RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_2261
ATGGCCTCCAAAACTTCTCCGCATCTCAGGGCACCCCCCCAACTGTCTGTGGATCTGGAGGCCTGGCATCTATGAGGATG

ACAAGGGGAGGACCTGGGTGACTGTGGTTGTGCGCCTCAGTCCCCTGCACAGAGAAAGGGCCAGGTGCTCAAGCTCCCAG

GGCAGCACATATGAACCTAGCATCACAGTGCACATGTGGTAGATGCCAGTGCACACCCGGGAGCCACTGTCCCCCAGCCA

GCTGCCCTTCTCCCACCTGCTCCCTGTGTGGCAGCTCTACCCCAAGAGGAGGTATCAAGCAGCAAATTCCAGTTTCTGGG

AAATAGTGGACCAGATCATCTCCATGGAGCAGCTGGTCCTAACATATTGGCCGGCAAGGAATAAC

ORF - retro_ptro_2261 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	68.7 %
Parental protein coverage:	100. %
Number of stop codons detected:	1
Number of frameshifts detected	1

Retrocopy - Parental Gene Alignment:

									ParentalMASEASVRL-GVPPGRLWIQRPGIYEDEEGRTWVTVVVRFNPSHREWAR--ASQGSRYEPSITVHLWQMA
		MAS..S..L.G.PP..LWI.RPGIYED..GRTWVTVVVR..P.HRE.AR...SQGS.YEPSITVH.W.M.
RetrocopyMASKTSPHL>GHPPNCLWIWRPGIYEDDKGRTWVTVVVRLSPLHRERARCSSSQGSTYEPSITVHMW*MP
ParentalVHTRELLSSGQMPFSQLPAVWQLYPGRKYRAADSSFWEIADHGQIDSMEQLVLTYQPERKD
		VHTRE.LS..Q.PFS.L..VWQLYP.R.Y.AA.SSFWEI.D..QI.SMEQLVLTY.P.R..
RetrocopyVHTREPLSPSQLPFSHLLPVWQLYPKRRYQAANSSFWEIVD--QIISMEQLVLTYWPARNN

							

							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 .02 RPM	0 .00 RPM
SRP007412_cerebellum	0 .07 RPM	0 .00 RPM
SRP007412_heart	0 .00 RPM	0 .00 RPM
SRP007412_kidney	0 .08 RPM	1 .99 RPM
SRP007412_liver	0 .00 RPM	0 .03 RPM
SRP007412_testis	0 .11 RPM	0 .11 RPM

ChIP-Seq - click to see more details

Pan troglodytes was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ptro_2261 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_2261 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_2261 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3183
Pongo abelii	retro_pabe_2642

Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000213231	1 retrocopy	retro_hsap_3183,
Gorilla gorilla	ENSGGOG00000013671	1 retrocopy	retro_ggor_1341,
Mus musculus	ENSMUSG00000060863	2 retrocopies	retro_mmus_1150, retro_mmus_1605,
Nomascus leucogenys	ENSNLEG00000000495	1 retrocopy	retro_nleu_1660,
Pongo abelii	ENSPPYG00000006118	1 retrocopy	retro_pabe_2642,
Pan troglodytes	ENSPTRG00000006694	1 retrocopy	retro_ptro_2261 ,

	RetrogeneDB ID:	retro_ptro_2261
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	5:49303232..49303617(-)
	Located in intron of:	ENSPTRG00000016935
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TCL1B
	Ensembl ID:	ENSPTRG00000006694
	Aliases:	None
	Description:	T-cell leukemia/lymphoma 1B [Source:HGNC Symbol;Acc:11649]

Parental	MASEASVRL-GVPPGRLWIQRPGIYEDEEGRTWVTVVVRFNPSHREWAR--ASQGSRYEPSITVHLWQMA
	MAS..S..L.G.PP..LWI.RPGIYED..GRTWVTVVVR..P.HRE.AR...SQGS.YEPSITVH.W.M.
Retrocopy	MASKTSPHL>GHPPNCLWIWRPGIYEDDKGRTWVTVVVRLSPLHRERARCSSSQGSTYEPSITVHMW*MP

Parental	VHTRELLSSGQMPFSQLPAVWQLYPGRKYRAADSSFWEIADHGQIDSMEQLVLTYQPERKD
	VHTRE.LS..Q.PFS.L..VWQLYP.R.Y.AA.SSFWEI.D..QI.SMEQLVLTY.P.R..
Retrocopy	VHTREPLSPSQLPFSHLLPVWQLYPKRRYQAANSSFWEIVD--QIISMEQLVLTYWPARNN

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

RetrogeneDB ID:

retro_ptro_2261