RetrogeneDB ID: retro_oruf_6

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 1:39747335..39748469(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI01G49270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI05G01180
• Aliases: None
• Description: None

Sequence

>retro_oruf_6
ATGGTGCAGCGCACTTCATCCGATTCGGCGGCGTCGGCTGAGGCCATGGTCATGGACCTGAGTCCCAAGCGTCCCGCCAA
GTCCTACGGCGGCGAAGGCGGCTCGTACTTTGATTGGTCCCCCTCCGAGCTGCCCATGCTCCGCGCCGCCTCCATCGGCG
CCGCCAAACTCTCGCTTGCCGCCGGAGGCCTCGCCCTCCCCTTCTACTCCGATTCGGCTAAGGTGGCCTACGTCCTCCAG
GGCAAGGGCACCTGCGCCGTTCTCCTCCCCGAGACCCCCTCCGAGAAGATCCTACCCATCAAAGAGGGCGACGCGCTCGC
CCTTCCATTCGGCGTTGTCACCTGGTGGCACAACCTGCACGCCGCCACCACCGAACTCGTCGTCCTCTTCCTCGGGGACA
CATCCAAGGGCCACACCGCCGGCCGCTTCACCAACATGCAGCTCACCGGCTCCACCGGCATCTTCACCGGCTTCTCCACC
GAGTTCGTCGCCCGCGCCTGGGACCTCCCGCAGGACGCCGCTGCCTCCCTCGTCTCCACCCAGCCCGGCGCCGGCATCGT
GAAGCTCAAGGATGGCTTCAGGATGCCCGAGGGTTGCGACAAGGACAGGGAGGGCATGGTGCTCAACTGCTTGGAGGCGC
CGCTGGACGTGGACATCAAGAACGGGGGCCGCGTGGTGGTGCTGAACACGCAGAACCTGCCGCTGGTGAAGGAGGTGGGG
CTGGGCGCCGACCTGGTGAGGATCGACGGCCACTCCATGTGCTCGCCGGGGTTCTCGTGCGACTCGGCGTACCAGGTGAC
GTACATCGTGCGGGGCAGCGGGCGCGTGCAGGTGGTGGGCATCGACGGGACGCGCGTGCTGGAGACCCGCGCCGAGGGTG
GCTGCCTCTTCATCGTCCCCAGGTTCTTCGTCGTCTCCAAGATCGCCGACGACACCGGCATGGAGTGGTTCTCCATCATC
ACCACTCCCAACCCCATCTTCTCCCACCTCGCCGGGAGGACCTCCGTCTGGAAGGCCATCTCCCCCGCCGTGCTCCAGGC
CTCCTTCAACACCACCCCGGAGATGGAGAACCTCTTCCGCTCCAAGAGGCTCGACTCCGAGATCTTCTTCGCCCCCAATT
CGAATTCGATTTGA

Alignment

ORF - retro_oruf_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.69 %
• Parental protein coverage: 99.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VDLTPRQARKAYGGDGGTYYEWSPADLPMLELANIGGAKLSLNAGGLALPSFSDSGKVAYVLQGKGTCGI
          .DL.P....K.YGG.GG.Y..WSP..LPML..A.IG.AKLSL.AGGLALP..SDS.KVAYVLQGKGTC..
Retrocopy MDLSPKRPAKSYGGEGGSYFDWSPSELPMLRAASIGAAKLSLAAGGLALPFYSDSAKVAYVLQGKGTCAV

Parental  VLPEASKEKVIAVKEGDSLALPFGVVTWWHNLPESPIELVILFLGDTSKAHKAGQFTNMQLTGATGIFTG
          .LPE...EK....KEGD.LALPFGVVTWWHNL.....ELV.LFLGDTSK.H.AG.FTNMQLTG.TGIFTG
Retrocopy LLPETPSEKILPIKEGDALALPFGVVTWWHNLHAATTELVVLFLGDTSKGHTAGRFTNMQLTGSTGIFTG

Parental  FSTEFVGRAWDLAESDAVKLVSSQPASGIVKIKSGQKLPEPSAADREGMALNCLEAPLDVDIKNGGRVVV
          FSTEFV.RAWDL....A..LVS.QP..GIVK.K.G...PE....DREGM.LNCLEAPLDVDIKNGGRVVV
Retrocopy FSTEFVARAWDLPQDAAASLVSTQPGAGIVKLKDGFRMPEGCDKDREGMVLNCLEAPLDVDIKNGGRVVV

Parental  LNTANLPMVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYFIRGSGRVQVVGADGKRVLDTHVEGGNLF
          LNT.NLP.VKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTY..RGSGRVQVVG.DG.RVL.T..EGG.LF
Retrocopy LNTQNLPLVKEVGLGADLVRIDGHSMCSPGFSCDSAYQVTYIVRGSGRVQVVGIDGTRVLETRAEGGCLF

Parental  IVPRFCVVSKIADASGLQWFSIITTPNPIFSHLAGKTSVWKAISPEVLEASFNATPEMEKLFRSKRIDSE
          IVPRF.VVSKIAD..G..WFSIITTPNPIFSHLAG.TSVWKAISP.VL.ASFN.TPEME.LFRSKR.DSE
Retrocopy IVPRFFVVSKIADDTGMEWFSIITTPNPIFSHLAGRTSVWKAISPAVLQASFNTTPEMENLFRSKRLDSE

Parental  IFFAPN
          IFFAPN
Retrocopy IFFAPN

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_6 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018931	1 retrocopy	retro_oind_1,
Oryza brachyantha	OB05G11140	1 retrocopy	retro_obra_13,
Oryza glumaepatula	OGLUM05G01170	1 retrocopy	retro_oglu_9,
Oryza nivara	ONIVA05G01190	1 retrocopy	retro_oniv_21,
Oryza punctata	OPUNC05G01050	1 retrocopy	retro_opun_21,
Oryza glaberrima	ORGLA05G0012000	1 retrocopy	retro_ogla_28,
Oryza rufipogon	ORUFI05G01180	1 retrocopy	retro_oruf_6 ,
Oryza sativa japonica	OS05G0116000	1 retrocopy	retro_osat_27,