNDRTMLAIASSYI<YKMDDTEHPEDGIFIHPVTDAETKPK

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

RetrogeneDB ID:

retro_mmul_1729