RetrogeneDB ID: retro_oglu_2

Retrocopy location

• Organism: Oryza glumaepatula
• Coordinates: 3:37109912..37111490(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OGLUM03G41100
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OGLUM03G39370
• Aliases: None
• Description: None

Sequence

>retro_oglu_2
ATGGCGGCAGCGGCCGGCGGCAAGATCAAGACGGTGGTGGTGGTGGTGATGGAGAACCGCTCCTTCGACCACATGCTGGG
CTGGATGAAGTCTCTCAACCCGGAGATCGACGGCGTCACCGGCGACGAGACCAACCACCTCGACGCCGCCGACCCAACCT
CCAGGGCCATCCGCTTCGGCGACGGCGCCGAGTACGTCGACCCTGACCCGGGCCACTCCATGCAGGCCATCTACGAGCAG
GTGTACGGCACGCCGTTCGTCGACGCGCGCGCCACGCCCATCACCCCTCCCGGCGTCCCCTCGCCGCCGATGGCCGGCTT
CGCGCAGCAGGCGGAGAAGGAGAAGCCCGGCATGGCGGACACCGTCATGAACGGCTTCCGGCCGGAGGCCGTGCCGGTGT
ACCGCGAGCTGGTCCGGCAGTTCGCCGTGTGCGACCGCTGGTTCGCGTCCAACCCGGCGTCGACGCAGCCCAACCGGCTG
TTCGTCCACTCGGCGACGTCGCACGGGCTCGTCAGCAACGACACCAAGCTGCTCGTCGCCGGCCTCCCGCAGCGCACCAT
CTTCGATTCGCTCCACGACGCCGGCTTCTCCTTCGGCATCTACTACCAGTACCCGCCGTCGACGCTCTTCTACCAGAGCT
TGCGCCAGCTCAAGTACGCCGGCAACTTCCACCCCTTCGACCTCGCGTTCCGGCGGCACTGCGCCGAGGGCAAGCTCCCC
AACTACGTCGTCGTCGAGCAGCGCTACTTCGACCTCAAGATGCTCCCCGGCAACGACGACCACCCCTCGCACGACGTCTC
CGAGGGCCAGCGCTTCGTCAAGGAGGTGTACGAGGCGCTGCGTGGCGGGCCACAGTGGGAGGAGGCGCTCCTCGTCGTCA
CCTACGACGAGCACGGCGGCTTCTACGACCACGTCCCGACGCCGGTGGGCGTGCCAAGCCCCGACGGCATCGTCAGCGCC
GCGCCATTCTTCTTCGAGTTCGACCGCCTCGGCGTCCGCGTCCCGGCGCTCTTCATCTCGCCGTGGATCGAGCCGGGCAC
GGTGGTGCACCGGCCGTCGGGGCCGTACCCGACGTCGGAGTTCGAGCACTCCTCCATCCCGGCCACCGTGAAGAAGCTCT
TCAACCTCAAGAGCTTCCTGACCAACCGCGACGCCTGGGCGGGCACCTTCGACGTCGTCCTCACGCGCGACGCGCCGCGC
ACCGACTGCCCCGCCACCCTGCCGGAGCCGGTGAAGATGAGGCCGACGACGGAGGCGGCGGAGCAGGCGGCGCTGACGGA
GTTCCAGGAGGAGCTGGTGCAGCTGGGGGCGGTGCTCAACGGCGACCACGCCGACGAGGACGTGTACCCGCGCAAGCTGG
TGGAGGGGATGACGGTGGCGGAGGCGGCCAGCTACTGCAACGCCGCCTTCAAGGCCTGGATGGACGAGTGCGACCGGTGC
AGGAAGTGCGGCGAGGACGGGTCCCACATCCCCACAGTGGTGAAGCCGCCGCCGCCGTCGACGTCGTCCTCAGGCTCTAG
CTCCTTTGCTTCCAAGTTGCTGTCTTGCTTTGCGTGTGGTCGTCCTAACAAGAATTAG

Alignment

ORF - retro_oglu_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.21 %
• Parental protein coverage: 75.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PMSGFAQNARGMGLGMPQNVMSGFKPESVPVYAALADEFAVFDRWFASVPTSTQPNRLYVHSATSHGLTF
          PM.GFAQ.A.....GM...VM.GF.PE.VPVY..L...FAV.DRWFAS.P.STQPNRL.VHSATSHGL..
Retrocopy PMAGFAQQAEKEKPGMADTVMNGFRPEAVPVYRELVRQFAVCDRWFASNPASTQPNRLFVHSATSHGLVS

Parental  NARKDLIHGFPQKTIFDSLEENGLSFGIYYQNIPATLFYQSLRRLKHLVKFHQYSLKFKLHAKWGKLPNY
          N..K.L..G.PQ.TIFDSL...G.SFGIYYQ..P.TLFYQSLR.LK....FH...L.F..H...GKLPNY
Retrocopy NDTKLLVAGLPQRTIFDSLHDAGFSFGIYYQYPPSTLFYQSLRQLKYAGNFHPFDLAFRRHCAEGKLPNY

Parental  AVIEQRYFDCEMFPANDDHPSHDVARGQRFVKEVYETLRASPQWNETALIITYDEHGGFYDHVPTPVVGV
          .V.EQRYFD..M.P.NDDHPSHDV..GQRFVKEVYE.LR..PQW.E..L..TYDEHGGFYDHVPTPV.GV
Retrocopy VVVEQRYFDLKMLPGNDDHPSHDVSEGQRFVKEVYEALRGGPQWEEALLVVTYDEHGGFYDHVPTPV-GV

Parental  PQPDGIVGPDPYYFKFDRLGVRVPSFLISPWIEKRTVIHEPNGPQDSSQYEHSSIPATVKKLFNLHSNFL
          P.PDGIV...P..F.FDRLGVRVP...ISPWIE..TV.H.P.GP...S..EHSSIPATVKKLFNL.S.FL
Retrocopy PSPDGIVSAAPFFFEFDRLGVRVPALFISPWIEPGTVVHRPSGPYPTSEFEHSSIPATVKKLFNLKS-FL

Parental  TKRDAWAGTFENYFKIRKTPRTDCPEKLPEVTKSLRPFGPKEDSSLSEFQVELIQLASQLNGDHV-LNTY
          T.RDAWAGTF......R..PRTDCP..LPE..K........E...L.EFQ.EL.QL...LNGDH.....Y
Retrocopy TNRDAWAGTFD-VVLTRDAPRTDCPATLPEPVKMRPTTEAAEQAALTEFQEELVQLGAVLNGDHADEDVY

Parental  P-DIGRTMTVGEANRYAEDAVARFLEAGRIALRAGANESALVTM--RPALTSRASPSSDLSSEL
          P......MTV.EA..Y...A..............G...S...T....P......S.SS...S.L
Retrocopy PRKLVEGMTVAEAASYCNAAFKAWMDECDRCRKCGEDGSHIPTVVKPPPPSTSSSGSSSFASKL

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza glumaepatula was not studied using ChIP-Seq data.

EST

Oryza glumaepatula was not studied using EST data.

TSS

Oryza glumaepatula was not studied using FANTOM5 data.

Lab

retro_oglu_2 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza glumaepatula 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
Oryza glumaepatula	OGLUM01G48550	1 retrocopy	retro_oglu_24,
Oryza glumaepatula	OGLUM03G39370	1 retrocopy	retro_oglu_2 ,
Oryza sativa japonica	OS03G0826600	1 retrocopy	retro_osat_36,