RetrogeneDB - Retrocopy retro_pabe

						
>retro_pabe_333
GGGGGGTCAACGTCCAGCCTTGCTCAGGCTCCCCTGCAAACTCTGAGTGTAACTGCACTGGTGGAACCCCATGGGTGCAT

CATGGGCCTGGACCTGCCAGATGGGGGCCACCTGACCCATGGGTTCATGACAGACAAAAAGAAAATCTCTGCCACGTCCA

TCTTTGAATCTATGCCCTATGAGGTGAACCCAGACACTGGCTACATCAACTATGACCAACTGGAGGAGAACGCCCGCCTC

TTCCACCCGAAGCTGATCACTGCAGGAACCAGCTGCTCCTCCTAAAACCTGGACTATGCCCGCTGCGGAAAAACTGCAGA

TGAGAATGGGCTGTATCTCATGGTGGACACGGCACATATCAGCAGGCTGGTGGAAGCTGGTATGGTTCCCTCCCCATTTA

ACACTGCCACGTGGTGACCACCACCACTGACAAGAACCTGAGAGGCTGCCAAGTTGGCATGATCTTCTACAGGAAAGGAG

TGCAAAGTATGGATCCCAAGACTGGCAAAGAGATTCTGTACAACCTGGAGTCCCTCATCAATTCTGCTGTGTTCCCTGGC

CTTCAGGGAGGTCCCCACAACCACGCCATTGCTGGGGTTGCTGTGGCCCTGAGGCAAGCTATGACTCTGGAATTTGAAGT

TTATCAGCACCAGGTGGTGGCCAACTGCAGGGCTCTGTCTGAGGCACTGACGCAGCTGGGCTACAAAACAGTCAGGTGGT

TCTGACAACCATTTCATCCTTGTGGATCTCCATTCAATCAAAGGCGCAGATGGCAGAAGGGCTGAGAAGGTCCTAGAAGC

CTGTTCTATTGCCTGCAACAAGAACACCTGCCCAGATGACAGAAGCACTCTACGGCCCAGTGGACTGCGGCTTGGGACCC

CAGCACTGACATCCCTCGGACTTTTGGAAAAAGGCTTCCAAAAGGTAGCTCACTTTATCCACGGAGGGATAGAGCTAACC

CTGCAGATCTAGAGCAACGCTGGCATCAGAACCACCCTGAAAGAGTTCAAGGAGAGACCAGCAGGGCATAAATACCAGGG

GGGTGTGCAGGCTCTCCAGGAGGAGGTTGAGAGCTTCACTCTCTCTTCCCTCTGCCTGGCCTGCCTGACTTC

ORF - retro_pabe_333 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	81.12 %
Parental protein coverage:	77.02 %
Number of stop codons detected:	2
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalGVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYI
		G.........P......TALVEPHG.IMGLDLPDGGHLTHGFMTDKKKISATSIF.ESMPY.VNPDTGYI
RetrocopyGGSTSSLAQAPLQTLSVTALVEPHGCIMGLDLPDGGHLTHGFMTDKKKISATSIF-ESMPYEVNPDTGYI
ParentalNYDQLEENARLFHPKLIIAGTSCYSRNLDYARLRKIADENGAYLMADMAHISGLVAAGVVPSPFE-HCHV
		NYDQLEENARLFHPKLI.AGTSC.S.NLDYAR..K.ADENG.YLM.D.AHIS.LV.AG.VPSPF..HCHV
RetrocopyNYDQLEENARLFHPKLITAGTSCSS*NLDYARCGKTADENGLYLMVDTAHISRLVEAGMVPSPFN<HCHV
ParentalVTTTTHKTLRGCRAGMIFYRKGVQSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAM
		VTTTT.K.LRGC..GMIFYRKGVQS.DPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVAL.QAM
RetrocopyVTTTTDKNLRGCQVGMIFYRKGVQSMDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALRQAM
ParentalTLEFKVYQHQVVANCRALSEALTELGYKIVT-GGSDNHLILVDLRS-KGTDGGRAEKVLEACSIACNKNT
		TLEF.VYQHQVVANCRALSEALT.LGYK.V..G.......LVDL.S.KG.DG.RAEKVLEACSIACNKNT
RetrocopyTLEFEVYQHQVVANCRALSEALTQLGYKTVR>GSDNHFI-LVDLHSIKGADGRRAEKVLEACSIACNKNT
ParentalCPGDRSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQ
		CP.DRS.LRPSGLRLGTPALTS.GLLEK.FQKVAHFIH.GIELTLQI.S..G.R.TLKEFKER.AG.KYQ
RetrocopyCPDDRSTLRPSGLRLGTPALTSLGLLEKGFQKVAHFIHGGIELTLQI*SNAGIRTTLKEFKERPAGHKYQ
ParentalGAVQALREKVESFA-SLFPLPGLPDF
		G.VQAL.E.VESF..SLFPLPGLPDF
RetrocopyGGVQALQEEVESFT<SLFPLPGLPDF

							

							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_prefrontal_cortex	0 .06 RPM	3 .15 RPM
SRP007412_cerebellum	0 .00 RPM	9 .24 RPM
SRP007412_heart	0 .03 RPM	1 .26 RPM
SRP007412_kidney	0 .03 RPM	191 .99 RPM
SRP007412_liver	0 .03 RPM	436 .75 RPM

ChIP-Seq - click to see more details

Pongo abelii was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_pabe_333 retrocopy.

TSS - click to see more details

Pongo abelii was not studied using FANTOM5 data.

Lab - click to see more details

retro_pabe_333 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_pabe_333 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Macaca mulatta	retro_mmul_487

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000013535	1 retrocopy	retro_mmul_487,
Pongo abelii	ENSPPYG00000008051	1 retrocopy	retro_pabe_333 ,

	RetrogeneDB ID:	retro_pabe_333
Retrocopy location	Organism:	*Orangutan (Pongo abelii)*
	Coordinates:	1:186058554..186059666(+)
	Located in intron of:	ENSPPYG00000001440
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	SHMT1
	Ensembl ID:	ENSPPYG00000008051
	Aliases:	None
	Description:	serine hydroxymethyltransferase, cytosolic [Source:RefSeq peptide;Acc:NP_001124622]

Parental	GVNVQPYSGSPANFAVYTALVEPHGRIMGLDLPDGGHLTHGFMTDKKKISATSIFFESMPYKVNPDTGYI
	G.........P......TALVEPHG.IMGLDLPDGGHLTHGFMTDKKKISATSIF.ESMPY.VNPDTGYI
Retrocopy	GGSTSSLAQAPLQTLSVTALVEPHGCIMGLDLPDGGHLTHGFMTDKKKISATSIF-ESMPYEVNPDTGYI

Parental	NYDQLEENARLFHPKLIIAGTSCYSRNLDYARLRKIADENGAYLMADMAHISGLVAAGVVPSPFE-HCHV
	NYDQLEENARLFHPKLI.AGTSC.S.NLDYAR..K.ADENG.YLM.D.AHIS.LV.AG.VPSPF..HCHV
Retrocopy	NYDQLEENARLFHPKLITAGTSCSS*NLDYARCGKTADENGLYLMVDTAHISRLVEAGMVPSPFN<HCHV

Parental	VTTTTHKTLRGCRAGMIFYRKGVQSVDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALKQAM
	VTTTT.K.LRGC..GMIFYRKGVQS.DPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVAL.QAM
Retrocopy	VTTTTDKNLRGCQVGMIFYRKGVQSMDPKTGKEILYNLESLINSAVFPGLQGGPHNHAIAGVAVALRQAM

Parental	TLEFKVYQHQVVANCRALSEALTELGYKIVT-GGSDNHLILVDLRS-KGTDGGRAEKVLEACSIACNKNT
	TLEF.VYQHQVVANCRALSEALT.LGYK.V..G.......LVDL.S.KG.DG.RAEKVLEACSIACNKNT
Retrocopy	TLEFEVYQHQVVANCRALSEALTQLGYKTVR>GSDNHFI-LVDLHSIKGADGRRAEKVLEACSIACNKNT

Parental	CPGDRSALRPSGLRLGTPALTSRGLLEKDFQKVAHFIHRGIELTLQIQSDTGVRATLKEFKERLAGDKYQ
	CP.DRS.LRPSGLRLGTPALTS.GLLEK.FQKVAHFIH.GIELTLQI.S..G.R.TLKEFKER.AG.KYQ
Retrocopy	CPDDRSTLRPSGLRLGTPALTSLGLLEKGFQKVAHFIHGGIELTLQI*SNAGIRTTLKEFKERPAGHKYQ

Parental	GAVQALREKVESFA-SLFPLPGLPDF
	G.VQAL.E.VESF..SLFPLPGLPDF
Retrocopy	GGVQALQEEVESFT<SLFPLPGLPDF

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

RetrogeneDB ID:

retro_pabe_333