RetrogeneDB - Retrocopy retro_pvam

						
>retro_pvam_804
CTGATGAACATATACAAGACTGATAACCACCTTAAACATTATTTACATATCACTGAAAATAAACCCTTGTACTCAGTAAT

CTATGATAGCAATGGTGGTGTCCTTTCAATGCCTTTGATCATCAATGGAAATAATTTCAAAATAATAGTAAATACTAGAA

ATGTGTTTATCGAATGCACAGGACCTGCCTTTACTAAGGCAAAAATAGTTCTTGATATTATTGTCACCGTGTTCAGTGAA

CATTGTGAGAATCTACTTACAGTTGAAGCAGCTGAGGTAGTTTTTCCTAATGGAAAATCATATATCTTTCCCGATCTGGC

TTTCTGAAAGGAGATGGTGAGAGCCTACCTAATTAACAAAAAAAGTTGCAATCAGAGAAACTCCAGAAAATCTTGCTAAT

CTTGTGACCAGGATGTACTTAAAGTCAGAAGTCCCTGGTGATGGGAATCAGATTGAGATTGAAAATCCCTCTGACCAAAG

CTGACATTGTCCACACAAGTGATATTGTAGAATTTACAGCTATTGCTTATGGATATAACAACTTTCAGATGACTCTCCCC

AAAACATACACCACAGCTAATCAATTTCTCCTTAATGATATCACAGAACTTCTAAGACATGACATGGCAGCCACCGGATT

CACCAAAGCACTTACCTTGCCTCTGTGCTCCCAAGAAGATACTGCTGATAAACTTGGCTTGGATATCTCTGCAACAAAGG

CAGTCCACATCAGTAATCCTAAAACAGCTGGATTTCAGATGGCAGCACTCCCCTTCTTCATGGCCTCCTAAAGACCATAG

CAGCAAATTGGAAGATGCCCCTTACTCTGAAACTGTTTGAAATCTCTGACTTTACAGTGAAAGATTCTAGCAGAGATGCA

GGTACAAGAAACTACACGCAGCTCTGTGCTGTTTATTACAACAAGATTCTTGGGTTTGAGATAATCCAAGGGCTACTGGA

CAGAATTATGCAGCGGCTTGATGTGCCTCCCAGGGAAGAGGGAATATGTGATCAAAGCATCAAAAGTCCCTGCTTTCTCC

CCAGGGCGATGTGCTGAGATCTCTTCCAGGGGTCAGAGCCTTGGACGGCTAGGGATTCCTCATCCTGACATTATCACCAA

ATTCCAGCTGACTGTGCCTTGCTCCTCCCTGGAAATCAATATCAAGCCCTTTTTG

ORF - retro_pvam_804 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.58 %
Parental protein coverage:	66.72 %
Number of stop codons detected:	1
Number of frameshifts detected	4

Retrocopy - Parental Gene Alignment:

									ParentalLMNIYKNDNHLKHYLHIIENKPLYPVICDSNGVILSMPPIINGNHSKITVNTRNVFIECTGTDFTKAKIV
		LMNIYK.DNHLKHYLHI.ENKPLY.VI.DSNG..LSMP.IINGN..KI.VNTRNVFIECTG..FTKAKIV
RetrocopyLMNIYKTDNHLKHYLHITENKPLYSVIYDSNGGVLSMPLIINGNNFKIIVNTRNVFIECTGPAFTKAKIV
ParentalLDIIVTTFSEYCENQFTVEAAEVVFPNGKSYTFPELAYRKEMVRADLIN-KKVGIRETPENLAKLLTRMY
		LDIIVT.FSE.CEN..TVEAAEVVFPNGKSY.FP.LA..KEMVRA.LIN.KKV.IRETPENLA.L.TRMY
RetrocopyLDIIVTVFSEHCENLLTVEAAEVVFPNGKSYIFPDLAF*KEMVRAYLIN>KKVAIRETPENLANLVTRMY
ParentalLKSEVIGDGNQIEIE-IPPTRADIIHACDIVEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRHDM
		LKSEV.GDGNQIEIE.IP.T.ADI.H..DIVE..AIAYGYNN.QMTLPKTYT.ANQF.LN..TELLRHDM
RetrocopyLKSEVPGDGNQIEIE>IPLTKADIVHTSDIVEFTAIAYGYNNFQMTLPKTYTTANQFLLNDITELLRHDM
ParentalAAAGFTEALTFALCSQEDIADKLGLDISATKAVHISNPKTAEFQVA-RTTLLPGLLKTIAANRKMPLPLK
		AA.GFT.ALT..LCSQED.ADKLGLDISATKAVHISNPKTA.FQ.A..T.LL.GLLKTIAAN.KMPL.LK
RetrocopyAATGFTKALTLPLCSQEDTADKLGLDISATKAVHISNPKTAGFQMA<STPLLHGLLKTIAANWKMPLTLK
ParentalLFEISDVVVKDPSRDVGARNYRHLCAIYYNKNPGFEIIHGLLDRIMQLLDVPPGEKKGGYVIKASEGPAF
		LFEISD..VKD.SRD.G.RNY..LCA.YYNK..GFEII.GLLDRIMQ.LDVPP.E...G........P.F
RetrocopyLFEISDFTVKDSSRDAGTRNYTQLCAVYYNKILGFEIIQGLLDRIMQRLDVPPREE--GICDQSIKSPCF
ParentalF-PGRCAEIFARGQSVGKLGVFHPDVITKFELTMPCSSLEINIEPFL
		..PGRCAEI..RGQS.G.LG..HPD.ITKF.LT.PCSSLEINI.PFL
RetrocopyL>PGRCAEISSRGQSLGRLGIPHPDIITKFQLTVPCSSLEINIKPFL

							

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

						

RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_804 was not experimentally validated.

Retrocopy orthology:

Pteropus vampyrus 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011649	1 retrocopy	retro_btau_1451,
Felis catus	ENSFCAG00000026772	1 retrocopy	retro_fcat_1179,
Gorilla gorilla	ENSGGOG00000017051	1 retrocopy	retro_ggor_598,
Pteropus vampyrus	ENSPVAG00000006985	1 retrocopy	retro_pvam_804 ,

	RetrogeneDB ID:	retro_pvam_804
Retrocopy location	Organism:	*Megabat (Pteropus vampyrus)*
	Coordinates:	scaffold_11909:17290..18465(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FARSB
	Ensembl ID:	ENSPVAG00000006985
	Aliases:	None
	Description:	phenylalanyl-tRNA synthetase, beta subunit [Source:HGNC Symbol;Acc:17800]

Parental	LMNIYKNDNHLKHYLHIIENKPLYPVICDSNGVILSMPPIINGNHSKITVNTRNVFIECTGTDFTKAKIV
	LMNIYK.DNHLKHYLHI.ENKPLY.VI.DSNG..LSMP.IINGN..KI.VNTRNVFIECTG..FTKAKIV
Retrocopy	LMNIYKTDNHLKHYLHITENKPLYSVIYDSNGGVLSMPLIINGNNFKIIVNTRNVFIECTGPAFTKAKIV

Parental	LDIIVTTFSEYCENQFTVEAAEVVFPNGKSYTFPELAYRKEMVRADLIN-KKVGIRETPENLAKLLTRMY
	LDIIVT.FSE.CEN..TVEAAEVVFPNGKSY.FP.LA..KEMVRA.LIN.KKV.IRETPENLA.L.TRMY
Retrocopy	LDIIVTVFSEHCENLLTVEAAEVVFPNGKSYIFPDLAF*KEMVRAYLIN>KKVAIRETPENLANLVTRMY

Parental	LKSEVIGDGNQIEIE-IPPTRADIIHACDIVEDAAIAYGYNNIQMTLPKTYTIANQFPLNKLTELLRHDM
	LKSEV.GDGNQIEIE.IP.T.ADI.H..DIVE..AIAYGYNN.QMTLPKTYT.ANQF.LN..TELLRHDM
Retrocopy	LKSEVPGDGNQIEIE>IPLTKADIVHTSDIVEFTAIAYGYNNFQMTLPKTYTTANQFLLNDITELLRHDM

Parental	AAAGFTEALTFALCSQEDIADKLGLDISATKAVHISNPKTAEFQVA-RTTLLPGLLKTIAANRKMPLPLK
	AA.GFT.ALT..LCSQED.ADKLGLDISATKAVHISNPKTA.FQ.A..T.LL.GLLKTIAAN.KMPL.LK
Retrocopy	AATGFTKALTLPLCSQEDTADKLGLDISATKAVHISNPKTAGFQMA<STPLLHGLLKTIAANWKMPLTLK

Parental	LFEISDVVVKDPSRDVGARNYRHLCAIYYNKNPGFEIIHGLLDRIMQLLDVPPGEKKGGYVIKASEGPAF
	LFEISD..VKD.SRD.G.RNY..LCA.YYNK..GFEII.GLLDRIMQ.LDVPP.E...G........P.F
Retrocopy	LFEISDFTVKDSSRDAGTRNYTQLCAVYYNKILGFEIIQGLLDRIMQRLDVPPREE--GICDQSIKSPCF

Parental	F-PGRCAEIFARGQSVGKLGVFHPDVITKFELTMPCSSLEINIEPFL
	..PGRCAEI..RGQS.G.LG..HPD.ITKF.LT.PCSSLEINI.PFL
Retrocopy	L>PGRCAEISSRGQSLGRLGIPHPDIITKFQLTVPCSSLEINIKPFL

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

RetrogeneDB ID:

retro_pvam_804