RetrogeneDB - Retrocopy retro_pvam

                        
>retro_pvam_313
GTGGATGCGCAGAACGAGGGCCTGCCTCACCTGTCACAGGACTCTCCGCGTGGCTCAGTCCACAGCATCCTCATTGCCAA

CACTGCCCCCTAGAGATGCTTCTACCTAGACACAGTCCCTGCACTCGACTTTGCTGCCAGGTGCAAGGAGGTGATCAATC

GACCTTCTACCAGTGAGAGCCTACAGCTTCATGTCTTGGCACCTGTTAAACTGTCTCAGAAAGGACAGCTAGGTCCTTCA

GAGGCAAAGAAAACTCGAGGCCCTGAGGAAGAGGAGATTGGGAATCCTGAGCCCCCCGCACTTCTAGCTTCTGCCTCCCA

GAAATTCAGCCCCCTACAGAAGCTAAGTAGCATGGACCCGGCCATGCTGGAGCGCCTCCTGAGCTTGGACCATTTGCTGG

GCTCCCGGGGAACCTGGGGGACCCCTCTGCTGAGCACCCCAAGACAAGAGTGGATGGTGCTCACGAAGACAGTGGAGGAA

AAGGATTGGAAGACTGAAAGGCTTAAGATAAAGCAAAAAGAACTGGAAGCCAAGGTGCTGGCCCGGGAAGCTGTGGACCC

GAAGGAGAACTGCTCTCCCACGATGCTCCGACCCTTCGCCCGCCGCATAGTCATGGTCGCTAAGCCCCTCGAGAAGGCTG

TGGAGATGCCCCTACAACTAATACAGGAGCAGGCAGCATCCCCAAATGCCGACATCCACACCCTGAAGAAAAGCTGCAAG

AGAAAGCTGGAGTGCCCGGATGGCTCGGAGCCGTTGGAGAAGGCTGAGGACTGTTGTGAGCTACGGATCAGCCCAGAGCT

ACCGGTCTGTGGGTGTCAGAAAATATTCGATCTGCTTCACGAAAGCTCAGCCTGGTATCTGCGCAGCCTGCAGCGCATTG

GCCAAAACAAGGCCCAGCTCATTGTGGGCTGGAGGAAGCTCCACGGCCCCTCCAGCCCGGTGGAAGACCTGGAACGTGTG

AAAGTCACGCCAGGGAAACAGCTGGTGTGATTCCTGAAGGCGAACATCCCGGGTCTCGCCGCTGTGGGTCAGTGCTGTGG

CCCTTCC

ORF - retro_pvam_313 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

Percent Identity:	79.2 %
Parental protein coverage:	52.94 %
Number of stop codons detected:	2
Number of frameshifts detected:	0

Retrocopy - Parental Gene Alignment:

                                ParentalVPYRDSKLTRLLQDSLGGSAHSILIANIAPERCFYLDTVSALNFAARSKEVINRPFTNESLQLHVLAPVK
V......L..L.QDS..GS.HSILIAN.AP.RCFYLDTV.AL.FAAR.KEVINRP.T.ESLQLHVLAPVK
RetrocopyVDAQNEGLPHLSQDSPRGSVHSILIANTAP*RCFYLDTVPALDFAARCKEVINRPSTSESLQLHVLAPVK
ParentalLSQKEQLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLSNMDPAMLKHLLSLDRLLGSQGTQG
LSQK.QLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLS.MDPAML..LLSLD.LLGS.GT.G
RetrocopyLSQKGQLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLSSMDPAMLERLLSLDHLLGSRGTWG
ParentalTPLLSTPRRERMVLMKTVEEKDLEIERLKMKQKELEAKVLAQEAVDPKEKEKRSPTMHQPLACRTVTVAK
TPLLSTPR.E.MVL.KTVEEKD...ERLK.KQKELEAKVLA.EAVDP..KE..SPTM..P.A.R.V.VAK
RetrocopyTPLLSTPRQEWMVLTKTVEEKDWKTERLKIKQKELEAKVLAREAVDP--KENCSPTMLRPFARRIVMVAK
ParentalPLKKAVVIPLQLIQEQAASPNVDIHILKKSRKRKLECLNGSEPLEKAEDCWELQISPELLVNGRQKILNL
PL.KAV..PLQLIQEQAASPN.DIH.LKKS.KRKLEC..GSEPLEKAEDC.EL.ISPEL.V.G.QKI..L
RetrocopyPLEKAVEMPLQLIQEQAASPNADIHTLKKSCKRKLECPDGSEPLEKAEDCCELRISPELPVCGCQKIFDL
ParentalLNEGSARDLRSLQRIGQKKAQLIVGWRKLHGPFSQVEDLERVKVMSGKQLESFLKANILGLAAAGQHCGP
L.E.SA..LRSLQRIGQ.KAQLIVGWRKLHGP.S.VEDLERVKV..GKQL..FLKANI.GLAA.GQ.CGP
RetrocopyLHESSAWYLRSLQRIGQNKAQLIVGWRKLHGPSSPVEDLERVKVTPGKQLV*FLKANIPGLAAVGQCCGP
ParentalS
S
RetrocopyS

                            

                            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_313 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007193	1 retrocopy	retro_cjac_144,
Mus musculus	ENSMUSG00000030677	1 retrocopy	retro_mmus_471,
Otolemur garnettii	ENSOGAG00000000266	1 retrocopy	retro_ogar_2234,
Pteropus vampyrus	ENSPVAG00000009856	1 retrocopy	retro_pvam_3,
Pteropus vampyrus	ENSPVAG00000017206	1 retrocopy	retro_pvam_313 ,

	RetrogeneDB ID:	retro_pvam_313
Retrocopy location	Organism:	*Megabat (Pteropus vampyrus)*
	Coordinates:	GeneScaffold_2482:213610..214657(+)
	Located in intron of:	ENSPVAG00000000855
Retrocopy information	Ensembl ID:	None
	Aliases:	None
	Status:	NOVEL
Parental gene information	Parental gene summary:
	Parental gene symbol:	KIF22
	Ensembl ID:	ENSPVAG00000017206
	Aliases:	None
	Description:	kinesin family member 22 [Source:HGNC Symbol;Acc:6391]

Parental	VPYRDSKLTRLLQDSLGGSAHSILIANIAPERCFYLDTVSALNFAARSKEVINRPFTNESLQLHVLAPVK
	V......L..L.QDS..GS.HSILIAN.AP.RCFYLDTV.AL.FAAR.KEVINRP.T.ESLQLHVLAPVK
Retrocopy	VDAQNEGLPHLSQDSPRGSVHSILIANTAP*RCFYLDTVPALDFAARCKEVINRPSTSESLQLHVLAPVK

Parental	LSQKEQLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLSNMDPAMLKHLLSLDRLLGSQGTQG
	LSQK.QLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLS.MDPAML..LLSLD.LLGS.GT.G
Retrocopy	LSQKGQLGPSEAKKTRGPEEEEIGNPEPPALLASASQKFSPLQKLSSMDPAMLERLLSLDHLLGSRGTWG

Parental	TPLLSTPRRERMVLMKTVEEKDLEIERLKMKQKELEAKVLAQEAVDPKEKEKRSPTMHQPLACRTVTVAK
	TPLLSTPR.E.MVL.KTVEEKD...ERLK.KQKELEAKVLA.EAVDP..KE..SPTM..P.A.R.V.VAK
Retrocopy	TPLLSTPRQEWMVLTKTVEEKDWKTERLKIKQKELEAKVLAREAVDP--KENCSPTMLRPFARRIVMVAK

Parental	PLKKAVVIPLQLIQEQAASPNVDIHILKKSRKRKLECLNGSEPLEKAEDCWELQISPELLVNGRQKILNL
	PL.KAV..PLQLIQEQAASPN.DIH.LKKS.KRKLEC..GSEPLEKAEDC.EL.ISPEL.V.G.QKI..L
Retrocopy	PLEKAVEMPLQLIQEQAASPNADIHTLKKSCKRKLECPDGSEPLEKAEDCCELRISPELPVCGCQKIFDL

Parental	LNEGSARDLRSLQRIGQKKAQLIVGWRKLHGPFSQVEDLERVKVMSGKQLESFLKANILGLAAAGQHCGP
	L.E.SA..LRSLQRIGQ.KAQLIVGWRKLHGP.S.VEDLERVKV..GKQL..FLKANI.GLAA.GQ.CGP
Retrocopy	LHESSAWYLRSLQRIGQNKAQLIVGWRKLHGPSSPVEDLERVKVTPGKQLV*FLKANIPGLAAVGQCCGP

Parental	S
	S
Retrocopy	S

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

RetrogeneDB ID:

retro_pvam_313