RetrogeneDB ID: retro_ogla_27

Retrocopy location

• Organism: African rice (Oryza glaberrima)
• Coordinates: 4:14319772..14320957(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORGLA04G0104000
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORGLA07G0032400
• Aliases: None
• Description: None

Sequence

>retro_ogla_27
ATGATGGACCCGGAGATGATGCGGGTGGCGCAGGAGCAGATGAGACGGATGCCCCCCGCCGCGCTCGCCGCGATGCAGCA
GCAGCTCACGTCCAACCCGAGCCTCCTCCGCTTCGCCACGGAGGGCATCAAGACCCTGACACCCGACGACCTCCGCCGCG
CCGGGGAGCAGATGAGCCGGACGAGCGCCGAGGAGGTGCTCGGCATGTCCCGGAGGCTCGCCGCCGCCAGCCCGGAGGAG
CTCGCCGCGACGATGAAGAACGCCCAGGCCGAGCAGCAGCGCGCGTCGTCCTACGCGGCGGTGTCCGGCGCCAGGGCGCT
CAAGGACCAGGGCAACGCGCTCTTCAGGCTCGCCCGCCACGCCGACGCCGCCGCCAAGTACGCGCTCGCCGTCGACAACC
TGCGGAGCGTCCCGTCGTCGGCGTCGCGGTCGCTGCGGGCGGTGTGCGGCGTCAACCTGATGGCGTGCCACCTCAAGACC
GGGAGGCTCGCCGAGTGCGTGGAGCTAGGCTCCGATGTGCTCGGCCTCGACCCGGGCAACGTCAAGGCGCACTACCGGAG
AGGGCAGGCGTACAGGGAGCTCGGGAGGATGGAGGCGGCCGTGGCCGACCTGAGGAGAGCGCACGAGCTCTCCCCCGAGG
AGGACGCCATCGCCGACGCTCTGCGAGACGCCGAAGAGAAGCTCGGGGCTCCCAGAGGCCTCGTCATTGAGGAAATCGTC
GAAGAAGAAGAAGAAGCACAAGGTTCAGAGATACTACCAACCAGTGGGGCAACTTCGTCTTCAACCTCTGGACACAGTGT
TCCATCGCCATCGCCATCGCCATCGCCGTCTGCTGCTGCTGCGGCTGAGATGATGAACTCCATGGGGGACCCGGCGATGG
GGAAGATGGTCGCGTCCGTGGTGCAGGGCATGGATCCGGAGACGGTGTCGATCATCGGGAAGCAGTTCGGGGTGGACCTG
TCCAGGGACGACGCTGCCAGGTTGCAGGACGCCATGAAGAAGCTGTCTCCGGAGAACCTGGAGAAGGTGATGGGTTGGGT
GAACCGGGCACGGCGCGCGGCGGAGGCCGCGAGGAAGGCCAAGGAGCTCCTCCTGGGCAGCAGGAGAGGCTGGCTGGTGC
TCGCCATTGTCGTGCTCGTCCTCGCGTTCGTCCTTCATCACCTGCTCGGGTTCATCGGAGCGTGA

Alignment

ORF - retro_ogla_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.06 %
• Parental protein coverage: 51.01 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMDPEMMRLAQEQMSKMSPADLARMQQQLLSNPNLVKLASESMKNMRADDFRRAAQQMNQTRPDEMLDMA
          MMDPEMMR.AQEQM..M.PA.LA.MQQQL.SNP.L...A.E..K....DD.RRA..QM..T...E.L.M.
Retrocopy MMDPEMMRVAQEQMRRMPPAALAAMQQQLTSNPSLLRFATEGIKTLTPDDLRRAGEQMSRTSAEEVLGMS

Parental  EKLANANPEEVAAM--KVQAEQQM--SYV-ISGAKMLKQQGNELHRCEQYSEAAAKYKLAKDNLKSIPSQ
          ..LA.A.PEE.AA.....QAEQQ...SY...SGA..LK.QGN.L.R......AAAKY.LA.DNL.S.PS.
Retrocopy RRLAAASPEELAATMKNAQAEQQRASSYAAVSGARALKDQGNALFRLARHADAAAKYALAVDNLRSVPSS

Parental  SAHSLQLVCTLNLMACYLKTRNFEECINEGSEVLTYDSSNVKAYYRRGQAYKELGNLEAAVGDLSKAHEL
          ...SL..VC..NLMAC.LKT....EC...GS.VL..D..NVKA.YRRGQAY.ELG..EAAV.DL..AHEL
Retrocopy ASRSLRAVCGVNLMACHLKTGRLAECVELGSDVLGLDPGNVKAHYRRGQAYRELGRMEAAVADLRRAHEL

Parental  SPDDETIAAVLRDAEEKLAVEGKGAKHPKGVVIEEVVDDASEPSSSQRSSSPGYTVSQPPEEGNSRPSGS
          SP....IA..LRDAEEKL.....G......V..EE..........S...SS.....S.P.......PS..
Retrocopy SPEEDAIADALRDAEEKLGAP-RGLVIEEIVEEEEEAQGSEILPTSGATSSSTSGHSVPSPSPSPSPSAA

Parental  SSID
          ....
Retrocopy AAAE

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_27 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI1G56980	1 retrocopy	retro_bdis_36,
Aegilops tauschii	F775_31516	1 retrocopy	retro_atau_10,
Hordeum vulgare	MLOC_56431	1 retrocopy	retro_hvul_94,
Oryza barthii	OBART07G03860	1 retrocopy	retro_obar_28,
Oryza glaberrima	ORGLA07G0032400	1 retrocopy	retro_ogla_27 ,