RetrogeneDB - Retrocopy retro_ogar

                        
>retro_ogar_1598
ATGCCCAAGCAGCTGCTGAGGCTCAGGTAGTTGAACCCCACTCCAATGGCTCTGTGGTTAATAGAACCAGCCCAGAGGAG

ACTAACTTGGAGGCCTTGCAGAAAAAGCTTGAAGAGCTGGAGTTTGATGAACAGCAGCAGAAGCACACTGAGGCCTCTCT

TACCTAGAAGCAGAAGTGGGGAGAATTAAAGGATGACAACTTCAAGAAATCAGTGAACTGGGGACTGGCAATGGCAGTGT

GCTGTTCAAGGTCTCCCTCAAGCATTCCAGTCTGGTCATAGCCAGAGAGCTAGTTCACCTGGACACCAACCCTGCAATCT

GGAACAAGGTCTTAAGGGAGCTGCAGATTCTACCTGAGTACAACTCTTCACACACTATGGCTACTATGATGCATTCTACA

GCGATGGAAAGATGGATATCTGCAAAGATCATATGGGAAGGGGTTCCTTGGGTCGAGTTCTGAAGAAAGCCATAAGAATT

CATGAACACATTTTAGGAGAAGTTAGGGTTGCTGTGTAAAAGACCTGACACATCTGAGGGAGAAGCACAAGATTGTGTAC

AGAGATGTCAAGCCCTTATCAACCTAGTCACCTCCTACGGGGAGATCAAGTTCTGTGAATTTGGGGTCAGTGGGCAGTGC

TTGGACTCCTTGGCCAGCTCCTCCATGGGCACAAGGTCCTATGTCACCAGAAAGACTCCAGAGAACTCTCTGCAGTCAGG

TATTTAGACAGTGGAACACTCCTTTCTGGTGGAGATAGTGGTTGGGAGGTATCTCTTTCCTCATCCAGATCCAAAGGAGC

TGGAGCTGATGTTCGGGTGCAGGTGGAGGAAGATGCAGCTGATACCCAACCCAGACCAAATCGTGGGAGGTCCCTCAGCG

CACATGGAATGGACAGCTGACCTCCTGTGGTGATTTTTGGGTTGTTGGTTACATAGTCAACGAGCCTCCTCCA

ORF - retro_ogar_1598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	61.93 %
Parental protein coverage:	82.19 %
Number of stop codons detected:	4
Number of frameshifts detected:	7

Retrocopy - Parental Gene Alignment:

                                ParentalMPKKKPTPIQLNPAP-DGSAVNGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFE
MPK.......LNP.P..GS.VN.TS..ETNLEALQKKLEELE.DEQQ.K..EA.LT.KQK.GELKDD.F.
RetrocopyMPKQLLRLR*LNPTP<NGSVVNRTSPEETNLEALQKKLEELEFDEQQQKHTEASLT*KQKWGELKDDNFK
ParentalK-ISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIV-GFYGAFYSDG
K.ISELG.GNG.V.FKVS.K.S.LV.AR.L.HL...PAI.N...RELQ.L.E.NS.....G.Y.AFYSDG
RetrocopyK<ISELGTGNGSVLFKVSLKHSSLVIARELVHLDTNPAIWNKVLRELQILPEYNSSHTM<GYYDAFYSDG
ParentalEISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAV-IKGLTYLREKHKIMHRDVKPSNI-LVNSRGEIK
...IC..HM..GSL..VLKKA.RI.E.ILG.V..AV..K.LT.LREKHKI..RDVKP....LV.S.GEIK
RetrocopyKMDICKDHMGRGSLGRVLKKAIRIHEHILGEVRVAV<VKDLTHLREKHKIVYRDVKPLST<LVTSYGEIK
ParentalLCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLS-LVEMAVGRYPIPPPDAKELELM
.C.FGVSGQ..DS.A.S..GTRSY...........S.QS.I.....S.LVE..VGRY..P.PD.KELELM
RetrocopyFCEFGVSGQCLDSLASSSMGTRSYVTRKTPEN---SLQSGI*TVEHSFLVEIVVGRYLFPHPDPKELELM
ParentalFGC-QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELL-DYIVNEPPP
FGC.QVE.DAA.T.PRP...GR.LS..GMDS.PP..IF.LL..YIVNEPPP
RetrocopyFGC<QVEEDAADTQPRPNR-GRSLSAHGMDS*PPVVIFGLL<GYIVNEPPP

                            

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

                        

RNA-Seq - click to see more details

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Otolemur garnettii was not studied using ChIP-Seq data.

EST - click to see more details

Otolemur garnettii was not studied using EST data.

TSS - click to see more details

Otolemur garnettii was not studied using FANTOM5 data.

Lab - click to see more details

retro_ogar_1598 was not experimentally validated.

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033983	1 retrocopy	retro_btau_1416,
Cavia porcellus	ENSCPOG00000003053	1 retrocopy	retro_cpor_483,
Gorilla gorilla	ENSGGOG00000003687	1 retrocopy	retro_ggor_2650,
Macaca mulatta	ENSMMUG00000016840	1 retrocopy	retro_mmul_2285,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Otolemur garnettii	ENSOGAG00000015876	1 retrocopy	retro_ogar_1598 ,
Ochotona princeps	ENSOPRG00000007770	1 retrocopy	retro_opri_846,
Pongo abelii	ENSPPYG00000006576	2 retrocopies	retro_pabe_3092, retro_pabe_3249,
Pan troglodytes	ENSPTRG00000007193	1 retrocopy	retro_ptro_2676,

	RetrogeneDB ID:	retro_ogar_1598
Retrocopy location	Organism:	*Bushbaby (Otolemur garnettii)*
	Coordinates:	GL873554.1:6408990..6409943(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	MAP2K1
	Ensembl ID:	ENSOGAG00000015876
	Aliases:	None
	Description:	mitogen-activated protein kinase kinase 1 [Source:HGNC Symbol;Acc:6840]

Parental	MPKKKPTPIQLNPAP-DGSAVNGTSSAETNLEALQKKLEELELDEQQRKRLEAFLTQKQKVGELKDDDFE
	MPK.......LNP.P..GS.VN.TS..ETNLEALQKKLEELE.DEQQ.K..EA.LT.KQK.GELKDD.F.
Retrocopy	MPKQLLRLRLNPTP<NGSVVNRTSPEETNLEALQKKLEELEFDEQQQKHTEASLTKQKWGELKDDNFK

Parental	K-ISELGAGNGGVVFKVSHKPSGLVMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIV-GFYGAFYSDG
	K.ISELG.GNG.V.FKVS.K.S.LV.AR.L.HL...PAI.N...RELQ.L.E.NS.....G.Y.AFYSDG
Retrocopy	K<ISELGTGNGSVLFKVSLKHSSLVIARELVHLDTNPAIWNKVLRELQILPEYNSSHTM<GYYDAFYSDG

Parental	EISICMEHMDGGSLDQVLKKAGRIPEQILGKVSIAV-IKGLTYLREKHKIMHRDVKPSNI-LVNSRGEIK
	...IC..HM..GSL..VLKKA.RI.E.ILG.V..AV..K.LT.LREKHKI..RDVKP....LV.S.GEIK
Retrocopy	KMDICKDHMGRGSLGRVLKKAIRIHEHILGEVRVAV<VKDLTHLREKHKIVYRDVKPLST<LVTSYGEIK

Parental	LCDFGVSGQLIDSMANSFVGTRSYMSPERLQGTHYSVQSDIWSMGLS-LVEMAVGRYPIPPPDAKELELM
	.C.FGVSGQ..DS.A.S..GTRSY...........S.QS.I.....S.LVE..VGRY..P.PD.KELELM
Retrocopy	FCEFGVSGQCLDSLASSSMGTRSYVTRKTPEN---SLQSGI*TVEHSFLVEIVVGRYLFPHPDPKELELM

Parental	FGC-QVEGDAAETPPRPRTPGRPLSSYGMDSRPPMAIFELL-DYIVNEPPP
	FGC.QVE.DAA.T.PRP...GR.LS..GMDS.PP..IF.LL..YIVNEPPP
Retrocopy	FGC<QVEEDAADTQPRPNR-GRSLSAHGMDS*PPVVIFGLL<GYIVNEPPP

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

RetrogeneDB ID:

retro_ogar_1598