RetrogeneDB ID: retro_oind_53

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02049242.1:13..1285(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA040335
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA014643
• Aliases: None
• Description: None

Sequence

>retro_oind_53
ATGTTGGATGCAGTATGTAAATACTTGCCTTCTCCATTGGATAAAGATGATATCAAAGGTACTGATCCGAGAACAGACGC
TGAAATTACAAGAAAACCATCTGTAGATGAGCCTTTCGCAGCTTTAGCATTTAAGATTGCTACTGACCCGTTCGTGGGAA
GATTAGCATTCTTCAGAGCTTACTCTGGAAGACTGGATGCTGGTTCTTATATCTTGAACTCTCGTTCAGGAGATAAAGAA
AGACTCTCAAGAATCTATCAGATGCACGCTAACAAACAAAACCCGGTAGAATATATTGAAGCTGGTGATATTGGTGCAGC
GGTAGGATTCAAATCTATCAAAACTGGTGATACGATGTGTGATGAGAAAAACCCAATCGTTCTTGAATCGATGGTTTTCC
CTGATCCGGTAATCGGTATCGCTGTTGAGCCTAAAACTAAAGCTGACCAGGATAAAATGGGTAACGCTCTAGCTAAATTG
GCTGAAGAAGATCCAACGTTTACTGTAAGAACTGACGAAGCTTCTGGACAAACGATCATCTCTGGTATGGGTGAGCTTCA
CTTAGATATCATTGTAGACCGTATGAAGAGAGAGTTCAAGGTTGAAGTAAACCAGAGACAACCTCAGGTAGAGTACAACA
GAACACTTAACAAAAGTTGCCAGCCACAGAGAAGTTACAAAAAGCCATCTGGAGGTCAAGGTCAATTTGCTGACATTGTA
TTTGAACTAGGACCTGCAGACGAAGGTAAAGTTGGTTTAGAATTCATCAATGAGATCAAAGGGGGTAACGTTCCTAGAGA
ATTCGTTCCTGCAATTGAAAAAGGATTTAAAGCTGCAATGAAGAACGGTCCATTGGCTGGTTTCGAAGTTGAAGGTATTA
AAGTTACTCTTAAAGATGGATCTTTCCACGCAGTGGATTCTGACGCTCGTTCTTTCGAAATGGCTGCTAAGCTAGGATTT
AAAGAAGCTGGTAAAGCTGCTAAACCAGTAATTATGGAGCCTATTATGAAACTGGAAGTTGTAACTCCGGAAGAATATAT
GGGTAACATCATTGGTGACCTTAACAAGAGAAGAGGTACTATCAGTGGCCAGGAAGAGAAAAACGGAGCTGTTGTAATCA
AAGGTTCTGTTCCACTTTCTGAAATGTTTGGATATGTAACAACTCTAAGAACACTTTCATCAGGAAGAGCTACTTCTTCT
ATGGAATTAGAGAAATACGCACCAACTCCACAAAACGTTGCTGAAGAAATCATAGCTAAAGCAAAAGGTTAA

Alignment

ORF - retro_oind_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.49 %
• Parental protein coverage: 54.26 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLDAVVDYLPSPLDLPPMKGTDPEDPELILERKPSDDEPFSGLAFKIMTDPFVGSLTFVRIYSGKLVAGS
          .LDAV..YLPSPLD....KGTDP........RKPS.DEPF..LAFKI.TDPFVG.L.F.R.YSG.L.AGS
Retrocopy MLDAVCKYLPSPLDKDDIKGTDPRT-DAEITRKPSVDEPFAALAFKIATDPFVGRLAFFRAYSGRLDAGS

Parental  YVLNANKDKKERIGRLLEMHANSKEDITVAVAGDIVALAGLKDTITGETLSDPDKPVVLERMEFPDPVIK
          Y.LN.....KER..R...MHAN.........AGDI.A..G.K...TG.T..D...P.VLE.M.FPDPVI.
Retrocopy YILNSRSGDKERLSRIYQMHANKQNPVEYIEAGDIGAAVGFKSIKTGDTMCDEKNPIVLESMVFPDPVIG

Parental  VAIEPKTKADADKMATGLIKLAQEDPSFHFSRDEETNQTVIEGMGELHLDIIVDRLKREFRVEANVGAPQ
          .A.EPKTKAD.DKM...L.KLA.EDP.F....DE...QT.I.GMGELHLDIIVDR.KREF.VE.N...PQ
Retrocopy IAVEPKTKADQDKMGNALAKLAEEDPTFTVRTDEASGQTIISGMGELHLDIIVDRMKREFKVEVNQRQPQ

Parental  VNYRESISKISEVQYVHKKQSGGSGQFADIIVRFEPLEAGS-GYEFKSEIKGGAVPKEYVPGVMKGIEES
          V.Y.....K....Q...KK.SGG.GQFADI.....P...G..G.EF..EIKGG.VP.E.VP...KG....
Retrocopy VEYNRTLNKSCQPQRSYKKPSGGQGQFADIVFELGPADEGKVGLEFINEIKGGNVPREFVPAIEKGFKAA

Parental  LPNGVLAGYPVVDLRAVLVDGSYHDVDSSVLAFQIAARGAFREGLRKAGPRLLEPIMKVEVITPEEHLGD
          ..NG.LAG..V......L.DGS.H.VDS....F..AA...F.E....A.P...EPIMK.EV.TPEE..G.
Retrocopy MKNGPLAGFEVEGIKVTLKDGSFHAVDSDARSFEMAAKLGFKEAGKAAKPVIMEPIMKLEVVTPEEYMGN

Parental  VIGDLNSRRGQVNSFGDKPGGLKVVDAFVPLAEMFQYVSTLRGMTKGRASYTMQLAKFDVVPQHIQNELS
          .IGDLN.RRG.......K.G...V....VPL.EMF.YV.TLR....GRA...M.L.K....PQ....E..
Retrocopy IIGDLNKRRGTISGQEEKNGAV-VIKGSVPLSEMFGYVTTLRTLSSGRATSSMELEKYAPTPQNVAEEII

Parental  A
          A
Retrocopy A

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_53 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA014643	1 retrocopy	retro_oind_53 ,