RetrogeneDB - Retrocopy retro_sscr

						
>retro_sscr_445
CTGGATGAGCAGGGTCAGCAGGAAGACCTTGAGGAGAAGTTTGTGGACTGCATCACAGACAAGAGTGCCAAGACCCAGCA

GGGTTCTCTTGAGAGCCTATGCCTGGCCTTGGCAGTTCACCTACTCCCCTACTTCTTGCTGAAGCTCTGCCTCACACTGA

TGGATGCTTTGGAAAAGTACCTCAAGAAGGGAAACTGGAGGGATAGGCCCTGGATGCTGCCATGCTTGGTGCTATGCATG

CACTGGTCCCTGGACCCAAGGGGAGGAGATATCCACAGCCTGCAGCCCCTACTGGTTTCTGTACTCAGTAGTGGCACAGC

TAGTCCTGCTGCCCAGCTCTACTGCACTTTTGCTCTTGGCTTAGGCTGCTCTGTGGCTGCTGCCAATGTACAAGACCTGG

TCTCTTGCCATACCCCCTTGGAAGGTGTTTTCAGCTGGACCTGTGGTATGGGTAGCTTCATAGCCTCTATGGTCCCTGCT

AGCCTTGGTGGCCTGCTTTGTGCTGCTCTGCAGGCCTGGGCATTGATACTCACCATTTGCTCCAGGGCCCACATCAGCTA

CTTCTTGGACAGACAGTTGCCCCAGCTTCCCTAGCTCTTGTCCAGTGAAACTGTGAACCTGTGGATTACCGGTGGAGAGA

CCATTGCATTGCTCTTTGAACTGGCCTGTGACCTGGAGAAGGATTTTGTTTATGAGGACATGGAGGCCCTCTGCAGTGCA

CTGCACACTCTGGCCATTGATAGTAAGTATCGTGCCAAGGCTGACCGTCAGTGCCAGTGCTTTACCTTCTGTGCTGTGCT

GCACTTTGTTTAGGGCAGCAAATGTGAGGAAGAGATAGTCTGCTTTGAGCTTGAGGTGCTTTATGTGGACAGCTGGGCTC

AGTGCTGGATCTACACCACTTTCAAGGATGTTCTGGGTTCTGGCATGCATCACCACCTCCAAAGCAACAAGCTGCTCCAT

GATATCTTTGGCCTGGGTGCTGTGCTGGTGCTGGATGCCACTGTCCTGAAGGCCTGCAAGATCTCATGGCTAGAA

ORF - retro_sscr_445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	73.24 %
Parental protein coverage:	79.64 %
Number of stop codons detected:	2
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalVDEQGQQEDLEEKLKEYVDCLTDKSSAKTRQGALESLRLALAAHLLPDFLLERCLTLADALEKCLKKGKG
		.DEQGQQEDLEEK....VDC.TDKS.AKT.QG.LESL.LALA.HLLP.FLL..CLTL.DALEK.LKKG..
RetrocopyLDEQGQQEDLEEK---FVDCITDKS-AKTQQGSLESLCLALAVHLLPYFLLKLCLTLMDALEKYLKKGNW
ParentalEEQ-ALAAAVLGLLCVQLGPGPKG-EEL-FHSLQPLLVSVLTDGTASPAARLHCASALGLGCYVAAADVQ
		....AL.AA.LG.....L.PGPKG.EE...HSLQPLLVSVL..GTASPAA.L.C..ALGLGC.VAAA.VQ
RetrocopyRDR<ALDAAMLGAMHA-LVPGPKG<EEI<IHSLQPLLVSVLSSGTASPAAQLYCTFALGLGCSVAAANVQ
ParentalDLVSCLTCLEGVFSRSCGVGGATAPMVPTSLHGLLCAALQAWALLLTICPSTHISHILDRQLPQLPQLLS
		DLVSC.T.LEGVFS..CG.G...A.MVP.SL.GLLCAALQAWAL.LTIC...HIS..LDRQLPQLP.LLS
RetrocopyDLVSCHTPLEGVFSWTCGMGSFIASMVPASLGGLLCAALQAWALILTICSRAHISYFLDRQLPQLP*LLS
ParentalSESVNLRIAAGETIALLFELARDLEEDFIYEDMEALCGALRTLATDSNKYRAKADRRRQRSTFRSVLHFV
		SE.VNL.I..GETIALLFELA.DLE.DF.YEDMEALC.AL.TLA.DS.KYRAKADR..Q..TF..VLHFV
RetrocopySETVNLWITGGETIALLFELACDLEKDFVYEDMEALCSALHTLAIDS-KYRAKADRQCQCFTFCAVLHFV
ParentalEGGECEEETVRFGLEVLYVDSWARRRIYAAFKDVLGSGMHHHLQNNELLRDIFGLGPVLVLDATALKACK
		.G..CEEE.V.F.LEVLYVDSWA...IY..FKDVLGSGMHHHLQ.N.LL.DIFGLG.VLVLDAT.LKACK
Retrocopy*GSKCEEEIVCFELEVLYVDSWAQCWIYTTFKDVLGSGMHHHLQSNKLLHDIFGLGAVLVLDATVLKACK
ParentalISRFE
		IS..E
RetrocopyISWLE

							

							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 .13 RPM	51 .50 RPM
SRP014902_testis	0 .00 RPM	65 .07 RPM
SRP018288_heart	0 .05 RPM	36 .83 RPM
SRP018288_kidney	0 .10 RPM	46 .20 RPM
SRP018288_liver	0 .16 RPM	43 .18 RPM
SRP018288_lung	0 .00 RPM	22 .30 RPM
SRP018856_adipose	0 .00 RPM	41 .01 RPM
SRP035408_brain	0 .00 RPM	14 .01 RPM
SRP035408_liver	0 .00 RPM	15 .03 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_445 retrocopy.

TSS - click to see more details

Sus scrofa was not studied using FANTOM5 data.

Lab - click to see more details

retro_sscr_445 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_sscr_445 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004993	1 retrocopy	retro_cjac_4213,
Macaca mulatta	ENSMMUG00000020119	1 retrocopy	retro_mmul_1073,
Otolemur garnettii	ENSOGAG00000012534	1 retrocopy	retro_ogar_2236,
Sus scrofa	ENSSSCG00000024363	1 retrocopy	retro_sscr_445 ,

	RetrogeneDB ID:	retro_sscr_445
Retrocopy location	Organism:	*Pig (Sus scrofa)*
	Coordinates:	14:100666330..100667365(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	IFRD2
	Ensembl ID:	ENSSSCG00000024363
	Aliases:	None
	Description:	interferon-related developmental regulator 2 [Source:HGNC Symbol;Acc:5457]

Parental	VDEQGQQEDLEEKLKEYVDCLTDKSSAKTRQGALESLRLALAAHLLPDFLLERCLTLADALEKCLKKGKG
	.DEQGQQEDLEEK....VDC.TDKS.AKT.QG.LESL.LALA.HLLP.FLL..CLTL.DALEK.LKKG..
Retrocopy	LDEQGQQEDLEEK---FVDCITDKS-AKTQQGSLESLCLALAVHLLPYFLLKLCLTLMDALEKYLKKGNW

Parental	EEQ-ALAAAVLGLLCVQLGPGPKG-EEL-FHSLQPLLVSVLTDGTASPAARLHCASALGLGCYVAAADVQ
	....AL.AA.LG.....L.PGPKG.EE...HSLQPLLVSVL..GTASPAA.L.C..ALGLGC.VAAA.VQ
Retrocopy	RDR<ALDAAMLGAMHA-LVPGPKG<EEI<IHSLQPLLVSVLSSGTASPAAQLYCTFALGLGCSVAAANVQ

Parental	DLVSCLTCLEGVFSRSCGVGGATAPMVPTSLHGLLCAALQAWALLLTICPSTHISHILDRQLPQLPQLLS
	DLVSC.T.LEGVFS..CG.G...A.MVP.SL.GLLCAALQAWAL.LTIC...HIS..LDRQLPQLP.LLS
Retrocopy	DLVSCHTPLEGVFSWTCGMGSFIASMVPASLGGLLCAALQAWALILTICSRAHISYFLDRQLPQLP*LLS

Parental	SESVNLRIAAGETIALLFELARDLEEDFIYEDMEALCGALRTLATDSNKYRAKADRRRQRSTFRSVLHFV
	SE.VNL.I..GETIALLFELA.DLE.DF.YEDMEALC.AL.TLA.DS.KYRAKADR..Q..TF..VLHFV
Retrocopy	SETVNLWITGGETIALLFELACDLEKDFVYEDMEALCSALHTLAIDS-KYRAKADRQCQCFTFCAVLHFV

Parental	EGGECEEETVRFGLEVLYVDSWARRRIYAAFKDVLGSGMHHHLQNNELLRDIFGLGPVLVLDATALKACK
	.G..CEEE.V.F.LEVLYVDSWA...IY..FKDVLGSGMHHHLQ.N.LL.DIFGLG.VLVLDAT.LKACK
Retrocopy	*GSKCEEEIVCFELEVLYVDSWAQCWIYTTFKDVLGSGMHHHLQSNKLLHDIFGLGAVLVLDATVLKACK

Parental	ISRFE
	IS..E
Retrocopy	ISWLE

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

RetrogeneDB ID:

retro_sscr_445