RetrogeneDB - Retrocopy retro_sscr

						
>retro_sscr_903
ATTTCGTGGGGCAGGGCAGGTGGCGCCCTGCTGAGCTCACTGCTGGAGGCCATGGAGGTGCCCTCGCTCATCCTGTGGGG

GCTCTTGGGCTGGGGCAAGACCTTGCTGGCCCACATTCTCACTAACAACAGCAAGAAACAGCGCAAGATTTGTGACCTTC

TCCGAAACCAGCTCCAAGACAACTGACTGGATGATGTCATCAAACAAGCTCAGAATGAGAAGAGCTTTTTCAAGAGGCAA

ACCATCCTTTATATTGACGAGATTTATCGATTCAATAAATCTCATCAGGACAGGTTCCTTCCTCACCTGGAGTATGAAAA

CCTGAACCTGATCTGGGCCACCACGCGGAACCCCTCTTTCCAGATCAATGCCGCTCTGCTGAGCCACTGTCAGGTGATCT

TCTTGAGAAGTTTCCAGTGGAGGCTGTGGTGACTGTCCTCACCCGGGTGACCAACTCCTTTGGGATCAAGGACCTGGACT

CTAGCTGCTCCGACGACCCTCTGAGCCACAGCAGCAACAGCAGTTCTGAGCCCCCCTTATTCACAGAGGACAAAGTGGTG

GACACACTGGCCCACCTCAGCGACAGGGACATCTGGGCTGGACTCAACAGACTGCTGATGGCAGTGGTGGCCAGGATCAG

CGCCAGGAAGGTTGTCGGGAAGAAGAGCAGGCAGACCTACCCTCCCAGCAGAGTCCTGGTCACCGAGAGTGACATGAAGA

AAGGCCTCCAGCACTCTCCCACCCTTTGTGACCACGCAGGAGAGGGCATTACCACTTCTGCGAGCTTCACACTGGCATGC

GGGGCTCTGAGCAGAGCGTGTCACTGCACAGGCTGGGCCATATGCTAGAGGGTAGAAAGGACCCACTCTATGCAGCCAGG

CAGCTCATGAAGTTTGCCAGAGAGGACCTGGGTCTGGCAGACCTGCCTGTATTAACCCAAGCCGTGGCCGCCCACCAGGG

CAGTCACTTTATTGGCAGGCTGAACGCCAGGTGCTCCTGGCCCAGTGCAGGGTCTACTTGGCCCGAGCCCCCAAGTCCAT

CGAGGTGTACAGCGCCTACCACAACGTTAAGGCCTGCCTGCGGAGCAACCAGGACCCCTGCGCCCCACTCCCC

ORF - retro_sscr_903 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	68.24 %
Parental protein coverage:	73.44 %
Number of stop codons detected:	0
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalVGQGRAVGPETLLRSLLEANEVPSLILWGPPGCGKTTLAHIIANNSKK-HSIRFVTLSATSAKTTD-VRD
		...GRA.G...LL.SLLEA.EVPSLILWG..G.GKT.LAHI...N..K..S.RFVT.S.TS.KTTD...D
RetrocopyISWGRAGG--ALLSSLLEAMEVPSLILWGLLGWGKTLLAHILT-NNSK>NSARFVTFSETSSKTTD<LDD
ParentalVIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVI-V
		VIKQAQNEKSFFKR.TIL.IDEI.RFNKS.QD.FLPH.E.....LI.ATT.NPSFQ.NAALLS.C.VI..
RetrocopyVIKQAQNEKSFFKRQTILYIDEIYRFNKSHQDRFLPHLEYENLNLIWATTRNPSFQINAALLSHCQVI<L
ParentalLEKLPVEAVVTILMRAINSLGIHVLDSSRPADPLSHSSNSSSEPSVFIEDKAVDTLAHLSDGDARAGLNG
		LEK.PVEAVVT.L.R..NS.GI..LDSS...DPLSHSSNSSSEP..F.EDK.VDTLAHLSD.D..AGLN.
RetrocopyLEKFPVEAVVTVLTRVTNSFGIKDLDSSCSDDPLSHSSNSSSEPPLFTEDKVVDTLAHLSDRDIWAGLNR
ParentalLQLAVLARLSARKVFGKKTGQTYPPGRVLVTEGDVKEGLQRSHILYDRAGE-EHYNCISALHKAMRGSDQ
		L..AV.AR.SARKV.GKK..QTYPP.RVLVTE.D.K.GLQ.S..L.D.AGE..HY.....LH..MRGS.Q
RetrocopyLLMAVVARISARKVVGKKSRQTYPPSRVLVTESDMKKGLQHSPTLCDHAGE<GHYH-FCELHTGMRGSEQ
ParentalNAALYWLGRMLEGGEDPLYVARRLVRFASEDVGLADPSALTQAVAAYQGCHFIG-MPECEVLLAQCVVYL
		...L..LG.MLEG..DPLY.AR.L..FA.ED.GLAD...LTQAVAA.QG.HFIG...E..VLLAQC.VYL
RetrocopySVSLHRLGHMLEGRKDPLYAARQLMKFAREDLGLADLPVLTQAVAAHQGSHFIG<QAERQVLLAQCRVYL
ParentalARAPKSIEVYSAYSNVKACLRSHQGPLPPVP
		ARAPKSIEVYSAY.NVKACLRS.Q.P..P.P
RetrocopyARAPKSIEVYSAYHNVKACLRSNQDPCAPLP

							

							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
SRP014902_placenta	0 .00 RPM	117 .33 RPM
SRP014902_testis	0 .00 RPM	152 .20 RPM
SRP018288_heart	0 .00 RPM	29 .89 RPM
SRP018288_kidney	0 .00 RPM	49 .94 RPM
SRP018288_liver	0 .00 RPM	31 .98 RPM
SRP018288_lung	0 .00 RPM	69 .34 RPM
SRP018856_adipose	0 .00 RPM	66 .49 RPM
SRP035408_brain	0 .00 RPM	85 .72 RPM
SRP035408_liver	0 .00 RPM	24 .63 RPM

ChIP-Seq - click to see more details

Sus scrofa was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_sscr_903 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_903 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_903 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002843	1 retrocopy	retro_chof_605,
Sus scrofa	ENSSSCG00000001010	1 retrocopy	retro_sscr_903 ,

	RetrogeneDB ID:	retro_sscr_903
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	7:58955487..58956600(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	WRNIP1
	Ensembl ID:	ENSSSCG00000001010
	Aliases:	None
	Description:	Werner helicase interacting protein 1 [Source:HGNC Symbol;Acc:20876]

Parental	VGQGRAVGPETLLRSLLEANEVPSLILWGPPGCGKTTLAHIIANNSKK-HSIRFVTLSATSAKTTD-VRD
	...GRA.G...LL.SLLEA.EVPSLILWG..G.GKT.LAHI...N..K..S.RFVT.S.TS.KTTD...D
Retrocopy	ISWGRAGG--ALLSSLLEAMEVPSLILWGLLGWGKTLLAHILT-NNSK>NSARFVTFSETSSKTTD<LDD

Parental	VIKQAQNEKSFFKRKTILFIDEIHRFNKSQQDTFLPHVECGTITLIGATTENPSFQVNAALLSRCRVI-V
	VIKQAQNEKSFFKR.TIL.IDEI.RFNKS.QD.FLPH.E.....LI.ATT.NPSFQ.NAALLS.C.VI..
Retrocopy	VIKQAQNEKSFFKRQTILYIDEIYRFNKSHQDRFLPHLEYENLNLIWATTRNPSFQINAALLSHCQVI<L

Parental	LEKLPVEAVVTILMRAINSLGIHVLDSSRPADPLSHSSNSSSEPSVFIEDKAVDTLAHLSDGDARAGLNG
	LEK.PVEAVVT.L.R..NS.GI..LDSS...DPLSHSSNSSSEP..F.EDK.VDTLAHLSD.D..AGLN.
Retrocopy	LEKFPVEAVVTVLTRVTNSFGIKDLDSSCSDDPLSHSSNSSSEPPLFTEDKVVDTLAHLSDRDIWAGLNR

Parental	LQLAVLARLSARKVFGKKTGQTYPPGRVLVTEGDVKEGLQRSHILYDRAGE-EHYNCISALHKAMRGSDQ
	L..AV.AR.SARKV.GKK..QTYPP.RVLVTE.D.K.GLQ.S..L.D.AGE..HY.....LH..MRGS.Q
Retrocopy	LLMAVVARISARKVVGKKSRQTYPPSRVLVTESDMKKGLQHSPTLCDHAGE<GHYH-FCELHTGMRGSEQ

Parental	NAALYWLGRMLEGGEDPLYVARRLVRFASEDVGLADPSALTQAVAAYQGCHFIG-MPECEVLLAQCVVYL
	...L..LG.MLEG..DPLY.AR.L..FA.ED.GLAD...LTQAVAA.QG.HFIG...E..VLLAQC.VYL
Retrocopy	SVSLHRLGHMLEGRKDPLYAARQLMKFAREDLGLADLPVLTQAVAAHQGSHFIG<QAERQVLLAQCRVYL

Parental	ARAPKSIEVYSAYSNVKACLRSHQGPLPPVP
	ARAPKSIEVYSAY.NVKACLRS.Q.P..P.P
Retrocopy	ARAPKSIEVYSAYHNVKACLRSNQDPCAPLP

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

RetrogeneDB ID:

retro_sscr_903