RetrogeneDB - Retrocopy retro_ttru

						
>retro_ttru_749
GTGATGAATGGTGCTATCCTTCAGCAAGTGTTTGTGGCGGATTATGTTGTTCAGGCCCGGATGTGTGGAGACTGCCACAG

AGTGGAAGCTGAGGATTTCTGGAAGGCTGTGGTGCAAGTCAGGCAAACGACTTTGCACAAAAGAACTTTCTACTGTCTAG

AACAGCTGATTTTGAAATGTGGCATGCACCGGAATACACTTCGTATCAAAGAGATTCATGATGGGCTGGATTTCTATTAT

TCCTCAAAACAACATGCTCAGAAGATGGTAGAATTTCTTCAGTGTACTGTTCCCACTAGATACAAAGCCTCACAGGGACT

GATCTCTCAGGATATCCATAGTAACACATACAATTACAAAAGCACCTTTTCTGTGGAAATTGTTCCAATATGCAAGGATA

ATGTTGTTTGTCTGTCTGCAAGACTGGCACAAATCCTGGGAAACATGAACCAGATTTGTGTGTGTATTCGAGTAACCAGC

GTCATCCATCTCATAGATCCAAATACCCTACAAGTTGCAGATATTGATGGGAGCGCTTTCTGGAGTCACCCTTTCAATAG

TTTATGCCACATCCCAAACAGCTAGAGGAGTTTATTGTTATGGAATGCAGCATAGTCCGAGATCTAAAACGCAGTGCAGG

TGCTGGAATGGTATCATAAAAGCATACCCTCGGGGAAGTCTGGGTACAGAAAACATCTGAAATGAGTACAGATAAACAGT

ATTTTTGTCGTACTCATTTGGGACATCTTCTGAATCCTGGAGACCTGGTGTTGGGGTTTGATCTGGCCAACTGTAACTTA

AATGATGAGCATATCAACAAAATGAAATCAGATAGAGTCCTAGATGTGGTGCTAGTCAAGAAGAGCTATGACCGTACCAA

ACGTCAGTGTCTTAGAAACCGGAAACTGAAAGAGCTTGCAAGAGATAGAGAAAACATGGATACAGATGATGAAAGGCAAT

ACCCAGATTTCCTTGAAGATCTGGAAGAAGATGAGGCAATTAGAAAAAGTGTGAATATTTATAGAGATTCAACGATTCCT

GTGGAAAGTGACACAGATGATGAAGGAGCACCTCGAATTAGTCTGGCTGAGATGCTTGAAGACCTTCACATTTCCCCAAG

ATGCTACTGGTGAAGAAGGTGAATCGATGATGACC

ORF - retro_ttru_749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	89.92 %
Parental protein coverage:	76.34 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalVMNGAILQQVFVVDYVVQPQMCGDCHRVEAKDFWKAVVQVRQKTLHKKTFYYLEQLILKYGMYQNTLRIK
		VMNGAILQQVFV.DYVVQ..MCGDCHRVEA.DFWKAVVQVRQ.TLHK.TFY.LEQLILK.GM..NTLRIK
RetrocopyVMNGAILQQVFVADYVVQARMCGDCHRVEAEDFWKAVVQVRQTTLHKRTFYCLEQLILKCGMHRNTLRIK
ParentalDIHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQRLISQDVHSNTYNYKSTFSVEIVPICKDNVVCLSP
		.IHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQ.LISQD.HSNTYNYKSTFSVEIVPICKDNVVCLS.
RetrocopyEIHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQGLISQDIHSNTYNYKSTFSVEIVPICKDNVVCLSA
ParentalKLAQSLGNMNQICVCIRVTSVIHLIDPNTLQVADIDGNTFWSH-PFN-SLCHPKQLEEFIVLECSIVRDL
		.LAQ.LGNMNQICVCIRVTSVIHLIDPNTLQVADIDG..FWSH.PF.....HPKQLEEFIV.ECSIVRDL
RetrocopyRLAQILGNMNQICVCIRVTSVIHLIDPNTLQVADIDGSAFWSH<PFQ*FMPHPKQLEEFIVMECSIVRDL
ParentalKRNAGAGMISKKHTLGEVWVQKTSEMNTDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEHVNKMKSDR
		KR.AGAGM.S.KHTLGEVWVQKTSEM.TDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEH.NKMKSDR
RetrocopyKRSAGAGMVS*KHTLGEVWVQKTSEMSTDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEHINKMKSDR
ParentalVPDVVLIKKSYDRTKRQRRRNWKLKELARDRENMDTDDERQYQDFLEDLEEDEAIRKNVNIYRDSTIPVE
		V.DVVL.KKSYDRTKRQ..RN.KLKELARDRENMDTDDERQY.DFLEDLEEDEAIRK.VNIYRDSTIPVE
RetrocopyVLDVVLVKKSYDRTKRQCLRNRKLKELARDRENMDTDDERQYPDFLEDLEEDEAIRKSVNIYRDSTIPVE
ParentalGDTDDEGAPRISLAEMLEDLHIS-QDATGEEGESMMT
		.DTDDEGAPRISLAEMLEDLHIS.QDATGEEGESMMT
RetrocopySDTDDEGAPRISLAEMLEDLHIS>QDATGEEGESMMT

							

							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_749 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_749 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000169251	1 retrocopy	retro_hsap_3855,
Pan troglodytes	ENSPTRG00000015586	1 retrocopy	retro_ptro_2627,
Tursiops truncatus	ENSTTRG00000012938	1 retrocopy	retro_ttru_749 ,

	RetrogeneDB ID:	retro_ttru_749
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	GeneScaffold_3267:201665..202820(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NMD3
	Ensembl ID:	ENSTTRG00000012938
	Aliases:	None
	Description:	NMD3 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:24250]

Parental	VMNGAILQQVFVVDYVVQPQMCGDCHRVEAKDFWKAVVQVRQKTLHKKTFYYLEQLILKYGMYQNTLRIK
	VMNGAILQQVFV.DYVVQ..MCGDCHRVEA.DFWKAVVQVRQ.TLHK.TFY.LEQLILK.GM..NTLRIK
Retrocopy	VMNGAILQQVFVADYVVQARMCGDCHRVEAEDFWKAVVQVRQTTLHKRTFYCLEQLILKCGMHRNTLRIK

Parental	DIHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQRLISQDVHSNTYNYKSTFSVEIVPICKDNVVCLSP
	.IHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQ.LISQD.HSNTYNYKSTFSVEIVPICKDNVVCLS.
Retrocopy	EIHDGLDFYYSSKQHAQKMVEFLQCTVPTRYKASQGLISQDIHSNTYNYKSTFSVEIVPICKDNVVCLSA

Parental	KLAQSLGNMNQICVCIRVTSVIHLIDPNTLQVADIDGNTFWSH-PFN-SLCHPKQLEEFIVLECSIVRDL
	.LAQ.LGNMNQICVCIRVTSVIHLIDPNTLQVADIDG..FWSH.PF.....HPKQLEEFIV.ECSIVRDL
Retrocopy	RLAQILGNMNQICVCIRVTSVIHLIDPNTLQVADIDGSAFWSH<PFQ*FMPHPKQLEEFIVMECSIVRDL

Parental	KRNAGAGMISKKHTLGEVWVQKTSEMNTDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEHVNKMKSDR
	KR.AGAGM.S.KHTLGEVWVQKTSEM.TDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEH.NKMKSDR
Retrocopy	KRSAGAGMVS*KHTLGEVWVQKTSEMSTDKQYFCRTHLGHLLNPGDLVLGFDLANCNLNDEHINKMKSDR

Parental	VPDVVLIKKSYDRTKRQRRRNWKLKELARDRENMDTDDERQYQDFLEDLEEDEAIRKNVNIYRDSTIPVE
	V.DVVL.KKSYDRTKRQ..RN.KLKELARDRENMDTDDERQY.DFLEDLEEDEAIRK.VNIYRDSTIPVE
Retrocopy	VLDVVLVKKSYDRTKRQCLRNRKLKELARDRENMDTDDERQYPDFLEDLEEDEAIRKSVNIYRDSTIPVE

Parental	GDTDDEGAPRISLAEMLEDLHIS-QDATGEEGESMMT
	.DTDDEGAPRISLAEMLEDLHIS.QDATGEEGESMMT
Retrocopy	SDTDDEGAPRISLAEMLEDLHIS>QDATGEEGESMMT

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

RetrogeneDB ID:

retro_ttru_749