RetrogeneDB - Retrocopy retro_ttru

						
>retro_ttru_1189
GAAGAAAGCGCCACAGGCGAGCCCAGCGCCCCGGGAGGGCCCTGACCCTTCCTCTCTGGGGAACGGGGGTCTTTTCCTGC

GGAGGCCGGTGCCTCCCCTCACCCCGGGCTGCCTTCCCTCCATCCACTCCAGGGACCTCACCCTCAGGGAGTCAAGAAGA

AAACCTGCACCCCAAATATCAGTCGTAAGATCAAGGAAGAGCCCAAGGAAGAAGTAACCGTCAAGAAGGAAAAGCGTGAA

AGGGATACAGACCGACAGCGAGAGGGCCATGGACAGGGCGGGGGACGCCCAGAAGTGTTCCGGTCCCACTCCATCTTTGA

GCAGGGCCCAGCTGAAATGATGAAGAAAAAGGGGAAATAAGGCTGTGAATGTGTCGGACATGGGGACCTCTCACAACATC

AACATCAAAAAGAACAAGAGGGAGACGGATGAAGAAACAGAACAGATCCTGTACACGCTGGAGAAGGATGATTTCATCGA

TGACCCTGGTCTGAGGAATGACACTCGAAATATACCTGTGCAGCTGCTTCTGGTTCACTCGGGCTGGCTTTTTAAGGAAG

AGAATGAAGAATCAGATGTTAAACCTTGGCTCAAGGAAGAGGACATGGAGGTGGGAGGGGCCTGCTGTGAAAGTGAAAGA

CGAGCCACGAGATGAGAGGAGGAGGCCAAGATGAAGGCTCCCCCCAGAGCAGCCAGGAAGCCCCCGGCCTCCCGAAGGAT

ATGTCTGTGGCAGAGGTTTCAGGAAGCTGAGCCTCACGCAGGAGGAAGAGCTGCTGTTCCTGCAGCTGCAAGACTGGCTC

CCC

ORF - retro_ttru_1189 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.36 %
Parental protein coverage:	68.84 %
Number of stop codons detected:	1
Number of frameshifts detected	7

Retrocopy - Parental Gene Alignment:

									ParentalEGDAAGEPSAPGGPRPLLSGARG-LIGRRPAPSLTPGRLPSIRSRDLTLG-GVKKKTFTPNIISRKVKEE
		E..A.GEPSAPGGP.P.LSG.RG.L..RRP.P.LTPG.LPSI.SRDLTL..GVKKKT.TPNI.SRK.KEE
RetrocopyEESATGEPSAPGGP*PFLSGERG>LFLRRPVPPLTPGCLPSIHSRDLTLR<GVKKKTCTPNI-SRKIKEE
ParentalPKEEVTVKKEKRDRDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKK-GNWDKTVDVSDMGPSHIIN
		PKEEVTVKKEKR.RD.DRQREGHG.G.GRPEV..SHSIFEQGPAEMMKKK.GN..K.V.VSDMG.SH.IN
RetrocopyPKEEVTVKKEKRERDTDRQREGHGQGGGRPEVFRSHSIFEQGPAEMMKKK>GN--KAVNVSDMGTSHNIN
ParentalIKKEKRETDEETKQILRMLEKDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEENEEPDVKPWLAGSKEED
		IKK.KRETDEET.QIL..LEKDDFIDDPGLRNDTRN.PVQL.L.HSGWLFKEENEE.DVKPWL...KEED
RetrocopyIKKNKRETDEETEQILYTLEKDDFIDDPGLRNDTRNIPVQLLLVHSGWLFKEENEESDVKPWL---KEED
ParentalMEV-DVPAVKVKEEPRDE-EEEAKMKASSRAARK-TPGLPKDVSVAEL-LRELSLTQEEELLFLQLPDSL
		MEV...PAVKVK.EPRDE.EEEAKMKA..RAARK..PGLPKD.SVAE...R.LSLTQEEELLFLQL.D.L
RetrocopyMEV>EGPAVKVKDEPRDE<EEEAKMKAPPRAARK<APGLPKDMSVAEV<FRKLSLTQEEELLFLQLQDWL
ParentalP
		P
RetrocopyP

							

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

						

RNA-Seq - click to see more details

Tursiops truncatus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Tursiops truncatus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ttru_1189 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1189 was not experimentally validated.

Retrocopy orthology:

Tursiops truncatus 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189 ,

	RetrogeneDB ID:	retro_ttru_1189
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	scaffold_106797:55760..56563(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	POLR3D
	Ensembl ID:	ENSTTRG00000012745
	Aliases:	None
	Description:	polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Parental	EGDAAGEPSAPGGPRPLLSGARG-LIGRRPAPSLTPGRLPSIRSRDLTLG-GVKKKTFTPNIISRKVKEE
	E..A.GEPSAPGGP.P.LSG.RG.L..RRP.P.LTPG.LPSI.SRDLTL..GVKKKT.TPNI.SRK.KEE
Retrocopy	EESATGEPSAPGGP*PFLSGERG>LFLRRPVPPLTPGCLPSIHSRDLTLR<GVKKKTCTPNI-SRKIKEE

Parental	PKEEVTVKKEKRDRDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKK-GNWDKTVDVSDMGPSHIIN
	PKEEVTVKKEKR.RD.DRQREGHG.G.GRPEV..SHSIFEQGPAEMMKKK.GN..K.V.VSDMG.SH.IN
Retrocopy	PKEEVTVKKEKRERDTDRQREGHGQGGGRPEVFRSHSIFEQGPAEMMKKK>GN--KAVNVSDMGTSHNIN

Parental	IKKEKRETDEETKQILRMLEKDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEENEEPDVKPWLAGSKEED
	IKK.KRETDEET.QIL..LEKDDFIDDPGLRNDTRN.PVQL.L.HSGWLFKEENEE.DVKPWL...KEED
Retrocopy	IKKNKRETDEETEQILYTLEKDDFIDDPGLRNDTRNIPVQLLLVHSGWLFKEENEESDVKPWL---KEED

Parental	MEV-DVPAVKVKEEPRDE-EEEAKMKASSRAARK-TPGLPKDVSVAEL-LRELSLTQEEELLFLQLPDSL
	MEV...PAVKVK.EPRDE.EEEAKMKA..RAARK..PGLPKD.SVAE...R.LSLTQEEELLFLQL.D.L
Retrocopy	MEV>EGPAVKVKDEPRDE<EEEAKMKAPPRAARK<APGLPKDMSVAEV<FRKLSLTQEEELLFLQLQDWL

Parental	P
	P
Retrocopy	P

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

RetrogeneDB ID:

retro_ttru_1189