RetrogeneDB ID: retro_ogla_41

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 1:20885961..20886993(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA01G0228400
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA08G0040000
• Aliases: None
• Description: None

Sequence

>retro_ogla_41
ATGAGGCGACCCATGGCTCGCGATTTTACGGCGACGTTTCTTCTGCTGCTCAGCGTCGCGTCGCTGCTGGTGATCTCGCC
GTGCGCGGCCCAGCAGATCAAGACCACCGACACGCGGTGGAGCTACCACCTCCCGCTTCCCGACGGCGTCAGCGGCGCCG
AGAGCCTCGCCTTCGACGGCAAGGACGGCCTCTACACCGGCGTCTCGGACGGCCGCGTGCTCAAGTGGGGAGGCAGCGCC
GCCGGCTGGACCACGTTCGCGTACAATGCGAACTACCGGAAAATCCCTCTCTGCTCGTCGTCCGAGGTGCCACCGGAGGA
GAGGGAGAGCATCTGCGGGCGCCCGCTGGGGATCCGGTTGTTCAGGAAGACCGGCGAGCTCTACATCGCCGACGCGTACA
AGGGGCTGATGAAGGTCGGGCCCGACGGCGGCGAGGCCCAGGTGGTCGCGACCGAGGCGGACGGCGTCCCCTTCCACTTC
CTCAATGGCCTTGACGTCGACCAAGCTACGGGTGATGCCTACTTCACCGACAGCAGCAGCACGTACACCCGCAGGTTCAA
CGGGGAGATCACGATGAACGCCGACGCGACAGGGCGGCTGCTCAAGTACGACGCGCGGACGCGGCGGGTCACCGTGCTGA
AGACCGACCTGCCGTACCCGAACGGCGTCGCCGTCAGCCGAGACAGGACGCACCTCGTCGTGGCGCACACCGTGCCGTGC
CAGGCGTTCCGGTACTGGCTGCGGGGCACCAAAGCCGGCGAGTACGAGCTCTTCGCCGACCTCCCGGGCTACCCCGACAA
CGTGAGGCGCGACACCAAGGGAGGCTACTGGGTGGCGCTCAACCAGGAGAGGATGCGGTTGGGCGCGGCGCCCGCAGCCA
AGCACCTGGTCGGCGTACGGCTCAACCCCGACGGCGTGGAGGTGGAGGAGTTGACGGCTGCCAAGGGCGTCACGCTCAGC
GAAGTGGCGGAGCAGAAGGGCAAGCTGTGGTTGGGCTCCGTCGAACTCGATTACATTGGCATGTTTGCTTGA

Alignment

ORF - retro_ogla_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.56 %
• Parental protein coverage: 88.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GPYTGFSDGRVLRWGGAAAGWTTFAHHQDYRKIPMCTTPVAPPEETESMCGRPLGLAFHDRTGDLYIADA
          G.YTG.SDGRVL.WGG.AAGWTTFA....YRKIP.C.....PPEE.ES.CGRPLG......TG.LYIADA
Retrocopy GLYTGVSDGRVLKWGGSAAGWTTFAYNANYRKIPLCSSSEVPPEERESICGRPLGIRLFRKTGELYIADA

Parental  YKGLMRVGPRGGEAEVLAAGADGVPFNFVNGIDVDQATGDVYFTDSSTTYPRRFNSEIMMNADATSRLLK
          YKGLM.VGP.GGEA.V.A..ADGVPF.F.NG.DVDQATGD.YFTDSS.TY.RRFN.EI.MNADAT.RLLK
Retrocopy YKGLMKVGPDGGEAQVVATEADGVPFHFLNGLDVDQATGDAYFTDSSSTYTRRFNGEITMNADATGRLLK

Parental  YDAATKQVTVLRSGLPYANGVAVSRNGSHAVVAHTVPCQAFRYWIKGPNAREYELLADLPGYPDNVRRDA
          YDA.T..VTVL...LPY.NGVAVSR...H.VVAHTVPCQAFRYW..G..A.EYEL.ADLPGYPDNVRRD.
Retrocopy YDARTRRVTVLKTDLPYPNGVAVSRDRTHLVVAHTVPCQAFRYWLRGTKAGEYELFADLPGYPDNVRRDT

Parental  RGGYWVALNQEKVRLDATAAVAPPAKHLVGVRLDGDGVEVEELTAAKGVTLSEVVERGGKLWLGSVELDF
          .GGYWVALNQE..RL.A....AP.AKHLVGVRL..DGVEVEELTAAKGVTLSEV.E..GKLWLGSVELD.
Retrocopy KGGYWVALNQERMRLGA----APAAKHLVGVRLNPDGVEVEELTAAKGVTLSEVAEQKGKLWLGSVELDY

Parental  IGL
          IG.
Retrocopy IGM

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_41 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA028079	1 retrocopy	retro_oind_6,
Oryza glumaepatula	OGLUM08G04830	1 retrocopy	retro_oglu_15,
Oryza meridionalis	OMERI08G04560	1 retrocopy	retro_omer_14,
Oryza punctata	OPUNC08G04420	1 retrocopy	retro_opun_39,
Oryza glaberrima	ORGLA08G0040000	1 retrocopy	retro_ogla_41 ,
Oryza rufipogon	ORUFI08G05030	1 retrocopy	retro_oruf_9,
Oryza sativa japonica	OS08G0175000	1 retrocopy	retro_osat_11,