RetrogeneDB ID: retro_omer_2

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 8:21318413..21319553(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI08G18200
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI11G07520
• Aliases: None
• Description: None

Sequence

>retro_omer_2
ATGGGTAGAGTGGTGGTCGTCGTGGCGGCGGCGGCGGTAGCCGTGGCCGTGGTGCTGCTGGGCGCGGCGGCGCCGGCGGC
GAGAGCGATGGAGTTCGGCGAGCGGGACGTGGCGTCGGACGAGGCGCTGTGGGAGCTGTACGAGCGGTGGCGCGGGCAGC
ACCGGGTGGCGCGGGACCTCGGCGAGAAGGCGCGGCGGTTCAACGTGTTCAAGGACAACGTCCGCCTCATCCACGAGTTC
AACCGCCGCGACGAGCCCTACAAGCTCCGCCTCAACCGCTTCGGCGACATGACCGCCGACGAGTTCCGCCGCGCCTACGC
CTCCTCCCGCGTCTCCCACCACCGCATGTTCCGCGGCGGCGAGAGGCGGAGCGGCTTCATGTACGCCGGCGCCCGCGACC
TGCCGGCGTCGGTGGACTGGCGCGAGAAGGGCGCCGTCGGGGCGGTCAAGGACCAGGGCCAGTGCGGCAGCTGCTGGGCG
TTCTCGACCATCGCCGCCGTGGAAGGGATCAACGCCATCCGCACCAGCAACCTCACCGCGCTGTCGGAGCAGCAGCTCGT
CGACTGCGACACCAAGACCGGCAACGCCGGCTGCGACGGCGGCCTCATGGACAACGCGTTCCAGTACATTGCCAAGCACG
GCGGCGTCGCCGCCTCCTCCGCCTACCCGTACCGCGCCCGCCAGAGCTCCTGCAAGAGCTCCGCGGCGTCGTCCCCCGCC
GTCACCATCGACGGGTACGAGGACGTGCCGGCGAACTCGGAGTCGGCGCTGAAGAAGGCGGTGGCGAACCAGCCGGTGTC
GGTGGCGATCGAGGCCGGGGGTTCGCACTTCCAGTTCTACTCGGAGGGGGTGTTCGCCGGGAAATGCGGGACGGAGCTCG
ACCATGGCGTGGCGGCGGTGGGGTACGGCACGACGGTGGACGGCACCAAGTACTGGATCGTCAGGAACTCGTGGGGCGCA
GACTGGGGGGAGAAGGGCTACATCCGCATGAAGCGCGACGTGTCCGCCAAGGAGGGTCTCTGCGGCATCGCCATGGAAGC
ATCCTACCCCGTCAAGACCTCGCCGAACCCCGCGCCCAAGAAGATCAAGAAGGTCACCGACGAAGACGACGATGACGAGC
ACCACCATGATGAGCTCTAA

Alignment

ORF - retro_omer_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 84.13 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGNDYVEARRRFNVFVENARYIHEANRRGGRPFRLALNKFADMTTDEFRRTYAGSRARHHRSLSGGRGGE
          V..D..E..RRFNVF..N.R.IHE.NRR...P..L.LN.F.DMT.DEFRR.YA.SR..HHR...GG....
Retrocopy VARDLGEKARRFNVFKDNVRLIHEFNRRD-EPYKLRLNRFGDMTADEFRRAYASSRVSHHRMFRGGERRS

Parental  GASFRYGGEDEDNLPPAVDWRERGAVTGIKDQGQCGSCWAFSAVAAVEGVNKIKTGRLVTLSEQELVDCD
          G..F.Y.G.....LP..VDWRE.GAV...KDQGQCGSCWAFS..AAVEG.N.I.T..L..LSEQ.LVDCD
Retrocopy G--FMYAGARD--LPASVDWREKGAVGAVKDQGQCGSCWAFSTIAAVEGINAIRTSNLTALSEQQLVDCD

Parental  TGD-NQGCDGGLMDYAFQFIKRNGGITTESNYPYRAEQGRCNKAKASSHDVTIDGYEDVPANDESALQKA
          T...N.GCDGGLMD.AFQ.I...GG....S.YPYRA.Q..C....ASS..VTIDGYEDVPAN.ESAL.KA
Retrocopy TKTGNAGCDGGLMDNAFQYIAKHGGVAASSAYPYRARQSSCKSSAASSPAVTIDGYEDVPANSESALKKA

Parental  VANQPVAVAIEASGQDFQFYSEGVFTGECGTDLDHGVAAVGYGITRDGTKYWIVKNSWGEDWGERGYIRM
          VANQPV.VAIEA.G..FQFYSEGVF.G.CGT.LDHGVAAVGYG.T.DGTKYWIV.NSWG.DWGE.GYIRM
Retrocopy VANQPVSVAIEAGGSHFQFYSEGVFAGKCGTELDHGVAAVGYGTTVDGTKYWIVRNSWGADWGEKGYIRM

Parental  QRGVSSDSNGLCGIAMEASYPIKSGAHDAAASDRVVKDE
          .R.VS....GLCGIAMEASYP.K.....A......V.DE
Retrocopy KRDVSA-KEGLCGIAMEASYPVKTSPNPAPKKIKKVTDE

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_2 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G19707	2 retrocopies	retro_bdis_26, retro_bdis_41,
Zea mays	GRMZM2G099765	1 retrocopy	retro_zmay_16,
Hordeum vulgare	MLOC_73076	2 retrocopies	retro_hvul_23, retro_hvul_68,
Oryza barthii	OBART11G08490	1 retrocopy	retro_obar_27,
Oryza glumaepatula	OGLUM05G09560	1 retrocopy	retro_oglu_31,
Oryza meridionalis	OMERI04G24530	1 retrocopy	retro_omer_32,
Oryza meridionalis	OMERI11G07520	1 retrocopy	retro_omer_2 ,
Setaria italica	Si026545m.g	1 retrocopy	retro_sita_27,