RetrogeneDB - Retrocopy retro_mdom

						
>retro_mdom_423
TCTTGCTTCACGCAGGCATCTCACTCGCTGAGAAGTTAAGTGTCCTCATCACCATGGTCCTGCAGGTGAACCTCTACAAA

CTGACCCCCAAGTGCTAGGGGCACCTGAGCCCCAGGAAGGATAAGATCGCTGTGGACATCGACGTGCCCTGGGGAGTGGA

CTCATTCATTACCCTGGTCTTCCAGGACTAGCCCTACCATGTGCCAACTGCGACTACTGTTTCCTGCGCAACAATGGGCA

CCTGGTGGAAAGACCTGAGAGGGGCACGATCTACATCCTGTAGTTCAGATCTGGCAAAGTGGCTTTCAGGGACTTCAAGG

ACCATTACCAGGAGCCAGTTGAACCCAACAGCACTCTTAAGGCAGGCATGAGCACCAAGATGGGCGAGATATACTCTTCT

TACTAGAACAGAATTGTCCCAAGGTGGTACTGCAGGAAGACAACCAGAGGAACATGTATGCTGGGCAGAAAATAGACCTC

TCTGCCAATTGGGATGAAGAGAGTGACTTAGAAATTTTCCCACTAGAGATCAATAGAGACACCAATAAATGTGCTCTCTG

GAGCAATACTGACAAATACTGGACCCTAACATTCAGTGGTGGCATACTTGTCCACTGCTTCGACCAAGACCGCCAACTAC

TGCTTTGACATAGAATGGTGTGACAAAGGCATCACTGTCAAAACTGCCAATGAGAAGTAGGTTACAACCTCAGAAAAATG

GAGAACTGGTGGCCTCTTTGGAAGCTGCAAAAGAAAATCGGCATTTGTTAAAATTGATCAAGAGACCCATCATCTTGTTC

TCAGGAATCTATGGCTTCATTGGATGCTAGAGAGTGAGTGGGATGGTGGATTCAGATTGCTCTTCATTCCAGTTGGAAGT

TAATAGTTGTGTCTACAATATCAAAGACTCTACTGGGAAGTATTGGATGATGGGAAATGAATCATCTATCATCAGTAGCA

GCAAAATTCCCAGAGACTTCTTTTTCAAGTTCTGTGACCATGACAAAGTAGCC

ORF - retro_mdom_423 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	64.84 %
Parental protein coverage:	69.23 %
Number of stop codons detected:	5
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalSCFAQT-ISPAEKWSVHIAMHPQVNIYSLTRKRYAHLSARQDEIAVDRDVPWGVDSLITLVFQDQRYSVQ
		SCF.Q..IS.AEK.SV.I.M..QVN.Y.LT.K...HLS.R.D.IAVD.DVPWGVDS.ITLVFQD..Y.V.
RetrocopySCFTQA<ISLAEKLSVLITMVLQVNLYKLTPKC*GHLSPRKDKIAVDIDVPWGVDSFITLVFQD*PYHVP
ParentalTA-DHRFLRNDGRLVESPEPGTGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKSTKVG-KDELFVLE
		TA.D..FLRN.G.LVE.PE.GT.Y.L.FRSGKVAFRD....Y..P..P..TLKAG.STK.G..D.LF.LE
RetrocopyTA<DYCFLRNNGHLVERPERGTIYIL*FRSGKVAFRDFKDHYQEPVEPNSTLKAGMSTKMG<RDILFLLE
ParentalQSCPQVVLQAGNQRNVSTRQGMDLSANQDEESDQETFQLEINRDTKKCAFRTHTGKYWTLTSNGGI-QST
		Q.CP.VVLQ..NQRN....Q..DLSAN.DEESD.E.F.LEINRDT.KCA....T.KYWTLT..GGI..ST
RetrocopyQNCPKVVLQEDNQRNMYAGQKIDLSANWDEESDLEIFPLEINRDTNKCALWSNTDKYWTLTFSGGI>LST
ParentalASTKNASCYFDIEWCDKRITLKAANGKYVTA-KKNGQLAASVEAAGETEHFLMKLINRPIIVFRGEHGFI
		ASTK.A...FDIEWCDK.IT.K.AN.K.VT...KNG.L.AS.EAA.E..H.L.KLI.RPII.F.G..GFI
RetrocopyASTKTANYCFDIEWCDKGITVKTANEK*VTT>QKNGELVASLEAAKENRH-LLKLIKRPIILFSGIYGFI
ParentalGCRKVTGTLDSNRSSYDVFQLEFNDGAYNIKDSTGKYWMVGNESSVTSSSNTPVDFFFEFCDYNKVA
		GC..V.G..DS..SS...FQLE.N...YNIKDSTGKYWM.GNESS..SSS..P.DFFF.FCD..KVA
RetrocopyGC*RVSGMVDSDCSS---FQLEVNSCVYNIKDSTGKYWMMGNESSIISSSKIPRDFFFKFCDHDKVA

							

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

						

RNA-Seq - click to see more details

(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	0 .00 RPM	0 .00 RPM
SRP007412_cerebellum	0 .00 RPM	0 .00 RPM
SRP007412_heart	0 .00 RPM	0 .00 RPM
SRP007412_kidney	0 .00 RPM	0 .00 RPM
SRP007412_liver	0 .00 RPM	0 .00 RPM
SRP007412_testis	6 .88 RPM	0 .00 RPM

ChIP-Seq - click to see more details

Monodelphis domestica was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_mdom_423 retrocopy.

TSS - click to see more details

Monodelphis domestica was not studied using FANTOM5 data.

Lab - click to see more details

retro_mdom_423 was not experimentally validated.

Retrocopy orthology:

Monodelphis domestica 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000075618	1 retrocopy	retro_hsap_1476,
Monodelphis domestica	ENSMODG00000001028	1 retrocopy	retro_mdom_423 ,
Ornithorhynchus anatinus	ENSOANG00000030243	1 retrocopy	retro_oana_11,
Pongo abelii	ENSPPYG00000017337	3 retrocopies	retro_pabe_1225, retro_pabe_3201, retro_pabe_3544,

	RetrogeneDB ID:	retro_mdom_423
Retrocopy location	Organism:	*Opossum (Monodelphis domestica)*
	Coordinates:	1:480153004..480154017(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	FSCN1
	Ensembl ID:	ENSMODG00000001028
	Aliases:	None
	Description:	fascin homolog 1, actin-bundling protein (Strongylocentrotus purpuratus) [Source:HGNC Symbol;Acc:11148]

Parental	SCFAQT-ISPAEKWSVHIAMHPQVNIYSLTRKRYAHLSARQDEIAVDRDVPWGVDSLITLVFQDQRYSVQ
	SCF.Q..IS.AEK.SV.I.M..QVN.Y.LT.K...HLS.R.D.IAVD.DVPWGVDS.ITLVFQD..Y.V.
Retrocopy	SCFTQA<ISLAEKLSVLITMVLQVNLYKLTPKCGHLSPRKDKIAVDIDVPWGVDSFITLVFQDPYHVP

Parental	TA-DHRFLRNDGRLVESPEPGTGYTLEFRSGKVAFRDCEGRYLAPSGPSGTLKAGKSTKVG-KDELFVLE
	TA.D..FLRN.G.LVE.PE.GT.Y.L.FRSGKVAFRD....Y..P..P..TLKAG.STK.G..D.LF.LE
Retrocopy	TA<DYCFLRNNGHLVERPERGTIYIL*FRSGKVAFRDFKDHYQEPVEPNSTLKAGMSTKMG<RDILFLLE

Parental	QSCPQVVLQAGNQRNVSTRQGMDLSANQDEESDQETFQLEINRDTKKCAFRTHTGKYWTLTSNGGI-QST
	Q.CP.VVLQ..NQRN....Q..DLSAN.DEESD.E.F.LEINRDT.KCA....T.KYWTLT..GGI..ST
Retrocopy	QNCPKVVLQEDNQRNMYAGQKIDLSANWDEESDLEIFPLEINRDTNKCALWSNTDKYWTLTFSGGI>LST

Parental	ASTKNASCYFDIEWCDKRITLKAANGKYVTA-KKNGQLAASVEAAGETEHFLMKLINRPIIVFRGEHGFI
	ASTK.A...FDIEWCDK.IT.K.AN.K.VT...KNG.L.AS.EAA.E..H.L.KLI.RPII.F.G..GFI
Retrocopy	ASTKTANYCFDIEWCDKGITVKTANEK*VTT>QKNGELVASLEAAKENRH-LLKLIKRPIILFSGIYGFI

Parental	GCRKVTGTLDSNRSSYDVFQLEFNDGAYNIKDSTGKYWMVGNESSVTSSSNTPVDFFFEFCDYNKVA
	GC..V.G..DS..SS...FQLE.N...YNIKDSTGKYWM.GNESS..SSS..P.DFFF.FCD..KVA
Retrocopy	GC*RVSGMVDSDCSS---FQLEVNSCVYNIKDSTGKYWMMGNESSIISSSKIPRDFFFKFCDHDKVA

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

RetrogeneDB ID:

retro_mdom_423