RetrogeneDB - Retrocopy retro_pvam

						
>retro_pvam_227
GAGCCTGAGAAGGATCTGTACAGCTGCCACAAGAAGCTACAGTAAGAGCTGGAGTTCCTGGAGGTGCAGGAGGAGTACAT

CAAGGATGAGCAGAAGAACCTGAAGAAGGAATTCCTCCACGCCCAGGAGGAGGTGAAGCGAATCCAGAGCATCCCGCTAG

TTATTGGGCAGTTTCTGGAGGCTGTGGATCAGAATACAGCTATAGTGGGCTCCACCACAGGCTCCAATTACTACATGCAC

ATCCTGAGCGCCATTGATGGGGAGCTACTCGAGCCCAGTGCTTTGGTGGCCCTCCACAAGCACAGCAATGCCCTGATGGA

TGTGCTGCCTCCTGAGGCCGACAGTAGCATCATGATGCTCACCTCAGACCAGAAGCTAGGTGTGATGTATGCAGACATCA

GGGGCATGGCCATCCAGAAGCAGGAGGTGCAGGAGGCTATGGAGCTTCTGCTTTATGCACTTTGAGCTGTATAAGCAGAT

TGGCATCAATCCCCCCACGAGGCGTCCTCATGTATGGCCTACCTGGCTGTGGGAAGACCATGCTGGCAAAGGCTGTGGCT

CATCACACCACCACTGCATTTAACCAGTTTGGGGGCTCGGAGTTCGTACAGAAGTACCTGGGCAAGGGCCCCCGCATGGT

CCAGGAAGTGTTCCGCCTGGCCAAGGAGAACACACCTGCCATCATCCTCATAGATGAGATCGATGCCATCGCCACCATGA

GATTTGATGCCCAGACAGGGACTGACAGGGAGGTTCAGAGAATCCTGCTGGAGCTGCTGAATCAAATGGACGGCTTCAAC

CAGAACATCAATGTCAAGGTGATCATGACCACAAACCGAGCAGACACCCTGGATCCTGCCCTGCTGTGGCCAGGACACCT

TGACCGTAAAATTAAATTTCCACTCCCTGACCCCCGCCAAAAGAGACTGATTTTCTCTACTATCACCAGCAAGATGAATC

TCTCTGAGGAGGGTGACTTGGAAGGTTATGTGGCCCAGCCAGATAAGATTTCAGGGGCTGCTATCAACTCAATCTGTCAG

GAGAGTGGAATGTTGGCCATCGGAGAGAACTGCTACATTGTTCTGGCCGAGGACTTCAAGAAAGCATACAGGACAGTCAT

CAAGAAGGATGAATAGGAGCCTGAGTTTTATAAG

ORF - retro_pvam_227 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	85.31 %
Parental protein coverage:	92.34 %
Number of stop codons detected:	2
Number of frameshifts detected	2

Retrocopy - Parental Gene Alignment:

									ParentalEPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI
		EPE...DLYS..KKLQ.ELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI
RetrocopyEPE--KDLYSCHKKLQ*ELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI
ParentalVGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDI
		VGSTTGSNYY..ILS.ID.ELL.P.A.VALHKHSNAL.DVLPPEADSSIMMLTSDQK..VMYADI.GM.I
RetrocopyVGSTTGSNYYMHILSAIDGELLEPSALVALHKHSNALMDVLPPEADSSIMMLTSDQKLGVMYADIRGMAI
ParentalQKQEVREAVELPL-THFELYKQIGIDPP-RGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
		QKQEV.EA.EL.L..HFELYKQIGI.PP.RGVLMYG.PGCGKTMLAKAVAHHTT.AF....GSEFVQKYL
RetrocopyQKQEVQEAMELLL>MHFELYKQIGINPP>RGVLMYGLPGCGKTMLAKAVAHHTTTAFNQFGGSEFVQKYL
ParentalGEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNVKVIMA
		G.GPRMV..VFRLAKEN.PAII.IDEIDAIAT.RFDAQTG.DREVQRILLELLNQMDGF.QN.NVKVIM.
RetrocopyGKGPRMVQEVFRLAKENTPAIILIDEIDAIATMRFDAQTGTDREVQRILLELLNQMDGFNQNINVKVIMT
ParentalTNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQ
		TNRADTLDPALL.PG.LDRKI.FPLPD.RQKRLIFSTITSKMNLSEE.DLE.YVA.PDKISGA.INSICQ
RetrocopyTNRADTLDPALLWPGHLDRKIKFPLPDPRQKRLIFSTITSKMNLSEEGDLEGYVAQPDKISGAAINSICQ
ParentalESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK
		ESGMLA..EN.YIVLA.DF.KAY.TVIKKDE.E.EFYK
RetrocopyESGMLAIGENCYIVLAEDFKKAYRTVIKKDE*EPEFYK

							

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

						

RNA-Seq - click to see more details

Pteropus vampyrus was not studied using RNA-Seq expression data.

ChIP-Seq - click to see more details

Pteropus vampyrus was not studied using ChIP-Seq data.

EST - click to see more details

Pteropus vampyrus was not studied using EST data.

TSS - click to see more details

Pteropus vampyrus was not studied using FANTOM5 data.

Lab - click to see more details

retro_pvam_227 was not experimentally validated.

Retrocopy orthology:

Pteropus vampyrus 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000004372	1 retrocopy	retro_pvam_227 ,
Rattus norvegicus	ENSRNOG00000018994	2 retrocopies	retro_rnor_1952, retro_rnor_2414,

	RetrogeneDB ID:	retro_pvam_227
Retrocopy location	Organism:	*Megabat (Pteropus vampyrus)*
	Coordinates:	GeneScaffold_2038:216867..218021(+)
	Located in intron of:	None
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	PSMC4
	Ensembl ID:	ENSPVAG00000004372
	Aliases:	None
	Description:	proteasome (prosome, macropain) 26S subunit, ATPase, 4 [Source:HGNC Symbol;Acc:9551]

Parental	EPEDLEDLYSRYKKLQQELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI
	EPE...DLYS..KKLQ.ELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI
Retrocopy	EPE--KDLYSCHKKLQ*ELEFLEVQEEYIKDEQKNLKKEFLHAQEEVKRIQSIPLVIGQFLEAVDQNTAI

Parental	VGSTTGSNYYVRILSTIDRELLKPNASVALHKHSNALVDVLPPEADSSIMMLTSDQKPDVMYADIGGMDI
	VGSTTGSNYY..ILS.ID.ELL.P.A.VALHKHSNAL.DVLPPEADSSIMMLTSDQK..VMYADI.GM.I
Retrocopy	VGSTTGSNYYMHILSAIDGELLEPSALVALHKHSNALMDVLPPEADSSIMMLTSDQKLGVMYADIRGMAI

Parental	QKQEVREAVELPL-THFELYKQIGIDPP-RGVLMYGPPGCGKTMLAKAVAHHTTAAFIRVVGSEFVQKYL
	QKQEV.EA.EL.L..HFELYKQIGI.PP.RGVLMYG.PGCGKTMLAKAVAHHTT.AF....GSEFVQKYL
Retrocopy	QKQEVQEAMELLL>MHFELYKQIGINPP>RGVLMYGLPGCGKTMLAKAVAHHTTTAFNQFGGSEFVQKYL

Parental	GEGPRMVRDVFRLAKENAPAIIFIDEIDAIATKRFDAQTGADREVQRILLELLNQMDGFDQNVNVKVIMA
	G.GPRMV..VFRLAKEN.PAII.IDEIDAIAT.RFDAQTG.DREVQRILLELLNQMDGF.QN.NVKVIM.
Retrocopy	GKGPRMVQEVFRLAKENTPAIILIDEIDAIATMRFDAQTGTDREVQRILLELLNQMDGFNQNINVKVIMT

Parental	TNRADTLDPALLRPGRLDRKIEFPLPDRRQKRLIFSTITSKMNLSEEVDLEDYVARPDKISGADINSICQ
	TNRADTLDPALL.PG.LDRKI.FPLPD.RQKRLIFSTITSKMNLSEE.DLE.YVA.PDKISGA.INSICQ
Retrocopy	TNRADTLDPALLWPGHLDRKIKFPLPDPRQKRLIFSTITSKMNLSEEGDLEGYVAQPDKISGAAINSICQ

Parental	ESGMLAVRENRYIVLAKDFEKAYKTVIKKDEQEHEFYK
	ESGMLA..EN.YIVLA.DF.KAY.TVIKKDE.E.EFYK
Retrocopy	ESGMLAIGENCYIVLAEDFKKAYRTVIKKDE*EPEFYK

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

RetrogeneDB ID:

retro_pvam_227