RetrogeneDB - Retrocopy retro_sscr

                        
>retro_sscr_192
CATTTCAACAAGATTCAAAATTTTAATGACACTTTCTATCTGCAATTTCATATAATTGTATGTGGACTGGACTCTGTTAT

GGCCAGAAGATGGATAAATGGCATGCTGGTATCGCTTCTAAATTATGAAGATGGTGTATTAGAGCCAAGTTCCATTGTCC

CTTTTTTACACAGGAGGACAGAAAGTTTTAAAGGAAGTGCCTGAGTAATTCTGCCTGGAATGACTGCTTGTATTGAATGT

ACACTGGCACTGTACCCATCACAGGTTAATTTTCCCATGTGTATTGTATTTTTGCCCAGGCTACCAGAGCTCTGTATTGA

GTATGTAAGGATATTGCAGTGGCCTAAGGAGCAGCTTTTTGGAGAAGGGGCAACATTAAGTGGAGATAATATTGATCATA

TTCAGTGGATTTTCCAAAAATCCCTAGAGAGAGCATCGCAATATAATATTAGAGGTGTTACGTAGAGATTCACTTAAGAG

GTGGTAAAATGAACAATTCTTGTAGTAGCTTCTATAAATGCAGTCATTGCAGCTGTATGTGCCACTGAGGTTTTTAAAAT

AGCCACAAGTGCATATATTCCCCTTAATAGTTACTTGGTATTCAGTGATATAGATGGAGTATACACATTCGCATCTGAAG

CAGAGAGAAAGGAAAACTTCCCAGCTCTTAGCCAGCTTCTGCACAACATTCAGTTCTCTCCATCAGCTAAACTGCAGGTG

ATTTTGGATTGTTTAACCAGTAGTGCTTCTCTGCAGATGAAATCTGTAGCCGTAACAGCCATATTAGAGGGAAAAAAAAA

TAAAACACTTTACTGACAGACAGTAACCTCCATTGAAGAGTGCACAAGGCCAAATCTCTCCAAGACATTGAAAGAATTGG

GACTCGTTCATGGGCAAGAACTGGCAGTTGCTGATGTCACCACACCACAGACTGTTCAAACTTCATTTTACTTC

ORF - retro_sscr_192 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	78.37 %
Parental protein coverage:	67.95 %
Number of stop codons detected:	5
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalHFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVI
HFNKIQ.FNDTFY.QFHIIVCGLDS..ARRWINGML.SLLNYEDGVL.PSSIVP.....TE.FKG.A.VI
RetrocopyHFNKIQNFNDTFYLQFHIIVCGLDSVMARRWINGMLVSLLNYEDGVLEPSSIVPFLHRRTESFKGSA*VI
ParentalLPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRILQWPKEQPFGEGVPLDGDDPDHIQWIFQ
LPGMTACIECTL.LYP.QVNFPMC.I...PRLPE.CIEYVRILQWPKEQ.FGEG..L.GD..DHIQWIFQ
RetrocopyLPGMTACIECTLALYPSQVNFPMC-IVFLPRLPELCIEYVRILQWPKEQLFGEGATLSGDNIDHIQWIFQ
ParentalKSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYT
KSLERASQYNIRGVT.R.T..VVK..I..VAS.NAVIAAVCATEVFKIATSAYIPLN.YLVF.D.DG.YT
RetrocopyKSLERASQYNIRGVT*RFT*EVVK*TILVVASINAVIAAVCATEVFKIATSAYIPLNSYLVFSDIDGVYT
ParentalYTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLE-GKNRTLYLQSVTSIE
...EAERKEN.PA.SQL..NIQFSPSAKLQ..LD.LT.SASLQMKS.A.TA.LE......LY.Q.VTSIE
RetrocopyFASEAERKENFPALSQLLHNIQFSPSAKLQVILDCLTSSASLQMKSVAVTAILEXXXXXXLY*QTVTSIE
ParentalERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHF
E.TRPNLSKTLKELGLV.GQELAVADVTTPQTV.....F
RetrocopyECTRPNLSKTLKELGLVHGQELAVADVTTPQTVQTSFYF

                            

                            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	24 .42 RPM
SRP014902_testis	0 .00 RPM	25 .74 RPM
SRP018288_heart	0 .16 RPM	52 .18 RPM
SRP018288_kidney	0 .20 RPM	49 .06 RPM
SRP018288_liver	0 .16 RPM	18 .07 RPM
SRP018288_lung	0 .20 RPM	30 .45 RPM
SRP018856_adipose	0 .00 RPM	29 .73 RPM
SRP035408_brain	0 .13 RPM	37 .19 RPM
SRP035408_liver	0 .09 RPM	20 .81 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_192 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_192 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_192 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010117	1 retrocopy	retro_amel_204,
Choloepus hoffmanni	ENSCHOG00000013626	2 retrocopies	retro_chof_1740, retro_chof_553,
Callithrix jacchus	ENSCJAG00000013395	2 retrocopies	retro_cjac_2827, retro_cjac_2986,
Erinaceus europaeus	ENSEEUG00000005430	2 retrocopies	retro_eeur_374, retro_eeur_663,
Otolemur garnettii	ENSOGAG00000007771	2 retrocopies	retro_ogar_1868, retro_ogar_2776,
Rattus norvegicus	ENSRNOG00000006221	1 retrocopy	retro_rnor_852,
Sus scrofa	ENSSSCG00000011506	1 retrocopy	retro_sscr_192 ,

	RetrogeneDB ID:	retro_sscr_192
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	1:242765102..242766056(-)
	Located in intron of:	ENSSSCG00000005215
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	UBA3
	Ensembl ID:	ENSSSCG00000011506
	Aliases:	None
	Description:	ubiquitin-like modifier activating enzyme 3 [Source:HGNC Symbol;Acc:12470]

Parental	HFNKIQDFNDTFYRQFHIIVCGLDSIIARRWINGMLISLLNYEDGVLDPSSIVPLIDGGTEGFKGNARVI
	HFNKIQ.FNDTFY.QFHIIVCGLDS..ARRWINGML.SLLNYEDGVL.PSSIVP.....TE.FKG.A.VI
Retrocopy	HFNKIQNFNDTFYLQFHIIVCGLDSVMARRWINGMLVSLLNYEDGVLEPSSIVPFLHRRTESFKGSA*VI

Parental	LPGMTACIECTLELYPPQVNFPMCTIASMPRLPEHCIEYVRILQWPKEQPFGEGVPLDGDDPDHIQWIFQ
	LPGMTACIECTL.LYP.QVNFPMC.I...PRLPE.CIEYVRILQWPKEQ.FGEG..L.GD..DHIQWIFQ
Retrocopy	LPGMTACIECTLALYPSQVNFPMC-IVFLPRLPELCIEYVRILQWPKEQLFGEGATLSGDNIDHIQWIFQ

Parental	KSLERASQYNIRGVTYRLTQGVVKRIIPAVASTNAVIAAVCATEVFKIATSAYIPLNNYLVFNDVDGLYT
	KSLERASQYNIRGVT.R.T..VVK..I..VAS.NAVIAAVCATEVFKIATSAYIPLN.YLVF.D.DG.YT
Retrocopy	KSLERASQYNIRGVTRFTEVVK*TILVVASINAVIAAVCATEVFKIATSAYIPLNSYLVFSDIDGVYT

Parental	YTFEAERKENCPACSQLPQNIQFSPSAKLQEVLDYLTNSASLQMKSPAITATLE-GKNRTLYLQSVTSIE
	...EAERKEN.PA.SQL..NIQFSPSAKLQ..LD.LT.SASLQMKS.A.TA.LE......LY.Q.VTSIE
Retrocopy	FASEAERKENFPALSQLLHNIQFSPSAKLQVILDCLTSSASLQMKSVAVTAILEXXXXXXLY*QTVTSIE

Parental	ERTRPNLSKTLKELGLVDGQELAVADVTTPQTVLFKLHF
	E.TRPNLSKTLKELGLV.GQELAVADVTTPQTV.....F
Retrocopy	ECTRPNLSKTLKELGLVHGQELAVADVTTPQTVQTSFYF

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

RetrogeneDB ID:

retro_sscr_192