RetrogeneDB - Retrocopy retro_ggor

						
>retro_ggor_2937
ATCTGTACCATGGGCGCCAATGCTTCGGCATTAGAGAAAGAGATTGGTCCAGAACAGTTTCCGGTCAACGAGCATTATTT

TGGATTAGTCAATTTTGGGAATACCTGCTACTGCAATTCAGTTCTTCAAGCACTTTATTTTTGTCGTCCGTTTCGGGAAA

AAGTTCTTGCATATAAGAGTCAACCTAGGAAAAAGGAGAGCCTTCTTACATGCTTAGCAGATCTCTTCCACAGCATAGCC

ACTCAGAAGAAAAAGGTTGGAGTAATACCTCCTAAGAAGTTCATCACAAGATTACAGAAAGAAAATGAGCTTTTCGACAA

CTACATGCAACAAGATGCCCGTGAATTCTTAAATTACCTGCTAAATACAATTGGTGATATTTTACAAGAAGAGAGAAAGC

AGGAAAAACAAAATGTTCGCTAACCTAATGATAATATTGATAATGAAAATAATAGCAGCACACCAGACCCAGCGTGGGTT

CATGAGATTTTTCGGGGAACATTAACTAATGAAACCAGACGTCTTACTTGTGAAACTATAAGCAGCAAAGATGAAGATTT

TTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATTACTCACTGCTTAAGGGGTTTCAGCAACACAGAAACTCTA

TGCAGTGAATACAAGTATTACTGTGAAGAGTGTCGCAGCAAACAGGAAGCACACAAACGGATGAAAGTTTAAAAACTGCC

CATGATTCTAGCTCTACACTTGAAGAGATTTAAATATATGGATCAACTTCATCGATATACAAAACTCTCTTACCGGGTGG

TTTTTCCTTTAGAACTTCGTCTATCTAACACTTCAGGTGATGCCACCAATCCAGATAGAATCTACAACCTTGTTGCTGTT

GTGGTTCACTGTGGAAGTGGTCCCAATCGAGGCCATTATATTGCGCTGGTTAAGAGTCATGATTTTGGGTTGTTGTTTGA

TGACGACATTGTAGAAAAAATAGATACACAAGCTATTGAAGAATTCTACGGGTTGACATCAGATACTCAAAGAACTCTGA

GTCTGGTTACATCCTTTTCTATCAGTCTCGGGAC

ORF - retro_ggor_2937 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	83.06 %
Parental protein coverage:	97.55 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalLCYPGTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQALYFCRPFRENVLAYKAQQKKKENLLT
		.C..G.NASALEK.IGPEQFP.NEHYFGLVNFGNTCYCNSVLQALYFCRPFRE.VLAYK.Q..KKE.LLT
RetrocopyICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLT
ParentalCLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDAHEFLNYLLNTIADILQEEKKQEKQNGK
		CLADLFHSIATQKKKVGVIPPKKFI.RL.KEN.LFDNYMQQDA.EFLNYLLNTI.DILQEE.KQEKQN..
RetrocopyCLADLFHSIATQKKKVGVIPPKKFITRLQKENELFDNYMQQDAREFLNYLLNTIGDILQEERKQEKQNVR
ParentalLKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSSKDED-FLDLSVDVEQNTSITHCLRDFSN
		..N.N.........P...WVHEIF.GTLTNETR.L.CET.SSKDED.FLDLSVDVEQNTSITHCLR.FSN
Retrocopy*PNDNIDNENNSSTPDPAWVHEIFRGTLTNETRRLTCETISSKDED>FLDLSVDVEQNTSITHCLRGFSN
ParentalTETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLKRFKYMEQLHRYTKLSYRVVFPLELRLFNTSS
		TETLCSE.KYYCE.C.SKQEA.KRM.V.KLPMILALHLKRFKYM.QLHRYTKLSYRVVFPLELRL.NTS.
RetrocopyTETLCSEYKYYCEECRSKQEAHKRMKV*KLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLSNTSG
ParentalDAVNLDRMYDLVAVVVHCGSGPNRGHYITIVKSHGFWLLFDDDIVEKIDAQAIEEFYGLTSD-ISKNSES
		DA.N.DR.Y.LVAVVVHCGSGPNRGHYI..VKSH.F.LLFDDDIVEKID.QAIEEFYGLTSD..SKNSES
RetrocopyDATNPDRIYNLVAVVVHCGSGPNRGHYIALVKSHDFGLLFDDDIVEKIDTQAIEEFYGLTSD<YSKNSES
ParentalGYILFYQSRE
		GYILFYQSR.
RetrocopyGYILFYQSRD

							

							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	2 .45 RPM	52 .17 RPM
SRP007412_cerebellum	1 .42 RPM	41 .33 RPM
SRP007412_heart	0 .34 RPM	10 .38 RPM
SRP007412_kidney	2 .86 RPM	25 .64 RPM
SRP007412_liver	0 .87 RPM	6 .86 RPM
SRP007412_testis	2 .80 RPM	26 .31 RPM

ChIP-Seq - click to see more details

Gorilla gorilla was not studied using ChIP-Seq data.

EST - click to see more details

Gorilla gorilla was not studied using EST data.

TSS - click to see more details

Gorilla gorilla was not studied using FANTOM5 data.

Lab - click to see more details

retro_ggor_2937 was not experimentally validated.

Retrocopy orthology:

Retrocopy retro_ggor_2937 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_4726
Homo sapiens	retro_hsap_4918
Pan troglodytes	retro_ptro_3143
Pongo abelii	retro_pabe_3672

Parental genes homology:

Parental genes homology involve 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007660	1 retrocopy	retro_cpor_1157,
Gorilla gorilla	ENSGGOG00000017197	3 retrocopies	retro_ggor_1767, retro_ggor_2223, retro_ggor_2937 ,

	RetrogeneDB ID:	retro_ggor_2937
Retrocopy location	Organism:	*Gorilla (Gorilla gorilla)*
	Coordinates:	X:87235624..87236698(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	USP46
	Ensembl ID:	ENSGGOG00000017197
	Aliases:	None
	Description:	Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G3RLX0]

Parental	LCYPGTNASALEKDIGPEQFPINEHYFGLVNFGNTCYCNSVLQALYFCRPFRENVLAYKAQQKKKENLLT
	.C..G.NASALEK.IGPEQFP.NEHYFGLVNFGNTCYCNSVLQALYFCRPFRE.VLAYK.Q..KKE.LLT
Retrocopy	ICTMGANASALEKEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLT

Parental	CLADLFHSIATQKKKVGVIPPKKFISRLRKENDLFDNYMQQDAHEFLNYLLNTIADILQEEKKQEKQNGK
	CLADLFHSIATQKKKVGVIPPKKFI.RL.KEN.LFDNYMQQDA.EFLNYLLNTI.DILQEE.KQEKQN..
Retrocopy	CLADLFHSIATQKKKVGVIPPKKFITRLQKENELFDNYMQQDAREFLNYLLNTIGDILQEERKQEKQNVR

Parental	LKNGNMNEPAENNKPELTWVHEIFQGTLTNETRCLNCETVSSKDED-FLDLSVDVEQNTSITHCLRDFSN
	..N.N.........P...WVHEIF.GTLTNETR.L.CET.SSKDED.FLDLSVDVEQNTSITHCLR.FSN
Retrocopy	*PNDNIDNENNSSTPDPAWVHEIFRGTLTNETRRLTCETISSKDED>FLDLSVDVEQNTSITHCLRGFSN

Parental	TETLCSEQKYYCETCCSKQEAQKRMRVKKLPMILALHLKRFKYMEQLHRYTKLSYRVVFPLELRLFNTSS
	TETLCSE.KYYCE.C.SKQEA.KRM.V.KLPMILALHLKRFKYM.QLHRYTKLSYRVVFPLELRL.NTS.
Retrocopy	TETLCSEYKYYCEECRSKQEAHKRMKV*KLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLSNTSG

Parental	DAVNLDRMYDLVAVVVHCGSGPNRGHYITIVKSHGFWLLFDDDIVEKIDAQAIEEFYGLTSD-ISKNSES
	DA.N.DR.Y.LVAVVVHCGSGPNRGHYI..VKSH.F.LLFDDDIVEKID.QAIEEFYGLTSD..SKNSES
Retrocopy	DATNPDRIYNLVAVVVHCGSGPNRGHYIALVKSHDFGLLFDDDIVEKIDTQAIEEFYGLTSD<YSKNSES

Parental	GYILFYQSRE
	GYILFYQSR.
Retrocopy	GYILFYQSRD

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

RetrogeneDB ID:

retro_ggor_2937