RetrogeneDB - Retrocopy retro_dmel

                        
>retro_dmel_74
ATGGGCAACGTAATGGCGTCCACCGCAGACGCTGAGTCCTCTCGTGGGCGTGGACATCTGTCCGCCGGACTACGCTTGCC

GGAGGCACCGCAGTATTCCGGCGGAGTGCCGCCACAGATGGTGGAGGCCTTAAAGGCGGAAGCTAAAAAGCCCGAATTGA

CAAATCCCGGAACTCTTGAGGAACTGCACAGTCGCTGTCGCGACATCCAGGCCAACACCTTCGAAGGCGCCAAAATTATG

GTGAACAAGGGTCTGAGCAACCACTTCCAAGTGACCCACACCATTAACATGAATTCGGCTGGTCCAAGTGGCTATCGTTT

TGGAGCTACCTACGTGGGTACCAAACAATACGGGCCGACTGAAGCCTTTCCGGTTCTTCTTGGCGAGATCGATCCGATGG

GCAATCTTAATGCAAACGTTATCCATCAACTGACCTCTCGTTTGAGGTGCAAGTTTGCCTCGCAGTTCCAGGACTCAAAG

CTGGTGGGCACCCAGCTGACGGGGGACTATCGCGGCAGAGACTACACGCTGACCCTGACAATGGGCAATCCGGGGTTTTT

TACGAGTTCCGGAGTATTTGTGTGCCAGTACTTGCAGTCCGTCACCAAACGTCTGGCGCTAGGATCGGAGTTCGCCTATC

ACTACGGGCCGAATGTGCCCGGACGCCAAGTGGCTGTATTATCAGCGGTGGGACGTTACGCCTTCGGTGATACCGTGTGG

TCTTGCACTTTGGGACCCGCCGGATTCCACCTTAGTTACTACCAGAAGGCCAGTGATCAGCTACAGATCGGAGTCGAGGT

GGAAACGAATATCCGCCAGCAAGAGTCGACGGCCACGGTGGCATACCAGATTGATCTGCCCAAGGCAGACCTAGTCTTCC

GCGGCAGTCTCGATTCCAATTGGCTTATTTCCGGAGTCCTTGAGAAAAGACTGCAGCCGCTACCGTTCTCGTTGGCCATT

AGCGGTCGTATGAATCACCAAAAAAATAGTTTTCGGCTGGGATGTGGCCTCATGATAGGATGA

ORF - retro_dmel_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	74.92 %
Parental protein coverage:	85.76 %
Number of stop codons detected:	0
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalAAAKDAALENPGTVEELHKKCKDIQAITFEGAKIMLNKGLSNHFQVSHTINMSNVVPSGYRFGATYVGTK
A.AK...L.NPGT.EELH..C.DIQA.TFEGAKIM.NKGLSNHFQV.HTINM....PSGYRFGATYVGTK
RetrocopyAEAKKPELTNPGTLEELHSRCRDIQANTFEGAKIMVNKGLSNHFQVTHTINMNSAGPSGYRFGATYVGTK
ParentalEFSPTEAFPVLLGDIDPAGNLNANVIHQFSARLRCKFASQIQESKVVASQLTTDYRGSDYTLSLTVANPS
...PTEAFPVLLG.IDP.GNLNANVIHQ...RLRCKFASQ.Q.SK.V..QLT.DYRG.DYTL.LT..NP.
RetrocopyQYGPTEAFPVLLGEIDPMGNLNANVIHQLTSRLRCKFASQFQDSKLVGTQLTGDYRGRDYTLTLTMGNPG
ParentalIFTNSGVVVGQYLQSVTPALALGSELAYQFGPNVPGRQIAIMSVVGRYTAGSSVWSGTLGQSGLHVCYYQ
.FT.SGV.V.QYLQSVT..LALGSE.AY..GPNVPGRQ.A..S.VGRY..G..VWS.TLG..G.H..YYQ
RetrocopyFFTSSGVFVCQYLQSVTKRLALGSEFAYHYGPNVPGRQVAVLSAVGRYAFGDTVWSCTLGPAGFHLSYYQ
ParentalKASDQLQIGAEVETSLRMQESVATLAYQIDLPKANLVFRGGIDSNWQIFGVLEKRLAPLPFTLALSGRMN
KASDQLQIG.EVET..R.QES.AT.AYQIDLPKA.LVFRG..DSNW.I.GVLEKRL.PLPF.LA.SGRMN
RetrocopyKASDQLQIGVEVETNIRQQESTATVAYQIDLPKADLVFRGSLDSNWLISGVLEKRLQPLPFSLAISGRMN
ParentalHVKNNFRLGCGLMIG
H.KN.FRLGCGLMIG
RetrocopyHQKNSFRLGCGLMIG

                            

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

                        

RNA-Seq - click to see more details

Drosophila melanogaster was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Drosophila melanogaster was not studied using ChIP-Seq data.

EST - click to see more details

2 EST(s) were mapped to retro_dmel_74 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BF488202	2113138	2113650	99.9	511	1	510
BF492366	2113140	2113705	99.7	563	2	561

TSS - click to see more details

Drosophila melanogaster was not studied using FANTOM5 data.

Lab - click to see more details

retro_dmel_74 was not experimentally validated.

Retrocopy orthology:

Drosophila melanogaster 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000004808	1 retrocopy	retro_eeur_472,
Echinops telfairi	ENSETEG00000015755	2 retrocopies	retro_etel_1124, retro_etel_1461,
Homo sapiens	ENSG00000130204	5 retrocopies	retro_hsap_1300, retro_hsap_1386, retro_hsap_2321, retro_hsap_2537, retro_hsap_3159,
Gorilla gorilla	ENSGGOG00000005720	2 retrocopies	retro_ggor_1075, retro_ggor_1761,
Gorilla gorilla	ENSGGOG00000023033	1 retrocopy	retro_ggor_1356,
Microcebus murinus	ENSMICG00000014041	1 retrocopy	retro_mmur_420,
Myotis lucifugus	ENSMLUG00000028928	1 retrocopy	retro_mluc_697,
Macaca mulatta	ENSMMUG00000014303	1 retrocopy	retro_mmul_1998,
Nomascus leucogenys	ENSNLEG00000001726	2 retrocopies	retro_nleu_2368, retro_nleu_2542,
Oryctolagus cuniculus	ENSOCUG00000023582	1 retrocopy	retro_ocun_1143,
Otolemur garnettii	ENSOGAG00000013733	1 retrocopy	retro_ogar_2524,
Pongo abelii	ENSPPYG00000025858	1 retrocopy	retro_pabe_174,
Pan troglodytes	ENSPTRG00000011126	1 retrocopy	retro_ptro_39,
Ictidomys tridecemlineatus	ENSSTOG00000003800	2 retrocopies	retro_itri_301, retro_itri_724,
Ictidomys tridecemlineatus	ENSSTOG00000009019	1 retrocopy	retro_itri_150,
Drosophila melanogaster	FBgn0016041	1 retrocopy	retro_dmel_74 ,

	RetrogeneDB ID:	retro_dmel_74
Retrocopy location	Organism:	*Fruit fly (Drosophila melanogaster)*
	Coordinates:	2R:2113229..2114252(+)
	Located in intron of:	FBgn0263144
Retrocopy information	Ensembl ID:	FBgn0033074
	Aliases:	None
	Status:	KNOWN_PROTEIN_CODING
Parental gene information	Parental gene summary:
	Parental gene symbol:	Tom40
	Ensembl ID:	FBgn0016041
	Aliases:	None
	Description:	Translocase of outer membrane 40 [Source:FlyBase gene name;Acc:FBgn0016041]

Parental	AAAKDAALENPGTVEELHKKCKDIQAITFEGAKIMLNKGLSNHFQVSHTINMSNVVPSGYRFGATYVGTK
	A.AK...L.NPGT.EELH..C.DIQA.TFEGAKIM.NKGLSNHFQV.HTINM....PSGYRFGATYVGTK
Retrocopy	AEAKKPELTNPGTLEELHSRCRDIQANTFEGAKIMVNKGLSNHFQVTHTINMNSAGPSGYRFGATYVGTK

Parental	EFSPTEAFPVLLGDIDPAGNLNANVIHQFSARLRCKFASQIQESKVVASQLTTDYRGSDYTLSLTVANPS
	...PTEAFPVLLG.IDP.GNLNANVIHQ...RLRCKFASQ.Q.SK.V..QLT.DYRG.DYTL.LT..NP.
Retrocopy	QYGPTEAFPVLLGEIDPMGNLNANVIHQLTSRLRCKFASQFQDSKLVGTQLTGDYRGRDYTLTLTMGNPG

Parental	IFTNSGVVVGQYLQSVTPALALGSELAYQFGPNVPGRQIAIMSVVGRYTAGSSVWSGTLGQSGLHVCYYQ
	.FT.SGV.V.QYLQSVT..LALGSE.AY..GPNVPGRQ.A..S.VGRY..G..VWS.TLG..G.H..YYQ
Retrocopy	FFTSSGVFVCQYLQSVTKRLALGSEFAYHYGPNVPGRQVAVLSAVGRYAFGDTVWSCTLGPAGFHLSYYQ

Parental	KASDQLQIGAEVETSLRMQESVATLAYQIDLPKANLVFRGGIDSNWQIFGVLEKRLAPLPFTLALSGRMN
	KASDQLQIG.EVET..R.QES.AT.AYQIDLPKA.LVFRG..DSNW.I.GVLEKRL.PLPF.LA.SGRMN
Retrocopy	KASDQLQIGVEVETNIRQQESTATVAYQIDLPKADLVFRGSLDSNWLISGVLEKRLQPLPFSLAISGRMN

Parental	HVKNNFRLGCGLMIG
	H.KN.FRLGCGLMIG
Retrocopy	HQKNSFRLGCGLMIG

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

RetrogeneDB ID:

retro_dmel_74