RetrogeneDB ID: retro_ogla_13

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 12:18764551..18765940(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA12G0173200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA12G0173300
• Aliases: None
• Description: None

Sequence

>retro_ogla_13
ATGGCAATGGAGGCGGCGTGCGTGCTCGCCGTGGTGGTGGTGGTGCTGGCGTTCTTGTCCTCGGCGGCGCGCGGCGGCGT
CACGAGCACGTACCGGAGGAGCCTGCAGGCGCTCCCAGACATGCCGATCGACGCCGACGTGTTCCGGCCGCCGCCCGGTT
TCAACGCGCCGGAGCAGGTCCACATCACGCTGGGCGACCAGACCGGCCGCGCCATGACCGTCTCCTGGGTGACGCCGAAG
CTCCCCGACAGCAACGTCGTCCGCTACGGCCTCCGCGCCGACAACCTCACCCACACCGCCAATGGCACCTTCCGGCGCTA
CTCCTTCGGGCGCAAGTACCGGTCGGGATTCATCCACCACGCCACCCTTACCGGCCTCGACTACGGCACCAAGTACCACT
ACGCCGTCGGCTCCGGCGACACCGCCAGCGCCAGGTCCTTCTCCTTCACGACGCCGCCCAAGCCCGGGCCCGACGTGCCG
TACAAGTTCGGGCTCATCGGCGACCTCGGGCAGACGTTCCACTCCAACGACACGCTGAGCCACTACGAGGCGTGCGGCGG
CGACGCGGTGCTGTTCATCGGCGACCTGTCGTACGCGGACAACCACCCGGGGCACGACAACAACCGGTGGGACACGTGGG
CGCGGTTCGTGGAGCGGAGCGTGGCGTACCAGCCGTGGATCTGGACGACGGGGAACCACGAGCTGGACTTCGCGCCGGAG
CTGGGGGAGACGACGCCGTTCAAGCCGTTCACGAACAGGTACCCGACGCCGTTCGGGGCGTCGGGGAGCACGCGGCCGCT
GTGGTACTCGGTGAGGATGGCGTCGGCGCACGTGATCGTGCTGGCGTCGTACGCGGCGTACGGCAAGTACACGCCGCAGT
GGAGGTGGCTGGAGGGGGAGCTGAGGCGCGTGGACAGGGCGGTGACGCCATGGCTGATCGTGTGCGTGCACTCGCCGTGG
TACAGCAGCAACGGATACCACTACATGGAGGGGGAGTCGATGCGCGTGGAGTTCGAGCGGTGGCTCGTCGACGCCAAGGC
CGACGTGGTGCTCGCCGGGCACGTCCACTCGTACGAGCGGACGCGGCGGGTGTCGAACGTGGCGTACGACATCGCCAACG
GGATGGCGACGCCGGTGTTCAACCGGTCGGCGCCGGTGTACATCAACATCGGCGACGGGGGGAACATCGAGGGGCTCGCC
GACGACTTCCGGTGGCCGCAGCCGGACTACTCGGTGTTCCGGGAGGCCAGCTTCGGCCACGCCACGCTGCAGATCGTCAA
CCGGACGCACGCCTTCTACGAGTGGCACCGCAACAGCGACGGCGTCAAGGTCGTCGCCGACCATGCCTGGTTCACCAACC
GATACTGGTTTCCCACCGACACCAACTAG

Alignment

ORF - retro_ogla_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.15 %
• Parental protein coverage: 96.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLLLLLAAATWTCAGAGAGVTSEYRRKLEATVDMPLDADVFRVPPGYNAPQQVHITLGDQTGTAMTVSWV
          .L.............A..GVTS.YRR.L.A..DMP.DADVFR.PPG.NAP.QVHITLGDQTG.AMTVSWV
Retrocopy VLAVVVVVLAFLSSAARGGVTSTYRRSLQALPDMPIDADVFRPPPGFNAPEQVHITLGDQTGRAMTVSWV

Parental  TANELGSNTVRYGSSPEKLDRAAEGSHTRYDYFN-YTSGFIHHCTLTGLTHATKYYYAMGFDHTV--RTF
          T.....SN.VRYG.....L...A.G...RY.....Y.SGFIHH.TLTGL...TKY.YA.G...T...R.F
Retrocopy TPKLPDSNVVRYGLRADNLTHTANGTFRRYSFGRKYRSGFIHHATLTGLDYGTKYHYAVGSGDTASARSF

Parental  SFTTPPKPAPDAPFKFGLIGDLGQTFDSNSTLAHYEANGGDAVLFVGDLSYADNYPLHDNNRWDTWARFV
          SFTTPPKP.PD.P.KFGLIGDLGQTF.SN.TL.HYEA.GGDAVLF.GDLSYADN.P.HDNNRWDTWARFV
Retrocopy SFTTPPKPGPDVPYKFGLIGDLGQTFHSNDTLSHYEACGGDAVLFIGDLSYADNHPGHDNNRWDTWARFV

Parental  ERSVAYQPWIWTAGNHELDYAPELGETVPFKPFTHRYPTPYRAAGSTEPFWYSVKIASAHVIVLASYSAY
          ERSVAYQPWIWT.GNHELD.APELGET.PFKPFT.RYPTP..A.GST.P.WYSV..ASAHVIVLASY.AY
Retrocopy ERSVAYQPWIWTTGNHELDFAPELGETTPFKPFTNRYPTPFGASGSTRPLWYSVRMASAHVIVLASYAAY

Parental  GKYTPQWTWLQEELATRVDRKLTPWLIVLMHSPWYNSNNYHYMEGETMRVQFERWLVDAKVDVVLAGHVH
          GKYTPQW.WL..EL..RVDR..TPWLIV..HSPWY.SN.YHYMEGE.MRV.FERWLVDAK.DVVLAGHVH
Retrocopy GKYTPQWRWLEGEL-RRVDRAVTPWLIVCVHSPWYSSNGYHYMEGESMRVEFERWLVDAKADVVLAGHVH

Parental  SYERSRRFANIEYNIVNGKATPAANVDAPVYITIGDGGNIEGIANNFTVPQPAYSAFREASFGHATLEIK
          SYER.RR..N..Y.I.NG.ATP..N..APVYI.IGDGGNIEG.A..F..PQP.YS.FREASFGHATL.I.
Retrocopy SYERTRRVSNVAYDIANGMATPVFNRSAPVYINIGDGGNIEGLADDFRWPQPDYSVFREASFGHATLQIV

Parental  NRTHAHYAWHRNHDGAKAVADAVWLTNRYWMPTN
          NRTHA.Y.WHRN.DG.K.VAD..W.TNRYW.PT.
Retrocopy NRTHAFYEWHRNSDGVKVVADHAWFTNRYWFPTD

Legend:

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

Expression

RNA-Seq

Oryza glaberrima was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza glaberrima was not studied using ChIP-Seq data.

EST

Oryza glaberrima was not studied using EST data.

TSS

Oryza glaberrima was not studied using FANTOM5 data.

Lab

retro_ogla_13 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glaberrima 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 glaberrima	ORGLA12G0173300	1 retrocopy	retro_ogla_13 ,