RetrogeneDB ID: retro_oruf_3

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:33990785..33992372(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G43080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI01G47680
• Aliases: None
• Description: None

Sequence

>retro_oruf_3
ATGGCGGCGGCGGCGGCCGGCGGCAAGATCAAGACGGTGGTGGTGCTGGTGATGGAGAACCGCTCCTTCGACCACATGCT
GGGCTGGATGAAGTCTCTCAACCCGGAGATCGACGGCGTCACCGGCGACGAGATCAACCACCTCGACGCCGCCGACCCGA
CCTCCAGGGCCATCCGCTTCGGCGACGGCGCCGAGTACGTCGACCCTGACCCGGGCCACTCCATGCAGGCCATCTACGAG
CAGGTGTACGGCACGCCGTTCGTCGACGCGCGCGCCACGCCCATCACCCCTCCCGGCGTCCCCTCGCCGCCGATGGCCGG
CTTCGCGCAGCAGGCGGAGAAGGAGAAGCCCGGCATGGCGGACACCGTCATGAACGGCTTCCGGCCGGAGGCCGTGCCGG
TGTACCGCGAGCTGGTGCGGCAGTTCGCCGTGTGCGACCGCTGGTTCGCGTCCAACCCGGCGTCGACGCAGCCCAACCGG
CTGTTCGTCCACTCAGCGACGTCGCACGGGCTCGTCAGCAACGACACCAAGCTGCTCGTCGCCGGCCTCCCGCAGCGCAC
CATCTTTGACTCCCTCCACGACGCCGGCTTCTCCTTCGGCATCTACTACCAGTACCCGCCGTCCACGCTCTTCTACCGGA
GCTTGCGCCAGCTCAAGTACGCCGGCAACTTCCACCCCTTCGACCTCGCGTTCCGGCGGCACTGCGCCGAGGGCAAGCTC
CCCAACTACGTCGTCGTCGAGCAGCGCTACTTCGACCTCAAGATGCTCCCCGGCAACGACGACCACCCCTCGCACGACGT
CTCCGAGGGCCAGCGATTCGTCAAGGAGGTGTACGAGGCGCTGCGTGGCGGGCCGCAGTGGGAGGAGGCGCTCCTCGTCG
TCACCTACGACGAGCACGGCGGCTTCTACGACCACGTCCCGACGCCGGTGGACGTGCCCAGCCCCGACGGCATCGTCAGC
GCCGCGCCATTCTTCTTCGAGTTCAACCGCCTCGGCGTCCGCGTCCCGGCGCTCTTCATCTCGCCGTGGATCGAGCCGGG
CACGGTGGTGCACCGGCCGTCGGGGCCGTACCCGACGTCGGAGTTCGAGCACTCCTCCATCCCGGCCACCGTGAAGAAGC
TCTTCAACCTCAAGAGCTTCCTGACCAACCGCGACGCCTGGGCGGGCACCTTCGACGTCGTCCTCACGCGCGACGCGCCG
CGCACCGACTGCCCCGCCACCCTGCCGGAGCCGGTGAAGATGAGGCCGGCGACGGAGGCGGCGGAGCAGGCGGCGCTGAC
GGAGTTCCAGGAGGAGCTGGTGCAGCTGGGGGCGGTGCTCAACGGCGACCACGCCGACGAGGACGTGTACCCGCGCAAGC
TGGTGGAGGGGATGACGGTGGCGGAGGCGGCCAGCTACTGCAACGCCGCCTTCAAGGCCTGGATGGACGAGTGCGACCGC
TGCAGGAAGTGCGGCGAGGACGGGTCCCACATCCCCACGGTGGTGAAGCCGCCGCCGCCGCCGCCGTCGACGTCGTCCTC
AGGCTCTAGCTCCTTTGCTTCCAAGTTGCTGTCTTGCTTTGCGTGTGGTCGTCCTAACAAGAATTAG

Alignment

ORF - retro_oruf_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.73 %
• Parental protein coverage: 65.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDGFVQQARSLGDNMTAAVMNGFSPDSVAVYRELVGEFAVFDRWFASVPSSTQPNRLFVHSATSGGATSN
          M.GF.QQA......M...VMNGF.P..V.VYRELV..FAV.DRWFAS.P.STQPNRLFVHSATS.G..SN
Retrocopy MAGFAQQAEKEKPGMADTVMNGFRPEAVPVYRELVRQFAVCDRWFASNPASTQPNRLFVHSATSHGLVSN

Parental  NPELLAKGYPQRTIFDNVHDAGLSFGVYYQDVPAVLFYRNLRKLKYLTKFHPFHGAFRDHAARGSLPNYA
          ...LL..G.PQRTIFD..HDAG.SFG.YYQ..P..LFYR.LR.LKY...FHPF..AFR.H.A.G.LPNY.
Retrocopy DTKLLVAGLPQRTIFDSLHDAGFSFGIYYQYPPSTLFYRSLRQLKYAGNFHPFDLAFRRHCAEGKLPNYV

Parental  VVEQHYMDSKSHPANDDHPSHDVFQGQMLVKEVYETLRASPQWNQTLMVVTYDEHGGFYDHVPTPVTGVP
          VVEQ.Y.D.K..P.NDDHPSHDV..GQ..VKEVYE.LR..PQW...L.VVTYDEHGGFYDHVPTPV..VP
Retrocopy VVEQRYFDLKMLPGNDDHPSHDVSEGQRFVKEVYEALRGGPQWEEALLVVTYDEHGGFYDHVPTPV-DVP

Parental  SPDGIVGPPPYNFAFDRLGVRVPAIVISPWINKGTVVHGPNGSPTATSEYEHSSIPATVKKLFDLPQDFL
          SPDGIV...P..F.F.RLGVRVPA..ISPWI..GTVVH.P.G.P..TSE.EHSSIPATVKKLF.L...FL
Retrocopy SPDGIVSAAPFFFEFNRLGVRVPALFISPWIEPGTVVHRPSG-PYPTSEFEHSSIPATVKKLFNL-KSFL

Parental  TKRDAWAGTFESVVQGRTEPRTDCPEQLPMPMRIR-LTEANEEAKLSEFQQELVQLASVLNGDH
          T.RDAWAGTF..VV..R..PRTDCP..LP.P...R..TEA.E.A.L.EFQ.ELVQL..VLNGDH
Retrocopy TNRDAWAGTFD-VVLTRDAPRTDCPATLPEPVKMRPATEAAEQAALTEFQEELVQLGAVLNGDH

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_3 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA000088	1 retrocopy	retro_oind_49,
Brachypodium distachyon	BRADI2G61140	1 retrocopy	retro_bdis_16,
Leersia perrieri	LPERR01G38640	1 retrocopy	retro_lper_20,
Oryza barthii	OBART01G44250	2 retrocopies	retro_obar_19, retro_obar_5,
Oryza glumaepatula	OGLUM01G48550	1 retrocopy	retro_oglu_24,
Oryza nivara	ONIVA01G50380	1 retrocopy	retro_oniv_1,
Oryza glaberrima	ORGLA01G0381200	1 retrocopy	retro_ogla_34,
Oryza rufipogon	ORUFI01G47680	2 retrocopies	retro_oruf_3 , retro_oruf_32,