RetrogeneDB ID: | retro_opun_29 | ||
Retrocopy location | Organism: | Red rice (Oryza punctata) | |
| Coordinates: | 2:508719..510792(-) | ||
| Located in intron of: | None | ||
Retrocopy information | Ensembl ID: | OPUNC02G00640 | |
| Aliases: | None | ||
| Status: | KNOWN_PROTEIN_CODING | ||
Parental gene information | Parental gene summary: | ||
| Parental gene symbol: | None | ||
| Ensembl ID: | OPUNC04G26930 | ||
| Aliases: | None | ||
| Description: | None |
Retrocopy-Parental alignment summary:
>retro_opun_29
ATGGCGGCGGAGGGGGAGGCGGAGGTGACGCGGGAGGTGATATCGATATCGACGGAGAAGGCGTTCGAGGGGAAGGCGTT
GCCGGCGTGGTCGGAGCAGATCACGGTGAGGTCGCTGGTGGTGAGCGCGCTCCTCGGCATGTTCCTGAGCTTCATCGTGA
TGAAGCTGAACCTCACCTCCGGCATCGTCCCTTCCCTCAACGTCTCCGCTGGTCTCCTCGCCTTCTTCCTCATGAAGACC
TGGACCAGCGCCCTCGAGCGCTGCGGCGTGTTCCCCAAGCCGTTCACCCGCCAGGAGAACACCGTCGTCCAGACCTGCGT
CATCTCCTGCTCCAGCATCGCCTTCTCCGGCGGATTCGGCACCTACATCCTCGGCATGAGCAAGAAGATCGCCGAGGGCT
TCGACGAGGCCGAGGCCAAGACCAGCATCAACGTCGAGGAGCCATCGCTGGGGCGCCTCATCGCCTTCCTCTTCCTCGTC
AGCTTCGTCGGCCTCTTCTCCATCGTGCCGCTTCGCAAGATCATGATCATCAGCTACAAGCTCACCTACCCGAGTGGATC
CGCCACCGCGCACCTCATCAACAGCTTCCACACGCCGCAGGGCGCCATCCAGGCCAAGCATCAGGTCTCCATCCTCTTCA
AATCCTTCGTCGGAAGCTTCCTCTGGTCGCTGTTCCAGTGGTTCTACGCCGCCGGACCGAGTTGTGGGTTCAGCTCGTTC
CCGACGTTCGGGATGGTGGCGTACAGCCGGCGATTCTACTTCGATTTCTCGGCAACCTACATCGGCGTCGGGATGATCTG
CCCCTACATTATCAACTTCTCGTTGCTCGTCGGCTCCATCGTGTCGTGGGGGATCATGTGGCCGTACATCGAGAGCAAGA
AGGGGAGCTGGTACGACGCGGGGCTCCCCAAGAGCAGCCTCCATGGGCTGAACGGATACCAGGTGTTCATCTCCATCGCC
ATGATCGTCGGCGACGGCCTCTTCAACTTCTTCTCCATCGTGCTACGCACCGCCTACGACCTCTACCTGAAGCGGCGCGG
CGGCGTCAACAAGCAGCAGCAGGAGATGCCGTTCGCCGGAGCCACGGGAACGGAGCGGCAGGTGCTCAGCTTCGACGACC
GGAGGCGGACGCAGGTGTTCCTCAAGGACCAGATCCCGACGACGATCGCGGCGGCGGCGTACGTGCTCCTCGCCGCCATA
TCGGTGGTCGCCATCCCGCACATCTTCCGGCAGCTGCGGCCCAAGCACGTGGTGTGGGCGTACGTGGTGGCGCCGCTCTT
CGCCTTCTGCAACGCCTACGGCACGGGGCTCACCGACTGGTCGCTCTCCAGCAGCTACGGCAAGCTCGCCATCTTCATCT
TCGGCGCAAACATCGGCGCCAAGGACGGCGGCGTCGTCGCCGGGCTCGCCGCCTGCGGGCTCATGATGGGCATCGTCTCC
ACCGCCTCCGACCTCGTCCAGGACTTCAAGACGGGATACCTCACCCTCACCTCGCCGCGCTCCATGTTCGTCAGCCAGGT
GTTGGGGACGGGGATGGGGTGCATAATAAGCCCGATGGTGTTCTGGATGTTCTACAAGGCGAACAACATCGGCATGGAGG
ACGGCTTCCCGGCGCCGTACGCCAAGATCTACAGGGGGATAGCTCTCCTGGGCGTCAATGGCTGGGACCAGCTGCCGCGC
TACTGCCTCCGCTTCTGCCTCGCCTTCTTCCTCCTCGCCATCGCCATCTGCGCGCTCAAGGAGGTCGCCAAGCAGCGCGG
GTGGTGGATCCAGGACTTCATCCCCAGCGCCCTCGGCATGGCCGTGCCCTTCTTCCTCGGCTCCTTCTTCACCATCGACA
TGTGCGTCGGTAGCCTCGTGCTCTTCCTCTGGTCCCGGAGTGATCCCGTCAGGGCGCACACCTTCGCCCCCGCCGTCGCC
TCCGGCCTCATCTGCGGCGACGGCATCTGGTCCTTGCCGGCGTCGATCCTCTCGCTGGCCAACGTCAGCCCGCCGATGTG
CATGCGCGTCTTCTCCACCGCCACCAACGAGAAGGTCCAGCTCTTCCTCAGGACGCTGCCCGCGCCGCCATGA
ORF - retro_opun_29 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
| Percent Identity: | 58.13 % |
| Parental protein coverage: | 82.33 % |
| Number of stop codons detected: | 0 |
| Number of frameshifts detected: | 0 |
Retrocopy - Parental Gene Alignment:
| Parental | IGGTGGFGSYIFAMSDRISD--QSGEARDEHNIKNPSLGWMIGFLFIVSFLGLFSVVPLRKIMIIDYKLI |
| I...GGFG.YI..MS..I.......EA....N...PSLG..I.FLF.VSF.GLFS.VPLRKIMII.YKL. | |
| Retrocopy | IAFSGGFGTYILGMSKKIAEGFDEAEAKTSINVEEPSLGRLIAFLFLVSFVGLFSIVPLRKIMIISYKLT |
| Parental | YPSGTATAHLINSFHTPQGAKLAKMQVKTLGKFFVMSFSWGFFQWFYTGGDGCGFMSFPTLGLEAYRNKF |
| YPSG.ATAHLINSFHTPQGA..AK.QV..L.K.FV.SF.W..FQWFY..G..CGF.SFPT.G..AY...F | |
| Retrocopy | YPSGSATAHLINSFHTPQGAIQAKHQVSILFKSFVGSFLWSLFQWFYAAGPSCGFSSFPTFGMVAYSRRF |
| Parental | FFDFSATYVGVGMICPYLVNISVLLGGVMSWGIMWPFIEQKKGDWYPADLKPSSLRGIVGYRVFISISLI |
| .FDFSATY.GVGMICPY..N.S.L.G...SWGIMWP.IE.KKG.WY.A.L..SSL.G..GY.VFISI..I | |
| Retrocopy | YFDFSATYIGVGMICPYIINFSLLVGSIVSWGIMWPYIESKKGSWYDAGLPKSSLHGLNGYQVFISIAMI |
| Parental | LGDGLYNFLKVMTRTTTALVMQVRAMMSEPTLPISGGSGGGGQTPEETFDDKRRTELFLKDQIPNWLALS |
| .GDGL.NF.....RT...L....R................G.......FDD.RRT..FLKDQIP...A.. | |
| Retrocopy | VGDGLFNFFSIVLRTAYDLYLKRRGGVNKQQQEMPFAGATGTERQVLSFDDRRRTQVFLKDQIPTTIAAA |
| Parental | AYVVIAAVSIATVPRIFQQLRWYHVAVSYVVAPVLAFCNAYGCGLTDWSLATTYGKLAIFTVGAWADASD |
| AYV..AA.S....P.IF.QLR..HV...YVVAP..AFCNAYG.GLTDWSL...YGKLAIF..GA...A.D | |
| Retrocopy | AYVLLAAISVVAIPHIFRQLRPKHVVWAYVVAPLFAFCNAYGTGLTDWSLSSSYGKLAIFIFGANIGAKD |
| Parental | GGIIAGLAACGVMIGIVSTASDLTQDFKTGYMTLASPRSMFVSQVIGTAMGCVIAPSVFWLFYKAFHDIG |
| GG..AGLAACG.M.GIVSTASDL.QDFKTGY.TL.SPRSMFVSQV.GT.MGC.I.P.VFW.FYKA...IG | |
| Retrocopy | GGVVAGLAACGLMMGIVSTASDLVQDFKTGYLTLTSPRSMFVSQVLGTGMGCIISPMVFWMFYKA-NNIG |
| Parental | MPGSEYPSPNALVYRNMAILGVQGLGSLPKHCLDLCIGFFVAAIAVNLARDLAAPK---VARFLPLPMAM |
| M.....P.P.A..YR..A.LGV.G...LP..CL..C..FF..AIA.......A.........F.P....M | |
| Retrocopy | MEDG-FPAPYAKIYRGIALLGVNGWDQLPRYCLRFCLAFFLLAIAICALKEVAKQRGWWIQDFIPSALGM |
| Parental | AIPFYLGPYFGIDMCIGSLIRFVWDRLDGARAKAFAPPVASGLICGDGIWTLPQSVLALAGVKPPICMKF |
| A.PF.LG..F.IDMC.GSL..F.W.R.D..RA..FAP.VASGLICGDGIW.LP.S.L.LA.V.PP.CM.. | |
| Retrocopy | AVPFFLGSFFTIDMCVGSLVLFLWSRSDPVRAHTFAPAVASGLICGDGIWSLPASILSLANVSPPMCMRV |
| Parental | LSRSTNVKVDAFIATLPS |
| .S..TN.KV..F..TLP. | |
| Retrocopy | FSTATNEKVQLFLRTLPA |
Legend:
| * | Stop codon |
| > | Forward frameshift by one nucleotide |
| < | Reverse frameshift by one nucleotide |
Oryza punctata was not studied using RNA-Seq expression data.
Oryza punctata was not studied using ChIP-Seq data.
Oryza punctata was not studied using EST data.
Oryza punctata was not studied using FANTOM5 data.
retro_opun_29 was not experimentally validated.
Retrocopy orthology:
Oryza punctata 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 | |
|---|---|---|---|
| Oryza punctata | OPUNC04G26930 | 1 retrocopy |
retro_opun_29 ,
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