RetrogeneDB - Retrocopy retro_ecab

						
>retro_ecab_627
CTGGAGCTGAGCGGCGACCGCAGCTGGAGCGTGGCCGTCTCAAGGCTCCTCTGAGCCGCGTCTACCCCGAGCGCCCGCGG

CCAGAGGACCAGAGGTTAATTTATTCTGGGGAGCCGTTGTTGGATCACCGGTGTCTTAGGGACTTGCTTCCAAAGCAGGA

GAAACGGCACGTTTCGCATCTGGTATGCAATGTGAAGAGTCCTTCCAAAATGCCAGAAACCACCGCGAAGGTTGCTGAAG

CCACAGAGCAGCCTACTGGTCTTAATCAGGGACAGTATTCTGGGGATTCGCCAAGTGATGGTTTAAGGCAAAGGGAGGCT

CTCCGGAACCTTTCTCCCTCTGGATAGGAGAACATCTCCAGACCTGAAGCTGCCCAGCCGGCGTTCCAAGGCCGGGGGCC

TGGTTTCTCGGGCTACACAACCTATGGGTGGCTGCAGCTCTCCTGGTTCTAGCAGACGGACGCACGGCAGTACTGCATGC

AGTATTCAGCGGCCACTGCTGCATCAGGGGCTTCTGTGCCCTCACCAAGTGCACAAGAGATACCTGTGGTCTCCGCTCCT

GCTCCAGCAGCTCCCATTCACAACCAGTTTCCAGCGGAAAACCAGCCGGCCAATCAGAATGCTGCCCCTCAAGTGGGTGG

TTAATGCTGGGGCCAATCAGAATTTGCGGATGACCGCACAAGGTGGCCCTATTGTGGAAGATGATGATGAGATCAACCGA

GATTGGTTGGATTGGACCTATTCAGCAGCTATGTTTTCGGTTTTTCTCAGTATCCTCTAATTCTACTCCTCTCTCAGCAG

ATTCCTCATGGTCATGGGAGCCACCGTGGTTACGTACCTGCATCACGTTGGACGGTTTCCATTTAGACAGAGGCCAGTTC

AGAACTTCCCGAAGGATGGGCCCCCTTATGAAGCTGTGAATCAGGACCCCTACAATAACTTACAGGAACGCCCTGACCCT

GAAATCGAAGATCCCAACCACGTTCCTCCAGACAAGGACGTTCTGGATGGCGTGCAGACCAGCCCTTCATTTTATGAGCA

CAACCTGGCTTGTTTTCAAGACTCTTTGCCTCTCTTCTTCCAGAAGGGCCCCCAGCTATAGCAAAC

ORF - retro_ecab_627 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	85.03 %
Parental protein coverage:	98.4 %
Number of stop codons detected:	3
Number of frameshifts detected	5

Retrocopy - Parental Gene Alignment:

									ParentalLELSGDRS-SV-GRLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPA
		LELSGDRS.SV.GRLKA.LSRVYPERPRPEDQRLIYSG..LLDH.CLRDLLPKQEKRHV.HLVCNVKSP.
RetrocopyLELSGDRSWSV<GRLKAPLSRVYPERPRPEDQRLIYSGEPLLDHRCLRDLLPKQEKRHVSHLVCNVKSPS
ParentalKMPETSAKVAEAPEQPAGLNQGQYPGDSPGDGLRPREPLRNLSPSGWENISRPEAAQPAFQGLGPGFSGL
		KMPET.AKVAEA.EQP.GLNQGQY.GDSP.DGLR.RE.LRNLSPSG.ENISRPEAAQPAFQG.GPGFSG.
RetrocopyKMPETTAKVAEATEQPTGLNQGQYSGDSPSDGLRQREALRNLSPSG*ENISRPEAAQPAFQGRGPGFSGY
ParentalTTYGWLQLSWLQQVYARQYYMQYLAATAASGAFVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA
		TTYGWLQLSW..Q..ARQY.MQY.AATAASGA.VPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA
RetrocopyTTYGWLQLSWF*QTDARQYCMQYSAATAASGASVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA
ParentalPQV-VVNPGANQNLRMNAQGGPVVEEDDELNRDWLDWTYSAATFSVFLSILYFYSSLSRFLMVMGATVVM
		PQV.VVN.GANQNLRM.AQGGP.VE.DDE.NRDWLDWTYSAA.FSVFLSIL.FYSSLSRFLMVMGATVV.
RetrocopyPQV>VVNAGANQNLRMTAQGGPIVEDDDEINRDWLDWTYSAAMFSVFLSIL*FYSSLSRFLMVMGATVVT
ParentalYLHHVGWFPFRQRPVQNFPNGGPPYDAVNQDPNNNLQEGPDPEIEDPSHGPPDRDALDGEQTSPS-FMST
		YLHHVG.FPFRQRPVQNFP..GPPY.AVNQDP.NNLQE.PDPEIEDP.H.PPD.D.LDG.QTSPS.FMST
RetrocopyYLHHVGRFPFRQRPVQNFPKDGPPYEAVNQDPYNNLQERPDPEIEDPNHVPPDKDVLDGVQTSPS>FMST
ParentalAWLVFKTFFAS-LLPEGP-PAIAN
		.WLVFKT...S.....GP.PAIAN
RetrocopyTWLVFKTLCLS<FFQKGP<PAIAN

							

							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
SRP021940_articular_cartilage	0 .18 RPM	49 .88 RPM
SRP021940_cerebellum	0 .47 RPM	50 .95 RPM
SRP021940_embryo	0 .18 RPM	23 .65 RPM
SRP021940_placental_villous	0 .43 RPM	50 .18 RPM
SRP021940_synovial_membrane	0 .14 RPM	33 .38 RPM
SRP021940_testis	0 .32 RPM	43 .23 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_627 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_627 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ecab_627 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000011366	1 retrocopy	retro_ecab_627 ,

	RetrogeneDB ID:	retro_ecab_627
Retrocopy location	Organism:	*Horse (Equus caballus)*
	Coordinates:	24:3540427..3541533(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	HERPUD1
	Ensembl ID:	ENSECAG00000011366
	Aliases:	None
	Description:	homocysteine-inducible, endoplasmic reticulum stress-inducible, ubiquitin-like domain member 1 [Source:HGNC Symbol;Acc:13744]

Parental	LELSGDRS-SV-GRLKAHLSRVYPERPRPEDQRLIYSGKLLLDHQCLRDLLPKQEKRHVLHLVCNVKSPA
	LELSGDRS.SV.GRLKA.LSRVYPERPRPEDQRLIYSG..LLDH.CLRDLLPKQEKRHV.HLVCNVKSP.
Retrocopy	LELSGDRSWSV<GRLKAPLSRVYPERPRPEDQRLIYSGEPLLDHRCLRDLLPKQEKRHVSHLVCNVKSPS

Parental	KMPETSAKVAEAPEQPAGLNQGQYPGDSPGDGLRPREPLRNLSPSGWENISRPEAAQPAFQGLGPGFSGL
	KMPET.AKVAEA.EQP.GLNQGQY.GDSP.DGLR.RE.LRNLSPSG.ENISRPEAAQPAFQG.GPGFSG.
Retrocopy	KMPETTAKVAEATEQPTGLNQGQYSGDSPSDGLRQREALRNLSPSG*ENISRPEAAQPAFQGRGPGFSGY

Parental	TTYGWLQLSWLQQVYARQYYMQYLAATAASGAFVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA
	TTYGWLQLSW..Q..ARQY.MQY.AATAASGA.VPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA
Retrocopy	TTYGWLQLSWF*QTDARQYCMQYSAATAASGASVPSPSAQEIPVVSAPAPAAPIHNQFPAENQPANQNAA

Parental	PQV-VVNPGANQNLRMNAQGGPVVEEDDELNRDWLDWTYSAATFSVFLSILYFYSSLSRFLMVMGATVVM
	PQV.VVN.GANQNLRM.AQGGP.VE.DDE.NRDWLDWTYSAA.FSVFLSIL.FYSSLSRFLMVMGATVV.
Retrocopy	PQV>VVNAGANQNLRMTAQGGPIVEDDDEINRDWLDWTYSAAMFSVFLSIL*FYSSLSRFLMVMGATVVT

Parental	YLHHVGWFPFRQRPVQNFPNGGPPYDAVNQDPNNNLQEGPDPEIEDPSHGPPDRDALDGEQTSPS-FMST
	YLHHVG.FPFRQRPVQNFP..GPPY.AVNQDP.NNLQE.PDPEIEDP.H.PPD.D.LDG.QTSPS.FMST
Retrocopy	YLHHVGRFPFRQRPVQNFPKDGPPYEAVNQDPYNNLQERPDPEIEDPNHVPPDKDVLDGVQTSPS>FMST

Parental	AWLVFKTFFAS-LLPEGP-PAIAN
	.WLVFKT...S.....GP.PAIAN
Retrocopy	TWLVFKTLCLS<FFQKGP<PAIAN

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

RetrogeneDB ID:

retro_ecab_627