RetrogeneDB - Retrocopy retro_ptro

						
>retro_ptro_1422
ACTGGAGCTGGACAAGGTGGACATTCTGACCTGAAGGGTGGCTCTGGGGGACAGGAGTGCTGGCCATGGGAGCAGGAGAG

GCTGCACATTTTGCTGCTTATGCTTTTGCACCTGCCATCTTGGTCACCCTCATCCCCCCGGCCCTCTGAGTGTTCTCATA

AGTGCAATATTATCTTCCTGTTTTTTAAACGAGCACTTGAACATTTATGGGAAAACAGGCTGCATATTGGGGTCAACTGT

GATGGTTATCCATGCCCCAGAAGAAGAGGAAGTCACTTCTTTGCATGAAATGGAAATGAAATTGAGAGACCCAGGATTTA

TTTCCTTTGCTGTGATCATAATTGTGATCTTGGTGCTGATTTTGATTGTGGCTCCCAAGAAAGGACAGACCAATATATTG

GTCTATATTTCAATCTGTTCATTTCCAGTTTCTCCTGCCAAAGGCCTGGGTATTGCCATTAAGGAATTACTAGAATGGAA

GCCAGTTTAGAAGCATCCCCTGGTCATTGTTTTGCTGGCTATACTTGTGTTTTTGGTGACTACACAGATTAACTATCTCA

AGGCACCAGACACCGTGAATACATCTCCTGTGACTCCCATTTATTTTGCGTTCTTCACATCCATGGTAGTGACTTGCTCT

GCCATCTTACTCCAAGAGTGGTATGGCATGAAAGCTGGAGATATCATCGAGACCCTGAATGGATTCTTCACTATTATCCT

TGGCATCTTTCTTCTACATGCTTTTAAAAATACTGACATTACCTGGAGTAAGCTGACATCCACTGCTAAGAAAGAAGTCA

TCTCTCTGAATGGCAATGAGAGCAGTCCTGTTTTACTAGAGAACTTGGAGTGTTCAGCCCTGGATACAATGATAACGTTA

CCTTGTTTAGCAGAACTGATGAT

ORF - retro_ptro_1422 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	77.39 %
Parental protein coverage:	75.37 %
Number of stop codons detected:	1
Number of frameshifts detected	3

Retrocopy - Parental Gene Alignment:

									ParentalTRAGQGGHSYLKE-WLWWVGLLSM-GAGEAANFAAYAFAPATL--VTPLGALSVLISAILSSYFLNEHLN
		T.AGQGGHS.LK..WLW..G.L.M.G......F....F....L....P.G.LSVLISAILSS.FLNEHLN
RetrocopyTGAGQGGHSDLKG<WLWGTGVLAM<GSRRGCTFCCLCFCTCHLGHPHPPGPLSVLISAILSSCFLNEHLN
ParentalIHGKIGCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIITVISLVLILIVAPKKGQTNIL
		I.GK.GC...ILGSTVMVIHAP.EEEVTSLHEMEMKLRDPGFISFAVII.VI.LVLILIVAPKKGQTNIL
RetrocopyIYGKTGC---ILGSTVMVIHAPEEEEVTSLHEMEMKLRDPGFISFAVIIIVI-LVLILIVAPKKGQTNIL
ParentalVYISICSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVTTQINYLNKALDTFNTSLVT
		VYISICS....F.VS..KGLGIAIKEL.EWKPV.KHPLV.VLLA.LV..VTTQINYL.KA.DT.NTS.VT
RetrocopyVYISICS----FPVSPAKGLGIAIKELLEWKPV*KHPLVIVLLAILVFLVTTQINYL-KAPDTVNTSPVT
ParentalPIYYVFFTSMVVTCSAILFQEWYGMTAGDIIGTLSGFFTIIIGIFLLHAFKNTDITWSELTSTAKKEAVS
		PIY..FFTSMVVTCSAIL.QEWYGM.AGDII.TL.GFFTII.GIFLLHAFKNTDITWS.LTSTAKKE..S
RetrocopyPIYFAFFTSMVVTCSAILLQEWYGMKAGDIIETLNGFFTIILGIFLLHAFKNTDITWSKLTSTAKKEVIS
ParentalLNVNENNYVLLENLECSA-PGYNDDVTLFSRTDD
		LN.NE...VLLENLECSA.PGYND.VTLFSRTDD
RetrocopyLNGNESSPVLLENLECSA<PGYNDNVTLFSRTDD

							

							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 .54 RPM
SRP007412_cerebellum	0 .00 RPM	0 .50 RPM
SRP007412_heart	0 .00 RPM	0 .29 RPM
SRP007412_kidney	0 .00 RPM	5 .26 RPM
SRP007412_liver	0 .00 RPM	5 .37 RPM
SRP007412_testis	0 .00 RPM	0 .74 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_1422 retrocopy.

TSS - click to see more details

Pan troglodytes was not studied using FANTOM5 data.

Lab - click to see more details

retro_ptro_1422 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ptro_1422 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2463
Gorilla gorilla	retro_ggor_1533

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422 ,

	RetrogeneDB ID:	retro_ptro_1422
Retrocopy location	Organism:	*Chimpanzee (Pan troglodytes)*
	Coordinates:	20:25325609..25326512(-)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	NIPAL1
	Ensembl ID:	ENSPTRG00000016038
	Aliases:	NIPAL1, NPAL1
	Description:	NIPA-like domain containing 1 [Source:HGNC Symbol;Acc:27194]

Parental	TRAGQGGHSYLKE-WLWWVGLLSM-GAGEAANFAAYAFAPATL--VTPLGALSVLISAILSSYFLNEHLN
	T.AGQGGHS.LK..WLW..G.L.M.G......F....F....L....P.G.LSVLISAILSS.FLNEHLN
Retrocopy	TGAGQGGHSDLKG<WLWGTGVLAM<GSRRGCTFCCLCFCTCHLGHPHPPGPLSVLISAILSSCFLNEHLN

Parental	IHGKIGCILSILGSTVMVIHAPQEEEVTSLHEMEMKLRDPGFISFAVIITVISLVLILIVAPKKGQTNIL
	I.GK.GC...ILGSTVMVIHAP.EEEVTSLHEMEMKLRDPGFISFAVII.VI.LVLILIVAPKKGQTNIL
Retrocopy	IYGKTGC---ILGSTVMVIHAPEEEEVTSLHEMEMKLRDPGFISFAVIIIVI-LVLILIVAPKKGQTNIL

Parental	VYISICSLIGAFSVSSVKGLGIAIKELIEWKPVYKHPLVFVLLAVLVLSVTTQINYLNKALDTFNTSLVT
	VYISICS....F.VS..KGLGIAIKEL.EWKPV.KHPLV.VLLA.LV..VTTQINYL.KA.DT.NTS.VT
Retrocopy	VYISICS----FPVSPAKGLGIAIKELLEWKPV*KHPLVIVLLAILVFLVTTQINYL-KAPDTVNTSPVT

Parental	PIYYVFFTSMVVTCSAILFQEWYGMTAGDIIGTLSGFFTIIIGIFLLHAFKNTDITWSELTSTAKKEAVS
	PIY..FFTSMVVTCSAIL.QEWYGM.AGDII.TL.GFFTII.GIFLLHAFKNTDITWS.LTSTAKKE..S
Retrocopy	PIYFAFFTSMVVTCSAILLQEWYGMKAGDIIETLNGFFTIILGIFLLHAFKNTDITWSKLTSTAKKEVIS

Parental	LNVNENNYVLLENLECSA-PGYNDDVTLFSRTDD
	LN.NE...VLLENLECSA.PGYND.VTLFSRTDD
Retrocopy	LNGNESSPVLLENLECSA<PGYNDNVTLFSRTDD

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

RetrogeneDB ID:

retro_ptro_1422