RetrogeneDB ID:

retro_pvam_999

Retrocopy
location
Organism:Megabat (Pteropus vampyrus)
Coordinates:scaffold_216:204857..206399(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GRIA3
Ensembl ID:ENSPVAG00000003139
Aliases:None
Description:glutamate receptor, ionotropic, AMPA 3 [Source:HGNC Symbol;Acc:4573]


Retrocopy-Parental alignment summary:






>retro_pvam_999
AACACTTTGACCTCATTCTGTGGGGCCCTGCACATGTCTTTTGTCATGCCCAGCTTCGTCACTGATGCAGATGTGCAGTT
TGTCATCCAGATATGCCCAGCCATGAAGGGTGCTATTCTGAGTCTTCTGGGTCACTATGAGTAGGAGAAGTTTGTGTACC
TCTATGACACAGAAAGAGGATTTTCCATCCTCCAAGCAATTATGGAAACAGCAGTGTAAAACAACTGGCAAGTGACTGCA
AGGTCTTTGGGAAACATAAAGGCTGTCTGAGAATTCAGGGGTATCATTGGAGTAATGGACACGGTGGCAGGAAAAGCAAT
ACTTGATTGACTACAAAGTCAAAAGGATTAACACAATTTTGGAACAGGTTTTGATTCTGGAGAAACATTCAAGAGCTTAT
CATTACATGCTTGTTAACCCAGATTTTACTAATATTTTGCTAGAAAGAGTCATGCCTGGAGGAGCCAAAATTATGAGATT
CCAGACTGTCAACAACGAAAATCCTATGATTCAGCAGTGCATACAGGACTCCGTGAGGCTGAATGAAAGGGAATTCCCTG
AAGCCAAGAACACACCACTGAAGTATACATTTGCATTGACGCATGACACATGACTGGTCAAAGCAGAAGCTTTCCGTATC
TGAGGAGGCAGTGAGTGGATGTATCCTTGAGAGGCAATGCTGGAGACTGCTTAGCAAATCCAGCTGTGCCTTGAAGTCAA
GGAATTGATATCCAGAGAGCTCTAAAAATGGTGCAAGTACAAGGAATGACTGGAAACATCCACTTTGACACTTATGGACG
TAAGACAAATTAATTATACCATTGATGTATATGAAATGAATCACTAGTTCTTGAAAAGCTTGCTACTGGAGTGAGTATGA
AAGGTTCGTGCCTTTCTCAGATCAGCAGATCAGCAACAATAGTGAATACTCAGAGAGCCGGACCACACTGGTGACTTCCA
TTCTGGAATCACTATATGTAATGGATGAGAAGAACCATGAGCAACTGGAAGGAAATGAGTGATATAAGGCTGTTGTGTAG
TCAGCCTATGAAATAGCCAAATGTGTAAGGATCAAATACAGATTGTCCATCGTCAACGATGGGAATCTTAGTGCAAGTAA
TCCAAAGACTAAAATATGGAATGGCATAGTTGGGCAACTTTTCTATAGGAGGGCTGATATAGCTGTTGCTCCACTCACTA
TAATGCTTGTCATAGATTTCTCAAAGTCATTTATGAGCCTGGGCATCTCCATCATGATAAAAAAGCCTCAGAAATCAGAA
CCAGGAGTATTCTCATTTCTGGATCTCTTGGCTGATGAAATCTGGATCTGCATCATTTTTGCTTACATTGGGATCAGTGT
AGTTCTTTTCCTAGTTAACAGATTCAGCCCTTAGGTACAGCAGTGGGAAGGCAACAGTGAAGGACCTCATGATCTGCAAA
GCCTTCCTGATCCTCCAAATGAATTGAAACATTTAACAGTCTGGTTTTTCTTGGGTGCCTTTTATGCAGCAAAGATGTGA
TATTTTCCAAAGGTTTGTTTCC

ORF - retro_pvam_999 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 71.37 %
Parental protein coverage: 58.05 %
Number of stop codons detected: 11
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalNTLTSFCGALHTSFVTPSFPTDADVQFVIQMRPALKGAILSLLGHYKWEKFVYLYDTERGFSILQAIMEA
NTLTSFCGALH.SFV.PSF.TDADVQFVIQ..PA.KGAILSLLGHY..EKFVYLYDTERGFSILQAIME.
RetrocopyNTLTSFCGALHMSFVMPSFVTDADVQFVIQICPAMKGAILSLLGHYE*EKFVYLYDTERGFSILQAIMET
ParentalAVQNNWQVTARSVGNIKDVQEFRRIIEEMD-RRQEKRFLIDCEVERINTILEQXXXXXXXXXXXXXXXXX
AV.NNWQVTARS.GNIK.V.EFR.II..MD.R.QEK..LID..V.RINTILEQ.................
RetrocopyAV*NNWQVTARSLGNIKAV*EFRGIIGVMD>RWQEKQYLIDYKVKRINTILEQVLILEKHSRAYHYMLVN
ParentalXGFTDILLERVMHGGANITGFQIVNNENPMVQQFIQRWMRLDEREFPEAKNAPLKYTSALTHDAILVIAE
..FT.ILLERVM.GGA.I..FQ.VNNENPM.QQ.IQ...RL.EREFPEAKN.PLKYT.ALTHD..LV.AE
RetrocopyPDFTNILLERVMPGGAKIMRFQTVNNENPMIQQCIQDSVRLNEREFPEAKNTPLKYTFALTHDT*LVKAE
ParentalAFR-YLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTN-YTIDVYE
AFR.YLRRQ.VDVS.RG.AGDCLANPAVP.SQGIDI.RALKMVQVQGMTGNI.FDTYGR.TN...I....
RetrocopyAFR<YLRRQ*VDVSLRGNAGDCLANPAVP*SQGIDIQRALKMVQVQGMTGNIHFDTYGRKTN<LIIPLMY
ParentalMK-VTGSRKAGYWNEYERFVPFSDQQISNDSASSENRTIVVTTILXSPYVMYKKDHEQLEGNERYEGYCV
MK..T.S.KA.YW.EYERFVPFSDQQISN.S..SE.RT..VT.IL.S.YVM..K.HEQLEGNE.Y....V
RetrocopyMK*ITSS*KACYWSEYERFVPFSDQQISNNSEYSESRTTLVTSILESLYVMDEKNHEQLEGNE*YKA-VV
ParentalDLAYEIAKHVRIKYKLSIVGDGKYGARNPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFM
..AYEIAK.VRIKY.LSIV.DG...A.NP.TKIWNG.VG.L.Y.RADIAVAPLTI.LV....IDFSK.FM
Retrocopy*SAYEIAKCVRIKYRLSIVNDGNLSASNPKTKIWNGIVGQLFYRRADIAVAPLTIMLV----IDFSKSFM
ParentalSLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHLEDNNEEPRDPQNP
SLGISIMIKKPQKS.PGVFSFLD.LA.EIW.CI.FAYIG.SVVLFLV.RFSP.....E.N.E.P.D.Q..
RetrocopySLGISIMIKKPQKSEPGVFSFLDLLADEIWICIIFAYIGISVVLFLVNRFSP*VQQWEGNSEGPHDLQSL
ParentalPDPPNEFGIFNSLWFSLGA-FMQQGCDISPRSLS
PDPPNE.......WF.LGA.FMQQ.CDI..R..S
RetrocopyPDPPNELKHL-TVWFFLGA>FMQQRCDIFQRFVS

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_999 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 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Pteropus vampyrus ENSPVAG00000003139 1 retrocopy
retro_pvam_999 ,


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