RetrogeneDB ID: retro_oind_64

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 12:22855404..22856793(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA035761
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA035760
• Aliases: None
• Description: None

Sequence

>retro_oind_64
ATGGTAATGGAGGCGGCGTGCGTGCTCGCCGTGGTGGTGGTGGTGCTGGCGTTCTTGTCCCCGGCGGCGCGCGGCGGCGT
CACGAGCACGTACCGGAGGAGCCTGCAGGCGCTCCCAGACATGCCGATCGACGCCGACGTGTTCCGGCCGCCGCCCGGGT
TCAACGCGCCGGAGCAGGTCCACATCACGCTGGGCGACCAGACCGGCCGCGCCATGACCGTCTCCTGGGTGACGCCGAAG
CTCCCCGACAGCAACGTCGTCCGCTACGGCCTCCGCGCCGACAACCTCACCCACACCGCCAATGGCACCTTCCGGCGCTA
CTCCTTCGGGCGCAAGTACCTGTCGGGATTCATCCACCACGCCACCCTCACCGGCCTCGACTACGGCACCAAGTACCACT
ACGCCGTCGGCTCCGGCGACACCGCCAGCGCCAGGTCCTTCTCCTTCACGACGCCGCCCAAGCCCGGGCCCGACGTGCCG
TACAAGTTCGGGCTCATCGGCGACCTCGGGCAGACGTTCCACTCCAACGACACGCTGAGCCACTACGAGGCGTGCGGCGG
CGACGCGGTGCTGTTCATCGGCGACCTGTCGTACGCGGACAACCACCCGGGGCACGACAACAACCGGTGGGACACGTGGG
CGCGGTTCGTGGAGCGGAGCGTGGCGTACCAGCCGTGGATCTGGACGACGGGGAACCACGAGCTGGACTTCGCGCCGGAG
CTGGGGGAGACGACGCCGTTCAAGCCGTTCACGAACAGGTACCCGACGCCGTTCGGGGCGTCGGGGAGCACGCGGCCGCT
GTGGTACTCGGTGAGGATGGCGTCGGCGCACGTGATCGTGCTGGCGTCGTACGCGGCGTACGGCAAGTACACGCCGCAGT
GGAGGTGGTTGGAGGGGGAGCTGAGGCGCGTGGACAGGGCGGTGACGCCATGGCTGATCGTGTGCGTGCACTCGCCGTGG
TACAGCAGCAACGGATACCACTACATGGAGGGGGAGTCGATGCGCGTGGAGTTCGAGCGGTGGCTCGTCGACGCCAAGGC
CGACGTGGTGCTCGCCGGGCACGTCCACTCGTACGAGCGGACGCGGCGGGTGTCGAACGTGGCGTACGACATCGCCAACG
GGATGGCGACGCCGGTGTTCAACCGGTCGGCGCCGGTGTACATCAACATCGGCGACGGGGGGAACATCGAGGGGCTCGCC
GACGACTTCCGGTGGCCGCAGCCGGACTACTCGGTGTTCCGGGAGGCCAGCTTCGGCCACGCCACGCTGCAGATCGTCAA
CCGGACGCACGCCTTCTACGAGTGGCACCGCAACAGCGACGGCGTCAAGGTCGTCGCCGACCATGCCTGGTTCACCAACC
GATACTGGTTTCCCACCGACACCAACTAG

Alignment

ORF - retro_oind_64 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.28 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRWGAHLLLLLLAAATWTCAGAGAGVTSEYRRKLEATVDMPLDADVFRVPPGYNAPQQVHITLGDQTGT
          M....A..L.............A..GVTS.YRR.L.A..DMP.DADVFR.PPG.NAP.QVHITLGDQTG.
Retrocopy MVMEAACVLAVVVVVLAFLSPAARGGVTSTYRRSLQALPDMPIDADVFRPPPGFNAPEQVHITLGDQTGR

Parental  AMTVSWVTANELGSNTVRYGRSPEKLDRAAEGSHTRYDYFN-YTSGFIHHCTLTGLTHATKYYYAMGFDH
          AMTVSWVT.....SN.VRYG.....L...A.G...RY.....Y.SGFIHH.TLTGL...TKY.YA.G...
Retrocopy AMTVSWVTPKLPDSNVVRYGLRADNLTHTANGTFRRYSFGRKYLSGFIHHATLTGLDYGTKYHYAVGSGD

Parental  TV--RTFSFTTPPKPAPDAPFKFGLIGDLGQTFDSNSTLAHYEANGGDAVLFVGDLSYADNYPLHDNNRW
          T...R.FSFTTPPKP.PD.P.KFGLIGDLGQTF.SN.TL.HYEA.GGDAVLF.GDLSYADN.P.HDNNRW
Retrocopy TASARSFSFTTPPKPGPDVPYKFGLIGDLGQTFHSNDTLSHYEACGGDAVLFIGDLSYADNHPGHDNNRW

Parental  DTWARFVERSVAYQPWIWTAGNHELDYAPELGETVPFKPFTHRYPTPYRAAGSTEPFWYSVKIASAHVIV
          DTWARFVERSVAYQPWIWT.GNHELD.APELGET.PFKPFT.RYPTP..A.GST.P.WYSV..ASAHVIV
Retrocopy DTWARFVERSVAYQPWIWTTGNHELDFAPELGETTPFKPFTNRYPTPFGASGSTRPLWYSVRMASAHVIV

Parental  LASYSAYGKYTPQWTWLQEELATRVDRKLTPWLIVLMHSPWYNSNNYHYMEGETMRVQFERWLVDAKVDV
          LASY.AYGKYTPQW.WL..EL..RVDR..TPWLIV..HSPWY.SN.YHYMEGE.MRV.FERWLVDAK.DV
Retrocopy LASYAAYGKYTPQWRWLEGEL-RRVDRAVTPWLIVCVHSPWYSSNGYHYMEGESMRVEFERWLVDAKADV

Parental  VLAGHVHSYERSRRFANIDYNIVNGKATPAANVDAPVYITIGDGGNIEGIANNFTVPQPAYSAFREASFG
          VLAGHVHSYER.RR..N..Y.I.NG.ATP..N..APVYI.IGDGGNIEG.A..F..PQP.YS.FREASFG
Retrocopy VLAGHVHSYERTRRVSNVAYDIANGMATPVFNRSAPVYINIGDGGNIEGLADDFRWPQPDYSVFREASFG

Parental  HATLEIKNRTHAHYAWHRNHDGAKAVAEAVWLTNRYWMPTN
          HATL.I.NRTHA.Y.WHRN.DG.K.VA...W.TNRYW.PT.
Retrocopy HATLQIVNRTHAFYEWHRNSDGVKVVADHAWFTNRYWFPTD

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_64 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.

---

Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA035760	1 retrocopy	retro_oind_64 ,
Oryza longistaminata	KN538756.1_FG066	1 retrocopy	retro_olon_2,
Oryza sativa japonica	OS12G0637100	1 retrocopy	retro_osat_32,