RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1123
GGGCCGCCGCTCGCCGCCAGCGCCAAAAGAAAGGGGCCCCCGGAATTCTCCAGCTACGTACGAGGAGCGCGAGCCCACAG

CCGTCTCGGCTCCGAGCCCGCCGCCGGCAGGAAAGCCACAAAGAAAACTGATAAACCCAGACAAGATGATAAAGACGATC

TAGATGTAACAGAACTCGCTAATGAAGATCCTTTGGATCAGCTTGTGAAATAGGAGTGAATTGTGGTCCTATTGTGGGAA

CAACCAGGAAGCTGTATGAGAAATAGCTTTTGAAACTGAGGGAGCAAGGAACAGAATCAAGATCGTCTCCTTCAGCAACA

ATTTCTTCTTCAGCAGAAAATACAAGGCAGAATGGAAGTAATGATTCTGACAGATATAGTGACAATGAAGAAGACTCTAA

AATAGAGCTCAAGTTTGAGAAGAGAGAACCGCTAAACAGCGGAGTAAAGACTCCAGTAACCCTCAAGCAAAGAAGAGTTG

AGCACAACGAGAGCTATTCTCAAGCTGGAATAACTGGGACTGAATGGACAAGTGGATCTTCAAAAGGCGGACTTCTGCAG

GCATTATTAACTAGGGAATCTACAAGAGGGTCAAGAAGAACTCCAAGCAAAAGGGTGCACACTTCAGAATATTTTCGTAT

AGATGGAGCAGTAATTTCAGCGAGTACTCCCATAGCTGAAACTATAATTGCTTCAAACAACGAATCCTTAATTGTCAATA

GGGTGACTGGAAATTTCAAGCATGCATTTCCTATTCTGCCAGTCACTGAATTCTCAGACATACCCAGAAGAACACCAAAG

AAACCACTGACAAGAGCTGAAGTGGGAGAAAAAAAACACAGGAAAGAAGAGTAGAAAGGGATATTCTTAAGGAAATGTTC

CCCTATGAAGCAACTACACCAACAAGAATTAGTGCTAGTTGCCGCAGAACAATCAAAGGAGCTGCAGGCCGGCCATTAGA

ACTCAGTGATTTGAGGATGGAGGAGTCGTTTTCATCTACATATCTTCCTAAGTATGTTCCCTTGGCAGATGTCAAGTGAG

AA

ORF - retro_ptro_1123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.27 %
Parental protein coverage:	75.55 %
Number of stop codons detected:	3
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalGPPDFSSDEEREPTPVLGS---GAAAAGR--SRAAVGRKATKKTDKPRQEDKDDLDVTELTNEDLLDQLV
		GPP.......R...P...S...GA.A..R..S..A.GRKATKKTDKPRQ.DKDDLDVTEL.NED.LDQLV
RetrocopyGPP-LAASAKRKGPPEFSSYVRGARAHSRLGSEPAAGRKATKKTDKPRQDDKDDLDVTELANEDPLDQLV
ParentalK-YGVNPGPIVGTTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSKIEL
		K..GVN.GPIVGTTRKLYEK.LLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRYSDNEEDSKIEL
RetrocopyK<IGVNCGPIVGTTRKLYEK*LLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYSDNEEDSKIEL
ParentalKLEKREPLKGRAKTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVE
		K.EKREPL....KTPVTLKQRRVEHN.SYSQAGIT.TEWTSGSSKGG.LQA.LTRESTRGSRRTP.KRV.
RetrocopyKFEKREPLNSGVKTPVTLKQRRVEHNESYSQAGITGTEWTSGSSKGGLLQALLTRESTRGSRRTPSKRVH
ParentalTSEHFRIEGPVISESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGE
		TSE.FRI.G.VIS.STPIAETI.AS.NESL.VNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVG.
RetrocopyTSEYFRIDGAVISASTPIAETIIASNNESLIVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGX
ParentalKTEERRVERDI-LKEMFP-YEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPFADVK
		..........I.L....P.YEA.TPT.ISASCRR.IKGAAGRPLELSD.RMEESFSS.Y.PKYVP.ADVK
RetrocopyXXHRKEE*KGIFLRKCSP<YEATTPTRISASCRRTIKGAAGRPLELSDLRMEESFSSTYLPKYVPLADVK
ParentalSE
		.E
Retrocopy*E

							

							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	11 .03 RPM
SRP007412_cerebellum	0 .07 RPM	23 .09 RPM
SRP007412_heart	0 .00 RPM	8 .60 RPM
SRP007412_kidney	0 .03 RPM	19 .69 RPM
SRP007412_liver	0 .03 RPM	18 .69 RPM
SRP007412_testis	6 .53 RPM	48 .69 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_1123 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1123 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1123 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1652
Gorilla gorilla	retro_ggor_1247
Pongo abelii	retro_pabe_1365

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Pongo abelii	ENSPPYG00000004857	1 retrocopy	retro_pabe_1365,
Pan troglodytes	ENSPTRG00000005331	1 retrocopy	retro_ptro_1123 ,

	RetrogeneDB ID:	retro_ptro_1123
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	16:74057967..74059009(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	TMPO
	Ensembl ID:	ENSPTRG00000005331
	Aliases:	None
	Description:	None

Parental	GPPDFSSDEEREPTPVLGS---GAAAAGR--SRAAVGRKATKKTDKPRQEDKDDLDVTELTNEDLLDQLV
	GPP.......R...P...S...GA.A..R..S..A.GRKATKKTDKPRQ.DKDDLDVTEL.NED.LDQLV
Retrocopy	GPP-LAASAKRKGPPEFSSYVRGARAHSRLGSEPAAGRKATKKTDKPRQDDKDDLDVTELANEDPLDQLV

Parental	K-YGVNPGPIVGTTRKLYEKKLLKLREQGTESRSSTPLPTISSSAENTRQNGSNDSDRYSDNEEDSKIEL
	K..GVN.GPIVGTTRKLYEK.LLKLREQGTESRSS.P..TISSSAENTRQNGSNDSDRYSDNEEDSKIEL
Retrocopy	K<IGVNCGPIVGTTRKLYEK*LLKLREQGTESRSS-PSATISSSAENTRQNGSNDSDRYSDNEEDSKIEL

Parental	KLEKREPLKGRAKTPVTLKQRRVEHNQSYSQAGITETEWTSGSSKGGPLQA-LTRESTRGSRRTPRKRVE
	K.EKREPL....KTPVTLKQRRVEHN.SYSQAGIT.TEWTSGSSKGG.LQA.LTRESTRGSRRTP.KRV.
Retrocopy	KFEKREPLNSGVKTPVTLKQRRVEHNESYSQAGITGTEWTSGSSKGGLLQALLTRESTRGSRRTPSKRVH

Parental	TSEHFRIEGPVISESTPIAETIMASSNESLVVNRVTGNFKHASPILPITEFSDIPRRAPKKPLTRAEVGE
	TSE.FRI.G.VIS.STPIAETI.AS.NESL.VNRVTGNFKHA.PILP.TEFSDIPRR.PKKPLTRAEVG.
Retrocopy	TSEYFRIDGAVISASTPIAETIIASNNESLIVNRVTGNFKHAFPILPVTEFSDIPRRTPKKPLTRAEVGX

Parental	KTEERRVERDI-LKEMFP-YEASTPTGISASCRRPIKGAAGRPLELSDFRMEESFSSKYVPKYVPFADVK
	..........I.L....P.YEA.TPT.ISASCRR.IKGAAGRPLELSD.RMEESFSS.Y.PKYVP.ADVK
Retrocopy	XXHRKEE*KGIFLRKCSP<YEATTPTRISASCRRTIKGAAGRPLELSDLRMEESFSSTYLPKYVPLADVK

Parental	SE
	.E
Retrocopy	*E

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

RetrogeneDB ID:

retro_ptro_1123