RetrogeneDB - Retrocopy retro_vpac

                        
>retro_vpac_127
AGCGATCTCGGCGAGCAAGCGGCGGAGCTGCGCCTCGGCCCGCTTTTCTCCCTGCTCAACGAGAACCCCTGGTAACAGAC

TACTTTGTGCGTATCCATCCTGGAGAGGTTGCTCCAAGCTTTGGACCCAGTTCACGTGGCCCGGAACTTCAGGAGTGACC

TGCAGAGGGGACTGACTCATCCCAATGATTCTGTGAAACTCCTTACTCTGTCCCAGGTTGGAAGAATTGTTGAAAATTCT

GATGCTGTTACTGACATTGTAAATAATGCTGAATTGCTAAAACAAATCGTTTGTTGTATTGGTGGCAAGAATCTATCTGT

AGCTAAAGCAGCCATTAAATCCCTGTCAAGAATGTCACTGACCCAAGCTGGCCTGGAGGCTTGCTTTGAAAGTAATCTGC

TGGATGATTTGAAAAGTGTAATGAAAACAAATGACATTGTTCGATACAGGGTGTATGAGCTAATTGTGGAGATTTCTTTT

GTGTCCCCAGAATCTTTAAAACTACTGTACCACCAGTGGATTGGTAACCCAGCTCCTTAAGGAACTGACTGATGAGGATG

TGCTGGTCAGAGCCACCTGTATAGAGATGGTGACATCACTGGCATGTACTCATTATGGACGACAGTACCTTGCTCGGGAA

GGAGTAATTGATCAGATTTCTAACATAATTGTGGGGGCCGATTCAGACCCTTTCGCTAGCTTCTATTTGCCAGGATTTGT

GAAGTTTTTTGGAAACCTAGCTATCATGGATAGCCCTCAACAGGTCTGTGAGCGTTATCCTTTTTTGTGGAAAAAGTCTT

TGAAATAAAGTCAGGACCCCACCATGAGTGGTGTAGCAGTGGACATGATTGGAATTCTGGGATCCAATGTTGAAGGAAAA

CAGGTTTTACAGAAAACAGGAACTCGCTTTGAACGCTTGCTCATGAGAATGGGATATCAAGCAAAGAAGCCTCAGTAGAG

CTCAAAATTAGGTGTTTGGATGCAGTTTCATCTCTTTTTTATTTACCGCCTGAGCAGCAGACTGATGACCTTAGGATGGC

AGAATCCTGGTTTTCTTCTTTATCTCGGGACCCACTGGAGCTCTTCCGTGGCATCAGCAATCAACCCTTCCCTGAACTAC

GCTGTGCTGCCCTGAAAGTGTTCACG

ORF - retro_vpac_127 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	87.86 %
Parental protein coverage:	76.39 %
Number of stop codons detected:	2
Number of frameshifts detected:	2

Retrocopy - Parental Gene Alignment:

                                ParentalSELRWDPLELHLGPLFSLLTYNHREQTTLCVSILERLLQALEPVHMARNLRSDLQRGLTHPNDSVKILTL
S.L.....EL.LGPLFSLL..N...QTTLCVSILERLLQAL.PVH.ARN.RSDLQRGLTHPNDSVK.LTL
RetrocopySDLGEQAAELRLGPLFSLLNENPW*QTTLCVSILERLLQALDPVHVARNFRSDLQRGLTHPNDSVKLLTL
ParentalSQVGRIVENSDAVTEILNNAELLKQIVYCIGGENLSVAKAAIKSLSRISLTQAGLEALFESNLLDDLKNV
SQVGRIVENSDAVT.I.NNAELLKQIV.CIGG.NLSVAKAAIKSLSR.SLTQAGLEA.FESNLLDDLK.V
RetrocopySQVGRIVENSDAVTDIVNNAELLKQIVCCIGGKNLSVAKAAIKSLSRMSLTQAGLEACFESNLLDDLKSV
ParentalMKTNDIVRYRVYELIVEISSVSPESL-NYCTTSGLVTQLLKELTGEDVLVRATCIEMVTSLACTHHGRQY
MKTNDIVRYRVYELIVEIS.VSPESL.NYCTTSGLVTQLLKELT.EDVLVRATCIEMVTSLACTH.GRQY
RetrocopyMKTNDIVRYRVYELIVEISFVSPESL>NYCTTSGLVTQLLKELTDEDVLVRATCIEMVTSLACTHYGRQY
ParentalLAQEGVIDQISNIIVGADSDPFSSFYLPGFVKFFGNLAIMDSPQQVCERYPVFVEKVFEMMESQDPTMIG
LA.EGVIDQISNIIVGADSDPF.SFYLPGFVKFFGNLAIMDSPQQVCERYP....K......SQDPTM.G
RetrocopyLAREGVIDQISNIIVGADSDPFASFYLPGFVKFFGNLAIMDSPQQVCERYPFLWKK--SLK*SQDPTMSG
ParentalVAVDTIGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK-NASTELKIRCLDAISSLFYLPPEQQTDDLLR
VAVD.IGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK..AS.ELKIRCLDA.SSLFYLPPEQQTDD.LR
RetrocopyVAVDMIGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK<EASVELKIRCLDAVSSLFYLPPEQQTDD-LR
ParentalMAESWFSSLSRDPLELFRGISNQPFPELHCAALKVFT
MAESWFSSLSRDPLELFRGISNQPFPEL.CAALKVFT
RetrocopyMAESWFSSLSRDPLELFRGISNQPFPELRCAALKVFT

                            

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

                        

RNA-Seq - click to see more details

Vicugna pacos was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Vicugna pacos was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_vpac_127 retrocopy.

TSS - click to see more details

Vicugna pacos was not studied using FANTOM5 data.

Lab - click to see more details

retro_vpac_127 was not experimentally validated.

Retrocopy orthology:

Vicugna pacos does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Monodelphis domestica	ENSMODG00000019635	1 retrocopy	retro_mdom_1523,
Vicugna pacos	ENSVPAG00000012577	1 retrocopy	retro_vpac_127 ,

	RetrogeneDB ID:	retro_vpac_127
Retrocopy location	Organism:	*Alpaca (Vicugna pacos)*
	Coordinates:	GeneScaffold_1966:1232410..1233556(-)
	Located in intron of:	ENSVPAG00000003118
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PSMD5
	Ensembl ID:	ENSVPAG00000012577
	Aliases:	None
	Description:	proteasome (prosome, macropain) 26S subunit, non-ATPase, 5 [Source:HGNC Symbol;Acc:9563]

Parental	SELRWDPLELHLGPLFSLLTYNHREQTTLCVSILERLLQALEPVHMARNLRSDLQRGLTHPNDSVKILTL
	S.L.....EL.LGPLFSLL..N...QTTLCVSILERLLQAL.PVH.ARN.RSDLQRGLTHPNDSVK.LTL
Retrocopy	SDLGEQAAELRLGPLFSLLNENPW*QTTLCVSILERLLQALDPVHVARNFRSDLQRGLTHPNDSVKLLTL

Parental	SQVGRIVENSDAVTEILNNAELLKQIVYCIGGENLSVAKAAIKSLSRISLTQAGLEALFESNLLDDLKNV
	SQVGRIVENSDAVT.I.NNAELLKQIV.CIGG.NLSVAKAAIKSLSR.SLTQAGLEA.FESNLLDDLK.V
Retrocopy	SQVGRIVENSDAVTDIVNNAELLKQIVCCIGGKNLSVAKAAIKSLSRMSLTQAGLEACFESNLLDDLKSV

Parental	MKTNDIVRYRVYELIVEISSVSPESL-NYCTTSGLVTQLLKELTGEDVLVRATCIEMVTSLACTHHGRQY
	MKTNDIVRYRVYELIVEIS.VSPESL.NYCTTSGLVTQLLKELT.EDVLVRATCIEMVTSLACTH.GRQY
Retrocopy	MKTNDIVRYRVYELIVEISFVSPESL>NYCTTSGLVTQLLKELTDEDVLVRATCIEMVTSLACTHYGRQY

Parental	LAQEGVIDQISNIIVGADSDPFSSFYLPGFVKFFGNLAIMDSPQQVCERYPVFVEKVFEMMESQDPTMIG
	LA.EGVIDQISNIIVGADSDPF.SFYLPGFVKFFGNLAIMDSPQQVCERYP....K......SQDPTM.G
Retrocopy	LAREGVIDQISNIIVGADSDPFASFYLPGFVKFFGNLAIMDSPQQVCERYPFLWKK--SLK*SQDPTMSG

Parental	VAVDTIGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK-NASTELKIRCLDAISSLFYLPPEQQTDDLLR
	VAVD.IGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK..AS.ELKIRCLDA.SSLFYLPPEQQTDD.LR
Retrocopy	VAVDMIGILGSNVEGKQVLQKTGTRFERLLMRMGYQAK<EASVELKIRCLDAVSSLFYLPPEQQTDD-LR

Parental	MAESWFSSLSRDPLELFRGISNQPFPELHCAALKVFT
	MAESWFSSLSRDPLELFRGISNQPFPEL.CAALKVFT
Retrocopy	MAESWFSSLSRDPLELFRGISNQPFPELRCAALKVFT

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

RetrogeneDB ID:

retro_vpac_127