RetrogeneDB ID: retro_oruf_12

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 2:22416358..22417570(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI02G25040
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G24680
• Aliases: None
• Description: None

Sequence

>retro_oruf_12
ATGGCGAGTAGGGTTCATCCACTCCTCGTCGCGTTCTTGGTGGTGCTCCTCGTCGGCACATGCCAGGCAAGGCCGGCTCC
GGGAAAGGCAGCGTCGTCGTCGTCATCGGGAGTGGTGGACGGCATCACGGCCATCTACAACTTCGGGGACTCCATCTCGG
ACACCGGCAACTACCTCCGAGAAGGAGCGGCCGCCGGCGCCATGATGGAGCACACCGTGGCGCCTCCCTACGGCGCGGCC
ATCGGCGGCGCCACGGGGCGGTGCTCCGACGGGTACCTCATGATCGACTACCTCGCCAAGGACCTCGGGCTGCCGCTGCT
CAACCCGTACCTCGACAAGGGCGCCGACTTCACCCACGGTGTCAACTTCGCCGTCACCGGCGCCACCGCCCTCGACGCGG
CGGCCCTCGCGAGGATCGGCGTCGCCGCGCCGCACACCAACAGCTCCCTGAGCGTCCAGCTCCAGTGGTTCAGGGACTTC
ATGAGCGCCACCACCAAGTCGCCCGCCGAGGTGCGCGACAAGCTGGCGAGCTCGCTGGTGATGGTGGGCGAGATCGGCGG
GAACGACTACAACTACGCCTTCGCCGCGAACCGGCCGCGGCCGGGAGGGCGCAGCGCCGCGGACGTCGGGCGCATGGTGA
CCGGCGTGGTGGAGTCGGTGGTGCTCGTCCCGGAGGTGGTGCGGTCCGTGGTGGGCGCGGCGAGGGAGGTGCTCGAGATG
GGCGCGACGCGGGTGGTGATCCCGGGCAACTTCCCGCTGGGTTGCGCGCCGAGCTACCTGGCGGCGGTGGACGAGACGGA
GCGCGCGGCGTACGACGGGAACGGGTGCCTCGTGGGTCTCAACCTGTTCGCGCAGATGCACAACGTGCTGCTGCAGCAGG
GGATCCGGGAGCTGAGGCGGTCGTACCCGGAGGCCACGGTCGCGTACGCCGACTACTTCGGCGCGTACGTGCGGATGCTG
GAGCGCGCGCGCGAGATGGGGTTCGACGGCACGGCGCTGACCAACGCGTGCTGCGGCGCGGGCGGCGGCAAGTACAACTT
CGAGATGGAGCGGATGTGCGGCGCGGGCGGGACGGCGGTGTGCGCGAGGCCCGAGGAGCGGATCAGCTGGGATGGCGTCC
ACCTGACGCAGCGCGCGTACAGCGTCATGGCCGAGCTTCTGTACCACAAGGGCTTCGCGTCCCCTGCACCCGTCAAGTTC
CCGCATCAGTAG

Alignment

ORF - retro_oruf_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.27 %
• Parental protein coverage: 92.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PAASAASTATRTVVVDGITAIYKPRRLAVGHRNLARQGATGG-LLRYTTRLPYGVTVGRATGRCSDGYLI
          PA...A.......VVDGITAIY..........N..R.GA..G.....T...PYG...G.ATGRCSDGYL.
Retrocopy PAPGKAASSSSSGVVDGITAIYNFGDSISDTGNYLREGAAAGAMMEHTVAPPYGAAIGGATGRCSDGYLM

Parental  IDFLARDLGLPLLNPYLDEGADFAHGVNFAVAGATALNTTALAARRITVPHTNSPLDGQLRFFLWFKEFM
          ID.LA.DLGLPLLNPYLD.GADF.HGVNFAV.GATAL...ALA......PHTNS.L..QL....WF..FM
Retrocopy IDYLAKDLGLPLLNPYLDKGADFTHGVNFAVTGATALDAAALARIGVAAPHTNSSLSVQLQ---WFRDFM

Parental  NSTTSSPQEIREKLSKSLVMLGEIGGNDYNYAFLQTWPMDGGYSLGNVTRMIESVATAVDLVPEVVQSIA
          ..TT.SP.E.R.KL..SLVM.GEIGGNDYNYAF....P..GG.S...V.RM...V...V.LVPEVV.S..
Retrocopy SATTKSPAEVRDKLASSLVMVGEIGGNDYNYAFAANRPRPGGRSAADVGRMVTGVVESVVLVPEVVRSVV

Parental  SAAKEVLDMGATRVVIPGNLPLGCVPSYMSAVNATDRAAYDARGCLVALNLFAALHNAWLRRAVGELRRA
          .AA.EVL.MGATRVVIPGN.PLGC.PSY..AV..T.RAAYD..GCLV.LNLFA..HN..L.....ELRR.
Retrocopy GAAREVLEMGATRVVIPGNFPLGCAPSYLAAVDETERAAYDGNGCLVGLNLFAQMHNVLLQQGIRELRRS

Parental  YRGAAVVAYADYSAAYAATLDGAAALGFDERRVFRACCGKGGGGAYGFDVRAMCGAPGTAACADPGRYVS
          Y...A.VAYADY..AY...L..A...GFD......ACCG..GGG.Y.F....MCGA.GTA.CA.P....S
Retrocopy Y-PEATVAYADYFGAYVRMLERAREMGFDGTALTNACCG-AGGGKYNFEMERMCGAGGTAVCARPEERIS

Parental  WDGVHLTQRAYGVMAELLFRRGLVHPPPINF
          WDGVHLTQRAY.VMAELL...G...P.P..F
Retrocopy WDGVHLTQRAYSVMAELLYHKGFASPAPVKF

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_12 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza nivara	ONIVA02G26140	1 retrocopy	retro_oniv_13,
Oryza glaberrima	ORGLA02G0200400	1 retrocopy	retro_ogla_1,
Oryza rufipogon	ORUFI02G24680	1 retrocopy	retro_oruf_12 ,
Oryza sativa japonica	OS02G0604000	1 retrocopy	retro_osat_12,
Sorghum bicolor	Sb04g025300	1 retrocopy	retro_sbic_16,