RetrogeneDB ID: retro_ogla_25

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 7:207706..208756(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA07G0002900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA05G0189300
• Aliases: None
• Description: None

Sequence

>retro_ogla_25
ATGGCCGCCGCGGCAGCAGCAAGAATCTCCTCGATGGCGTCGCAGCTGCGGCTGTCATGGCTCATGGTGATGCTCATGCT
AGTGGCGTCGAATAATAATGCTGCTGCTGCTCCACCGGCAGCGGCAGCTGGGCAGCTGCGGACGGGGTACTACCGGGAGA
CGTGCCCGCACGCAGAGGAGATGGTGTTCCGGGAGACGGCGAGGATCATCCGTGCGTCCCCCGACCTCGCCGCCGCGCTG
CTCCGCCTCCACTACCACGACTGCTTCGTCCAGGGCTGCGACGCCTCCGTCCTCCTCGACTCCACCCCCGCCAACGCCGC
CGAGAGGGACTCCGACCCCAACAAGTCCCTCCGTGGCTTCGACTCCGTCGCCCGCGTCAAGGCCAAGCTCGAGGCCGCCT
GCCCTGCCACCGTCTCCTGCGCCGACCTCCTCGCCCTCATGGCCCGCGACGCCGTCGTCCTCGCCAAGGGCCCCTACTGG
CACGTCCCGCTCGGCCGCAGGGACGGCCGCTCCTCCACCGCCGCCAGCTGCGGCGGTCAGCTTCCCCCGCTCTGCGGCAA
CGTCTCCCGCATGGTGGACTCCTTCGCCGCCAAGGGCCTCGACGTCAAGGACCTCGTCGTGCTCTCCGCCGCCCACACCC
TCGGGAAGGCGCACTGCCCAAACTTCGCCGACCGCCTCTACGGCCCCGGCGCCGACCCGCCGCTCAAGCTCGACGGCGCG
TACGCCGACAGGCTGCGGAAGCAGTGCAAGGAGGGCGCCCCGCCGTACGACGGGAACGTGACGGCGGAGATGGACCCCGG
GAGCTTCACGAGGTTCGACAGCAGCTACTTCCGGCAGGTGGCGAGGAGGCGGGCGCTGCTCCGGTCGGACGCCTGCCTCA
TGGACCACCCCTTCACCAGCGCCTACATCCGCCTCGCCGCCACCGGCAGGTACGACGGCCACTTCTTCCAGGATTTCGCT
CACTCCATGGTGAAGATGGGCGCCATCGGCGTGCTCACCGGCGACCAGGGCGAGATCCGCCTCAAGTGCAACGTCGTCAA
CTCAACCTAG

Alignment

ORF - retro_ogla_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.97 %
• Parental protein coverage: 96.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAAVMASSAQLDEKFYSNSCPSVEAVVRKEMVRALAAAPSLAGPLLRMHFHDCFVRGCDGSVLLDSAGN
          AAA...A...QL....Y...CP..E..V..E..R...A.P.LA..LLR.H.HDCFV.GCD.SVLLDS...
Retrocopy AAAPPAAAAGQLRTGYYRETCPHAEEMVFRETARIIRASPDLAAALLRLHYHDCFVQGCDASVLLDSTPA

Parental  STAEKDATPNQTLRGFGFVERVKAAVEKACPGTVSCADVLALMARDAVWLSKGPFWAVPLGRRDGRVSIA
          ..AE.D..PN..LRGF..V.RVKA..E.ACP.TVSCAD.LALMARDAV.L.KGP.W.VPLGRRDGR.S.A
Retrocopy NAAERDSDPNKSLRGFDSVARVKAKLEAACPATVSCADLLALMARDAVVLAKGPYWHVPLGRRDGRSSTA

Parental  NET-DQLPPPTANFTELTQMFAAKNLDLKDLVVLSAGHTIGTSHCFSFTDRLYNFTGLDNAHDIDPTLEL
          .....QLPP...N.......FAAK.LD.KDLVVLSA.HT.G..HC..F.DRLY...G.D.....D.....
Retrocopy ASCGGQLPPLCGNVSRMVDSFAAKGLDVKDLVVLSAAHTLGKAHCPNFADRLYG-PGADPPLKLDGAYAD

Parental  QYMARLRSKCTSLQDNTTLVEMDPGSFKTFDLGYFKNVAKRRGLFHSDGELLTNGFTRAYVQRHAGGGYK
          ...............N.T..EMDPGSF..FD..YF..VA.RR.L..SD..L....FT.AY....A.G.Y.
Retrocopy RLRKQCKEGAPPYDGNVT-AEMDPGSFTRFDSSYFRQVARRRALLRSDACLMDHPFTSAYIRLAATGRYD

Parental  DEFFADFAASMVKMGGVEVLTGSQGEIRKKCNVVN
          ..FF.DFA.SMVKMG...VLTG.QGEIR.KCNVVN
Retrocopy GHFFQDFAHSMVKMGAIGVLTGDQGEIRLKCNVVN

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_25 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Hordeum vulgare	MLOC_71584	1 retrocopy	retro_hvul_29,
Oryza glaberrima	ORGLA05G0189300	1 retrocopy	retro_ogla_25 ,
Triticum aestivum	Traes_4BL_4CC0E0AAA	1 retrocopy	retro_taes_34,