RetrogeneDB - Retrocopy retro_shar

                        
>retro_shar_692
GTAGAGGCCCCTTTCACATCCTTAAGGGCCTCCACTGGGCTTCCCATAGGAGGCATTCAGCAGCAGTTCTCACTCCCACA

GAACATCCAGCTCTCTTTCTTCTTCATTGAATTTCTCCATAACGTCAATGAATACCTTGCTGTTCCTGATGAGTCTCCCC

TAGATATTCAGTTTAATCCTTCAGGTTATCTTTTGCTGGCTTCAAAAGAAAAGGTTTCAGTGATGGATCACAATGTAAAA

ATACAGAGGTAAGAAGGAGCTAAAGTGTGTCTGCTGTCCTCCAAACTATTCAAAAACAAATTTCCCCAGATCAACACAGA

AGGCATGGCCTTGGCATCATATGGGCTGGAGAATGAGGACTGGTTTGATCCACGGTGATCTGCTTCAGGGACTGCGCCAA

AAGGCTCTGTCGATGGGGGTACATCATAGCCGTGGGAAAGTCATAGATTTAGTCTCTTCAGTAAGGTCTATGGTGACTTC

CAGTGGAGAACAAATAGACCTTAAAGGCTTTATGAAATCCATGTGAAGGTGGACAACATCCTGGAGTATCAACCTGTGGA

GTGTACAATAGTAATCAATGCTACTGGGGCCTGGTCTGGGCAATTAGTAGAGCTAGCTGGTATTGGCATTGGGTCCCCAG

GCACTTTGCAAAGCACCAGACTTCCTGTGGAGCCAAGAAAAAGGTATGGGTATGTTTGGCATTGCCCACAAGGACCTGGC

TTGGAGGCCCCATTACTTACATACATCACTGGAAGCTATTTCAGACAAGAAGGATTAGGTGACTACTTCTTAGGTGGCTG

TGGTCCCATGAGTAAGAAGAACCAGATACTTAAGATCTAGAAGTAGATCAGGACTTGTTTCAGAAAAAGGTGTGGCCTAT

CTGGGCCAGAGAATTCCAGCTTTCAATTCCCTGAAGGTCTGGAGCGTTTGGGCTAGCTTCTATAATTACAACACATTTGA

CCAGAATGGAATAGTGGGCCCCCATCCACTGGTTTCCAACATGTACTTTGCCATAGGCTTCAGTGGCCATGGGCCGCAAC

ACGTCCTTTCTGTGGGATGGGCTGTGGCAGAAACACTGCTGAAAGAAATTTCGACAGTATTCATCTTAACCTATTCTCCT

TCAACCGATTCTATCAGGGTGAAAAGGTCCTGGAGAACAATATCATC

ORF - retro_shar_692 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.49 %
Parental protein coverage:	80.25 %
Number of stop codons detected:	3
Number of frameshifts detected:	5

Retrocopy - Parental Gene Alignment:

                                ParentalVEQDPTYSMASTGLSIGGIRQQFSLPQNIQLSLFSIEFLRNINEYLAVPDEPLLDIQFNPSGYLLLASEE
VE...T...ASTGL.IGGI.QQFSLPQNIQLS.F.IEFL.N.NEYLAVPDE..LDIQFNPSGYLLLAS.E
RetrocopyVEAPFTSLRASTGLPIGGIQQQFSLPQNIQLSFFFIEFLHNVNEYLAVPDESPLDIQFNPSGYLLLASKE
ParentalKAAVMEHNVKIQRQEGAKVCLLSPKQLKDKFPWINTEGIALASYGLENEGWFDP-WCLLQGLRRKALSMG
K..VM.HNVKIQR.EGAKVCLLS.K..K.KFP.INTEG.ALASYGLENE.WFDP...LLQGLR.KALSMG
RetrocopyKVSVMDHNVKIQR*EGAKVCLLSSKLFKNKFPQINTEGMALASYGLENEDWFDP>GDLLQGLRQKALSMG
ParentalVYHSHGKVVNLVSSVRSMMTSSGEQVDLK-RIYEVHVKVDNSLECQPVECAIVINAAGAWSGEVAELAGI
V.HS.GKV..LVSSVRSM.TSSGEQ.DLK.R.YE.HVKVDN.LE.QPVEC.IVINA.GAWSG...ELAGI
RetrocopyVHHSRGKVIDLVSSVRSMVTSSGEQIDLK<RLYEIHVKVDNILEYQPVECTIVINATGAWSGQLVELAGI
ParentalGIGSPGTLQGTRLPVEPRKRYVYVWHCPEGPGLEAPLLTDITGSYFRREGLGGYYLGGCSPM-EEEEPDT
GIGSPGTLQ.TRLPVEPRKRY.YVWHCP.GPGLEAPLLT.ITGSYFR.EGLG.Y.LGGC.PM.E.EEPDT
RetrocopyGIGSPGTLQSTRLPVEPRKRYGYVWHCPQGPGLEAPLLTYITGSYFRQEGLGDYFLGGCGPM<E*EEPDT
ParentalKDLEVDHDFFQKKVWP-YLAQRIPAFNSLKVRSAWAGFYDYNTFDQNGIVGPHPLVSNMYFATGFSGHGL
.DLEVD.D.FQKKVWP.YL.QRIPAFNSLKV.S.WA.FY.YNTFDQNGIVGPHPLVSNMYFA.GFSGHG.
Retrocopy*DLEVDQDLFQKKVWP<YLGQRIPAFNSLKVWSVWASFYNYNTFDQNGIVGPHPLVSNMYFAIGFSGHGP
ParentalQHAPGVGRAVAEVLL-NGNFNTIDLNPFSFNRFYRGKKVLENNII
QH...VG.AVAE.LL...NF..I.LN.FSFNRFY.G.KVLENNII
RetrocopyQHVLSVGWAVAETLL<ERNFDSIHLNLFSFNRFYQGEKVLENNII

                            

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

                        

RNA-Seq - click to see more details

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST - click to see more details

Sarcophilus harrisii was not studied using EST data.

TSS - click to see more details

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab - click to see more details

retro_shar_692 was not experimentally validated.

Retrocopy orthology:

Sarcophilus harrisii 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000009226	1 retrocopy	retro_shar_692 ,

	RetrogeneDB ID:	retro_shar_692
Retrocopy location	Organism:	*Tasmanian devil (Sarcophilus harrisii)*
	Coordinates:	GL857275.1:49025..50192(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FOXRED1
	Ensembl ID:	ENSSHAG00000009226
	Aliases:	None
	Description:	FAD-dependent oxidoreductase domain containing 1 [Source:HGNC Symbol;Acc:26927]

Parental	VEQDPTYSMASTGLSIGGIRQQFSLPQNIQLSLFSIEFLRNINEYLAVPDEPLLDIQFNPSGYLLLASEE
	VE...T...ASTGL.IGGI.QQFSLPQNIQLS.F.IEFL.N.NEYLAVPDE..LDIQFNPSGYLLLAS.E
Retrocopy	VEAPFTSLRASTGLPIGGIQQQFSLPQNIQLSFFFIEFLHNVNEYLAVPDESPLDIQFNPSGYLLLASKE

Parental	KAAVMEHNVKIQRQEGAKVCLLSPKQLKDKFPWINTEGIALASYGLENEGWFDP-WCLLQGLRRKALSMG
	K..VM.HNVKIQR.EGAKVCLLS.K..K.KFP.INTEG.ALASYGLENE.WFDP...LLQGLR.KALSMG
Retrocopy	KVSVMDHNVKIQR*EGAKVCLLSSKLFKNKFPQINTEGMALASYGLENEDWFDP>GDLLQGLRQKALSMG

Parental	VYHSHGKVVNLVSSVRSMMTSSGEQVDLK-RIYEVHVKVDNSLECQPVECAIVINAAGAWSGEVAELAGI
	V.HS.GKV..LVSSVRSM.TSSGEQ.DLK.R.YE.HVKVDN.LE.QPVEC.IVINA.GAWSG...ELAGI
Retrocopy	VHHSRGKVIDLVSSVRSMVTSSGEQIDLK<RLYEIHVKVDNILEYQPVECTIVINATGAWSGQLVELAGI

Parental	GIGSPGTLQGTRLPVEPRKRYVYVWHCPEGPGLEAPLLTDITGSYFRREGLGGYYLGGCSPM-EEEEPDT
	GIGSPGTLQ.TRLPVEPRKRY.YVWHCP.GPGLEAPLLT.ITGSYFR.EGLG.Y.LGGC.PM.E.EEPDT
Retrocopy	GIGSPGTLQSTRLPVEPRKRYGYVWHCPQGPGLEAPLLTYITGSYFRQEGLGDYFLGGCGPM<E*EEPDT

Parental	KDLEVDHDFFQKKVWP-YLAQRIPAFNSLKVRSAWAGFYDYNTFDQNGIVGPHPLVSNMYFATGFSGHGL
	.DLEVD.D.FQKKVWP.YL.QRIPAFNSLKV.S.WA.FY.YNTFDQNGIVGPHPLVSNMYFA.GFSGHG.
Retrocopy	*DLEVDQDLFQKKVWP<YLGQRIPAFNSLKVWSVWASFYNYNTFDQNGIVGPHPLVSNMYFAIGFSGHGP

Parental	QHAPGVGRAVAEVLL-NGNFNTIDLNPFSFNRFYRGKKVLENNII
	QH...VG.AVAE.LL...NF..I.LN.FSFNRFY.G.KVLENNII
Retrocopy	QHVLSVGWAVAETLL<ERNFDSIHLNLFSFNRFYQGEKVLENNII

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

RetrogeneDB ID:

retro_shar_692