RetrogeneDB - Retrocopy retro_ogar

                        
>retro_ogar_338
GGAGCTCTATACTTTTGTCAGAAATAATCTCTTGGGCACTGAAGGCATAGATAGATTTACAATCAACCATTTATATGCAG

ATATTCAATGCTAGAAAATCAGTCCTGAAGGAAAAGCTAAAATTCAGCTTCAGCTGGTCTTGCATGCAGGGGACACAACT

AACTCCCATTTTTTCAATGAAAGCACAACAGTGAAAGAGCAAAATGCAGTAAAAGACCTTCTTCAGCAGCTGCTGCCTAA

ATTCAAGAGGAAAGCAAATAAAGAACTGGAAGAAGAAAACAGAGTGCTGCAAGAAGAACCTGTCTTGTTTCAGCAAAAAG

ACCTTGTTGTGAGCCAAGTGATCAGCGCTGAGGAATTCTGGGCCAATCTTTTAAACGTGAACGCAACAGAGTTCTTCGAC

ATCCAATCTTAAGCAGGATGTTGGCATTTCTGCAGCATTTCTGGCTGATGTTCAGCCCCAAACTTACGGCTGCAATGGTC

TGAGATATAATTTAACCTCTGATATTACTGAGTCTATATTTAGGATCTATCCAAAGTAAAAATGAAATACACAGAAAATG

TTCCCCACAACATGATAGAGAAGGAATTCTGGACACGTTTTCTCCAGTTCCATTATTTTCAAAGGAACTTACTGAATACA

GGGTCAAAGGATCTCTTTGCAGAATGCACCAAAATAGGGTTAAAAACAATGGTTTCATTAGGAGTGAAAAATCCATTACT

CGATTTGACGGCTTTGGAAGATAAATCATTAGATGGGGGCTATGGCATTTCCTCTATGCCAACTACTTCCAATTCTAAAT

CCATAAAGGAAAATAGTAATGCTGCCATCATCAAGAGGTTTAACTATTGTAGTGACATGGTCCTGGCAGCAGGACTCAGG

AAACAAGAAGCACAAAACGAATAAAATGGTGAGCTCAGCAGCATGGATGGAAATTCTAGAGATGCAGATTGCTTTCAGCC

TGCAGGAAAAAGGGCGAAGTTACAAGAGTCTGTTAAATATGAAGACCTGGCAAAAAAAAATTCTGTAAATTCT

ORF - retro_ogar_338 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	82.49 %
Parental protein coverage:	63.87 %
Number of stop codons detected:	2
Number of frameshifts detected:	4

Retrocopy - Parental Gene Alignment:

                                ParentalGALY-LMAERIAWA-PEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKER
GALY.L..E.I.WA..EG.DRFTI.H.YADI.C.KISPEGKAKIQLQLVLHAGDTTN.HF.NEST.VKE.
RetrocopyGALY<LLSEIISWA<TEGIDRFTINHLYADIQC*KISPEGKAKIQLQLVLHAGDTTNSHFFNESTTVKEQ
ParentalDAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNAAE-SSSTS
.AVKDLLQQLLPKFKRKANKELEE.NR.LQE.PVLFQ..KDLVVSQVISAEEFWAN.LNVNA.E.SS.TS
RetrocopyNAVKDLLQQLLPKFKRKANKELEEENRVLQEEPVLFQ-QKDLVVSQVISAEEFWANLLNVNATE>SS-TS
ParentalNHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYP-AVKMKYAENVPHNMTEKEFWTRFFQS
N.KQDVGISAAFLADV.PQT.GCNGLRYNLTSDI.ESIFR.YP..VKMKY.ENVPHNM.EKEFWTRF.Q.
RetrocopyNLKQDVGISAAFLADVQPQTYGCNGLRYNLTSDITESIFRIYP<KVKMKYTENVPHNMIEKEFWTRFLQF
ParentalHYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPTTSNSKSIKE
HYF.R..LNTGSKDLFAEC.KI...GLKTMVSLGVKNPLLDLTALEDK.LD.GYGISS.PTTSNSKSIKE
RetrocopyHYFQRNLLNTGSKDLFAECTKI---GLKTMVSLGVKNPLLDLTALEDKSLDGGYGISSMPTTSNSKSIKE
ParentalNSNAAIIKRFNHHSAMVLAAGLRKQEAQNEQNGEPSSMDGNSGDADCFQPAVKRAKLQESIEYEDLAKNN
NSNAAIIKRFN..S.MVLAAGLRKQEAQNE.NGE.SSMDGNS.DADCFQPA.KRAKLQES..YEDL....
RetrocopyNSNAAIIKRFNYCSDMVLAAGLRKQEAQNE*NGELSSMDGNSRDADCFQPAGKRAKLQESVKYEDLXXXX
ParentalSVKT
SV..
RetrocopySVNS

                            

                            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_338 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000110768	1 retrocopy	retro_hsap_1892,
Gorilla gorilla	ENSGGOG00000008405	1 retrocopy	retro_ggor_1385,
Monodelphis domestica	ENSMODG00000006540	1 retrocopy	retro_mdom_1210,
Nomascus leucogenys	ENSNLEG00000017760	1 retrocopy	retro_nleu_1473,
Otolemur garnettii	ENSOGAG00000000710	1 retrocopy	retro_ogar_338 ,
Pan troglodytes	ENSPTRG00000003420	1 retrocopy	retro_ptro_1269,

	RetrogeneDB ID:	retro_ogar_338
Retrocopy location	Organism:	*Bushbaby (Otolemur garnettii)*
	Coordinates:	GL873520.1:33856845..33857878(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	GTF2H1
	Ensembl ID:	ENSOGAG00000000710
	Aliases:	None
	Description:	general transcription factor IIH, polypeptide 1, 62kDa [Source:HGNC Symbol;Acc:4655]

Parental	GALY-LMAERIAWA-PEGKDRFTISHMYADIKCQKISPEGKAKIQLQLVLHAGDTTNFHFSNESTAVKER
	GALY.L..E.I.WA..EG.DRFTI.H.YADI.C.KISPEGKAKIQLQLVLHAGDTTN.HF.NEST.VKE.
Retrocopy	GALY<LLSEIISWA<TEGIDRFTINHLYADIQC*KISPEGKAKIQLQLVLHAGDTTNSHFFNESTTVKEQ

Parental	DAVKDLLQQLLPKFKRKANKELEEKNRMLQEDPVLFQLYKDLVVSQVISAEEFWANRLNVNAAE-SSSTS
	.AVKDLLQQLLPKFKRKANKELEE.NR.LQE.PVLFQ..KDLVVSQVISAEEFWAN.LNVNA.E.SS.TS
Retrocopy	NAVKDLLQQLLPKFKRKANKELEEENRVLQEEPVLFQ-QKDLVVSQVISAEEFWANLLNVNATE>SS-TS

Parental	NHKQDVGISAAFLADVRPQTDGCNGLRYNLTSDIIESIFRTYP-AVKMKYAENVPHNMTEKEFWTRFFQS
	N.KQDVGISAAFLADV.PQT.GCNGLRYNLTSDI.ESIFR.YP..VKMKY.ENVPHNM.EKEFWTRF.Q.
Retrocopy	NLKQDVGISAAFLADVQPQTYGCNGLRYNLTSDITESIFRIYP<KVKMKYTENVPHNMIEKEFWTRFLQF

Parental	HYFHRDRLNTGSKDLFAECAKIDEKGLKTMVSLGVKNPLLDLTALEDKPLDEGYGISSVPTTSNSKSIKE
	HYF.R..LNTGSKDLFAEC.KI...GLKTMVSLGVKNPLLDLTALEDK.LD.GYGISS.PTTSNSKSIKE
Retrocopy	HYFQRNLLNTGSKDLFAECTKI---GLKTMVSLGVKNPLLDLTALEDKSLDGGYGISSMPTTSNSKSIKE

Parental	NSNAAIIKRFNHHSAMVLAAGLRKQEAQNEQNGEPSSMDGNSGDADCFQPAVKRAKLQESIEYEDLAKNN
	NSNAAIIKRFN..S.MVLAAGLRKQEAQNE.NGE.SSMDGNS.DADCFQPA.KRAKLQES..YEDL....
Retrocopy	NSNAAIIKRFNYCSDMVLAAGLRKQEAQNE*NGELSSMDGNSRDADCFQPAGKRAKLQESVKYEDLXXXX

Parental	SVKT
	SV..
Retrocopy	SVNS

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

RetrogeneDB ID:

retro_ogar_338