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:
| Parental | NTLTSFCGALHTSFVTPSFPTDADVQFVIQMRPALKGAILSLLGHYKWEKFVYLYDTERGFSILQAIMEA |
| NTLTSFCGALH.SFV.PSF.TDADVQFVIQ..PA.KGAILSLLGHY..EKFVYLYDTERGFSILQAIME. | |
| Retrocopy | NTLTSFCGALHMSFVMPSFVTDADVQFVIQICPAMKGAILSLLGHYE*EKFVYLYDTERGFSILQAIMET |
| Parental | AVQNNWQVTARSVGNIKDVQEFRRIIEEMD-RRQEKRFLIDCEVERINTILEQXXXXXXXXXXXXXXXXX |
| AV.NNWQVTARS.GNIK.V.EFR.II..MD.R.QEK..LID..V.RINTILEQ................. | |
| Retrocopy | AV*NNWQVTARSLGNIKAV*EFRGIIGVMD>RWQEKQYLIDYKVKRINTILEQVLILEKHSRAYHYMLVN |
| Parental | XGFTDILLERVMHGGANITGFQIVNNENPMVQQFIQRWMRLDEREFPEAKNAPLKYTSALTHDAILVIAE |
| ..FT.ILLERVM.GGA.I..FQ.VNNENPM.QQ.IQ...RL.EREFPEAKN.PLKYT.ALTHD..LV.AE | |
| Retrocopy | PDFTNILLERVMPGGAKIMRFQTVNNENPMIQQCIQDSVRLNEREFPEAKNTPLKYTFALTHDT*LVKAE |
| Parental | AFR-YLRRQRVDVSRRGSAGDCLANPAVPWSQGIDIERALKMVQVQGMTGNIQFDTYGRRTN-YTIDVYE |
| AFR.YLRRQ.VDVS.RG.AGDCLANPAVP.SQGIDI.RALKMVQVQGMTGNI.FDTYGR.TN...I.... | |
| Retrocopy | AFR<YLRRQ*VDVSLRGNAGDCLANPAVP*SQGIDIQRALKMVQVQGMTGNIHFDTYGRKTN<LIIPLMY |
| Parental | MK-VTGSRKAGYWNEYERFVPFSDQQISNDSASSENRTIVVTTILXSPYVMYKKDHEQLEGNERYEGYCV |
| MK..T.S.KA.YW.EYERFVPFSDQQISN.S..SE.RT..VT.IL.S.YVM..K.HEQLEGNE.Y....V | |
| Retrocopy | MK*ITSS*KACYWSEYERFVPFSDQQISNNSEYSESRTTLVTSILESLYVMDEKNHEQLEGNE*YKA-VV |
| Parental | DLAYEIAKHVRIKYKLSIVGDGKYGARNPETKIWNGMVGELVYGRADIAVAPLTITLVREEVIDFSKPFM |
| ..AYEIAK.VRIKY.LSIV.DG...A.NP.TKIWNG.VG.L.Y.RADIAVAPLTI.LV....IDFSK.FM | |
| Retrocopy | *SAYEIAKCVRIKYRLSIVNDGNLSASNPKTKIWNGIVGQLFYRRADIAVAPLTIMLV----IDFSKSFM |
| Parental | SLGISIMIKKPQKSKPGVFSFLDPLAYEIWMCIVFAYIGVSVVLFLVSRFSPYEWHLEDNNEEPRDPQNP |
| SLGISIMIKKPQKS.PGVFSFLD.LA.EIW.CI.FAYIG.SVVLFLV.RFSP.....E.N.E.P.D.Q.. | |
| Retrocopy | SLGISIMIKKPQKSEPGVFSFLDLLADEIWICIIFAYIGISVVLFLVNRFSP*VQQWEGNSEGPHDLQSL |
| Parental | PDPPNEFGIFNSLWFSLGA-FMQQGCDISPRSLS |
| PDPPNE.......WF.LGA.FMQQ.CDI..R..S | |
| Retrocopy | PDPPNELKHL-TVWFFLGA>FMQQRCDIFQRFVS |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Pteropus vampyrus was not studied using RNA-Seq expression data.
Pteropus vampyrus was not studied using ChIP-Seq data.
Pteropus vampyrus was not studied using EST data.
Pteropus vampyrus was not studied using FANTOM5 data.
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 ,
|