RetrogeneDB - Retrocopy retro_ttru

                        
>retro_ttru_1807
GTTAAGCAAATGATAACTAAAGAATATGAACTGTTTGAATTCCGGCAGACTGAGGTTCCTCCCTTGCTACTTATTTTAGA

TCGCTGCGATGATGCCATCACCCCATTGCTAAACCAGTGGACATATCAGGCCATGGTCCATGAACTACTGGGCATAAACA

ACAATCGGATTGATCTTTCCAGAGTGCCAGGGATCAGTAAAGACATGAGAGAGGTGGTCCTATCTGCTGAAAATGATGAA

TTCTACACTAACAATATGTACCTGAACTTTGCTGAGATTGGTTGCAACATAAAGAATCTCATGGAAGACTTTCAGAAGAA

GAAACCAAAAGAACAGCAAAAACTAGAATCAATAGCAGACATGAAGGCCTTTGTGGAGAATTACCCACAATTCAAGAAGA

TGTCTGGGACTGTATCAAAGCACATGACAGTGGTTGGAGAGCTGTCTCAGTTGGTCAGTGAGTGGAATCTGCTGGAGGTT

TTGGAGGTTGAGCAAGAACTGGCCTGTCAAAATGACCATTCTAGTGCTCTCCAGAATGTAAAGAGGCTCCTGCAGAACCC

CAAAGTGACAGAGTTTGATGCGTGCAGCCTGGTGATGCTTTATCCTCTACATTATGAGCGACACAGCAGCAATAGCCTAC

CAGGATTATGATGGACCTTAGGAATAAAGGTGTTTCTGAGAAGTATCGAAAGCTTGTGTCTACAGTTGTTGAATATGGTG

GTAAACGGGTCAGAGGAAGTGACCTCTTCAGCCCCAAAGACGCTGTGGCTATTACCAAACATTTCCTCAAAGGATTGAAG

GGAGTAGAAAATGTATATGCTCAGCATCAGCCTTTCTTACATGAGAACCTGGACCATCTCATCAAAGGAAAGCTTAAGGA

AAACCTGTATCCTTATCTAGGCCCCAGCACACTCAGAGACAGACATCAGGATATCATTGTGTTTATAATTGGAGGAGCCA

CCTATGAAGAGGCTCTAACAGTTTATAACCTGAACCGCACCACTCCCGGAGTGAGGATTGTCCTGGGGGGAACCCCTGTG

CATAACACGAAAAGTTTCCCAGATGAAGTTCTTGCTTCTGGACTGCACAGCCGAAGCAAGGACAGCTCTCAAGTTACATC

AAAGTTAGCAAGCAGAAGA

ORF - retro_ttru_1807 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	94.23 %
Parental protein coverage:	66.67 %
Number of stop codons detected:	0
Number of frameshifts detected:	1

Retrocopy - Parental Gene Alignment:

                                ParentalVKQVITKEYELFEFRRTEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKDLR
VKQ.ITKEYELFEFR.TEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKD.R
RetrocopyVKQMITKEYELFEFRQTEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKDMR
ParentalEVVLSAENDEFYANNMYLNFAEIGSNIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK
EVVLSAENDEFY.NNMYLNFAEIG.NIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK
RetrocopyEVVLSAENDEFYTNNMYLNFAEIGCNIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK
ParentalHVTVVGELSRLVSERNLLEVSEVEQELACQNDHSSALQNVKRLLQNPKVTEFDAARLVMLYALHYERHSS
H.TVVGELS.LVSE.NLLEV.EVEQELACQNDHSSALQNVKRLLQNPKVTEFDA..LVMLY.LHYERHSS
RetrocopyHMTVVGELSQLVSEWNLLEVLEVEQELACQNDHSSALQNVKRLLQNPKVTEFDACSLVMLYPLHYERHSS
ParentalNSLPGL-MMDLRNKGVSEKYRKLVSTVVEYGGKRIRGSDLFSPKDAVAITKQFLKGLKGVENVYTQHQPF
NSLPGL.MMDLRNKGVSEKYRKLVSTVVEYGGKR.RGSDLFSPKDAVAITK.FLKGLKGVENVY.QHQPF
RetrocopyNSLPGL<MMDLRNKGVSEKYRKLVSTVVEYGGKRVRGSDLFSPKDAVAITKHFLKGLKGVENVYAQHQPF
ParentalLHETLDHLIKGKLKENLYPYLGPSTLRDRPQDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGTTVHN
LHE.LDHLIKGKLKENLYPYLGPSTLRDR.QDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGT.VHN
RetrocopyLHENLDHLIKGKLKENLYPYLGPSTLRDRHQDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGTPVHN
ParentalTKSFLEEVLASGLHSRSKDSSQVTSRLASRR
TKSF..EVLASGLHSRSKDSSQVTS.LASRR
RetrocopyTKSFPDEVLASGLHSRSKDSSQVTSKLASRR

                            

                            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_1807 retrocopy.

TSS - click to see more details

Tursiops truncatus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ttru_1807 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
Choloepus hoffmanni	ENSCHOG00000000501	1 retrocopy	retro_chof_1315,
Tupaia belangeri	ENSTBEG00000010744	1 retrocopy	retro_tbel_107,
Tursiops truncatus	ENSTTRG00000005060	1 retrocopy	retro_ttru_1807 ,

	RetrogeneDB ID:	retro_ttru_1807
Retrocopy location	Organism:	*Dolphin (Tursiops truncatus)*
	Coordinates:	scaffold_92498:224547..225686(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	VPS45
	Ensembl ID:	ENSTTRG00000005060
	Aliases:	None
	Description:	vacuolar protein sorting 45 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:14579]

Parental	VKQVITKEYELFEFRRTEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKDLR
	VKQ.ITKEYELFEFR.TEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKD.R
Retrocopy	VKQMITKEYELFEFRQTEVPPLLLILDRCDDAITPLLNQWTYQAMVHELLGINNNRIDLSRVPGISKDMR

Parental	EVVLSAENDEFYANNMYLNFAEIGSNIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK
	EVVLSAENDEFY.NNMYLNFAEIG.NIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK
Retrocopy	EVVLSAENDEFYTNNMYLNFAEIGCNIKNLMEDFQKKKPKEQQKLESIADMKAFVENYPQFKKMSGTVSK

Parental	HVTVVGELSRLVSERNLLEVSEVEQELACQNDHSSALQNVKRLLQNPKVTEFDAARLVMLYALHYERHSS
	H.TVVGELS.LVSE.NLLEV.EVEQELACQNDHSSALQNVKRLLQNPKVTEFDA..LVMLY.LHYERHSS
Retrocopy	HMTVVGELSQLVSEWNLLEVLEVEQELACQNDHSSALQNVKRLLQNPKVTEFDACSLVMLYPLHYERHSS

Parental	NSLPGL-MMDLRNKGVSEKYRKLVSTVVEYGGKRIRGSDLFSPKDAVAITKQFLKGLKGVENVYTQHQPF
	NSLPGL.MMDLRNKGVSEKYRKLVSTVVEYGGKR.RGSDLFSPKDAVAITK.FLKGLKGVENVY.QHQPF
Retrocopy	NSLPGL<MMDLRNKGVSEKYRKLVSTVVEYGGKRVRGSDLFSPKDAVAITKHFLKGLKGVENVYAQHQPF

Parental	LHETLDHLIKGKLKENLYPYLGPSTLRDRPQDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGTTVHN
	LHE.LDHLIKGKLKENLYPYLGPSTLRDR.QDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGT.VHN
Retrocopy	LHENLDHLIKGKLKENLYPYLGPSTLRDRHQDIIVFIIGGATYEEALTVYNLNRTTPGVRIVLGGTPVHN

Parental	TKSFLEEVLASGLHSRSKDSSQVTSRLASRR
	TKSF..EVLASGLHSRSKDSSQVTS.LASRR
Retrocopy	TKSFPDEVLASGLHSRSKDSSQVTSKLASRR

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

RetrogeneDB ID:

retro_ttru_1807