RetrogeneDB - Retrocopy retro_ttru

                        
>retro_ttru_1858
ATGTCTGACCGTGGAGATGTGAGCCTCCCACCCGAAGACCGGGTGAGGGCTCTCTCCCAGATGGGTAGCGCAGTCTAGAT

AAACGAAGACATTCCACCCCGTTGGTACTTCCGCTCTGGAGTGGAGATTATACGAATGACATCTATTTACTCTGAGGAAG

GCAACACTGAACATGCGTTCATCCTCTATAACAAGTATATCACGCTTTTTATTGAGAAACTACCAAAGCATTGAGATTAC

AAATCGGCTGTCATTCCTGAAAAGAAAGACACAGTAAAGAAATTAAAGGAGATTGCATTTCCCAAAGCAGAAGAGCTGAA

AGCAGAACTGTTAAAACGATATACCAAAGAATATATAGACTATAATGAAGAAAAAAAGAAGGAAGAGGAAGAATTTGCCC

GAAACGTAGCCATCCAGCAAGAGCTGGAAAAGGAAAGACAGAGGGTGGCACAACAGAAGCAGCAACAGTTGGAGCAGCAA

CAGTTCCATGCCTTTGAGGAGATGATCCAGAACCAGAAACTAGAAAAAGAATGACTGAAAATTGTACAGGAGTTTGGGAA

AGTGGAACCTGGCCTGGACGGCCCACTGGTACCTGACTTAGAGAAGCCCTCCCTAGATGTGTTCCCCACGGCACCTGTTA

TATACACACAGCCTTCGGACTGTAATACAACTGTAAGGCCTGCCAAGCCACCTGTAGTGGGTAGATCCTTGAAACCTGGA

GCATTGAGCAACTCGGAAGCTCCTACAATTGATGGACTGCACCACATGGTGGTACCTGGGAAGCTCTGCCCACAGTTTCT

CCAGTTAGCCAGTGCCAACACTGTCCGGGGAGTAGAGACACGTGGAATTCTCTGTGGAAAACTGATGAGGAATGAATTTA

CCATTACCCATATCCTCATCTCCAAGCAAAGTGATGCGTCTGATTATTGCAACACCGAGAACGAAGAAGAGCTTTTCCTC

ATACAGGATCAGCAGGGCATCACACTGGGCTGGATTCACACTCATCCCACGCAGACTGCCTTCCTCTCCAGTGTTGACCT

ACACGCTCACTGCTCCTACCAGATGGTGTTGCCAGAGTCGATAGCCATTGTTTGTTCCCCCAAGTTCCAGGAAACTGGAT

TCTTTAGACTAACTGACCATGGACTAGAGGAGATTTCTTCCTGTCACCAGAAAGGATTTCATCCACACAGCAAGGATCCA

CCTCTCTTCTGT

ORF - retro_ttru_1858 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	91.63 %
Parental protein coverage:	100.0 %
Number of stop codons detected:	3
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalMSDRGDVSLPPEDRVRALSQMGSAVEINEDIPPRRYFRSGMEIIRMASIYSEEGNIEHAFILYNKYITLF
MSDRGDVSLPPEDRVRALSQMGSAV.INEDIPPR.YFRSG.EIIRM.SIYSEEGN.EHAFILYNKYITLF
RetrocopyMSDRGDVSLPPEDRVRALSQMGSAV*INEDIPPRWYFRSGVEIIRMTSIYSEEGNTEHAFILYNKYITLF
ParentalIEKLPKHRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
IEKLPKH.DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
RetrocopyIEKLPKH*DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
ParentalELEKERQRVAQQKQQQLEQEQFHAFEEMIRNQELEKERLKIVQEFGKVDPGL-GPLLPDLEKPSLDVFPT
ELEKERQRVAQQKQQQLEQ.QFHAFEEMI.NQ.LEKE.LKIVQEFGKV.PGL.GPL.PDLEKPSLDVFPT
RetrocopyELEKERQRVAQQKQQQLEQQQFHAFEEMIQNQKLEKE*LKIVQEFGKVEPGLDGPLVPDLEKPSLDVFPT
ParentalAPVIYTQPSDCNTTV-PAKPPVXXXXXKPGALSNSEGTPTIDGLRHVVVPGKLCPRFLQLASANTARGVE
APVIYTQPSDCNTTV.PAKPPV.....KPGALSNSE..PTIDGL.H.VVPGKLCP.FLQLASANT.RGVE
RetrocopyAPVIYTQPSDCNTTVRPAKPPVVGRSLKPGALSNSE-APTIDGLHHMVVPGKLCPQFLQLASANTVRGVE
ParentalTCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLH
T.GILCGKLMRNEFTITH.LI.KQS..SDYCNTENEEELFLIQDQQG.ITLGWIHTHPTQTAFLSSVDLH
RetrocopyTRGILCGKLMRNEFTITHILISKQSDASDYCNTENEEELFLIQDQQG-ITLGWIHTHPTQTAFLSSVDLH
ParentalTHCSYQMMLPESIAIVCSPKFQETGFFRLTDHGLEEISSCRQKGFHPHSKDPPLFC
.HCSYQM.LPESIAIVCSPKFQETGFFRLTDHGLEEISSC.QKGFHPHSKDPPLFC
RetrocopyAHCSYQMVLPESIAIVCSPKFQETGFFRLTDHGLEEISSCHQKGFHPHSKDPPLFC

                            

                            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_1858 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1858 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000009888	1 retrocopy	retro_itri_1154,
Tursiops truncatus	ENSTTRG00000015478	1 retrocopy	retro_ttru_1858 ,

	RetrogeneDB ID:	retro_ttru_1858
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	scaffold_95091:232556..233768(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	STAMBP
	Ensembl ID:	ENSTTRG00000015478
	Aliases:	None
	Description:	STAM binding protein [Source:HGNC Symbol;Acc:16950]

Parental	MSDRGDVSLPPEDRVRALSQMGSAVEINEDIPPRRYFRSGMEIIRMASIYSEEGNIEHAFILYNKYITLF
	MSDRGDVSLPPEDRVRALSQMGSAV.INEDIPPR.YFRSG.EIIRM.SIYSEEGN.EHAFILYNKYITLF
Retrocopy	MSDRGDVSLPPEDRVRALSQMGSAV*INEDIPPRWYFRSGVEIIRMTSIYSEEGNTEHAFILYNKYITLF

Parental	IEKLPKHRDYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
	IEKLPKH.DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ
Retrocopy	IEKLPKH*DYKSAVIPEKKDTVKKLKEIAFPKAEELKAELLKRYTKEYIDYNEEKKKEEEEFARNVAIQQ

Parental	ELEKERQRVAQQKQQQLEQEQFHAFEEMIRNQELEKERLKIVQEFGKVDPGL-GPLLPDLEKPSLDVFPT
	ELEKERQRVAQQKQQQLEQ.QFHAFEEMI.NQ.LEKE.LKIVQEFGKV.PGL.GPL.PDLEKPSLDVFPT
Retrocopy	ELEKERQRVAQQKQQQLEQQQFHAFEEMIQNQKLEKE*LKIVQEFGKVEPGLDGPLVPDLEKPSLDVFPT

Parental	APVIYTQPSDCNTTV-PAKPPVXXXXXKPGALSNSEGTPTIDGLRHVVVPGKLCPRFLQLASANTARGVE
	APVIYTQPSDCNTTV.PAKPPV.....KPGALSNSE..PTIDGL.H.VVPGKLCP.FLQLASANT.RGVE
Retrocopy	APVIYTQPSDCNTTVRPAKPPVVGRSLKPGALSNSE-APTIDGLHHMVVPGKLCPQFLQLASANTVRGVE

Parental	TCGILCGKLMRNEFTITHVLIPKQSAGSDYCNTENEEELFLIQDQQGLITLGWIHTHPTQTAFLSSVDLH
	T.GILCGKLMRNEFTITH.LI.KQS..SDYCNTENEEELFLIQDQQG.ITLGWIHTHPTQTAFLSSVDLH
Retrocopy	TRGILCGKLMRNEFTITHILISKQSDASDYCNTENEEELFLIQDQQG-ITLGWIHTHPTQTAFLSSVDLH

Parental	THCSYQMMLPESIAIVCSPKFQETGFFRLTDHGLEEISSCRQKGFHPHSKDPPLFC
	.HCSYQM.LPESIAIVCSPKFQETGFFRLTDHGLEEISSC.QKGFHPHSKDPPLFC
Retrocopy	AHCSYQMVLPESIAIVCSPKFQETGFFRLTDHGLEEISSCHQKGFHPHSKDPPLFC

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

RetrogeneDB ID:

retro_ttru_1858