RetrogeneDB ID: retro_oniv_13

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 2:23772699..23773911(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA02G26460
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA02G26140
• Aliases: None
• Description: None

Sequence

>retro_oniv_13
ATGGCGAGTAGGGTTCATCCACTCCTCGTCGCGTTCTTGGTGGTGCTCCTCGTCGGCACATGCCAGGCAAGGCCGGCTCC
GGGAAAGGCAGCGTCGTCGTCGTCATCGGGAGTGGTGGACGGCATCACGGCCATCTACAACTTCGGGGACTCCATCTCGG
ACACCGGCAACTACCTCCGAGAAGGAGCGGCCGCCGGCGCCATGATGGAGCACACCGTGGCGCCTCCCTACGGCGCGGCC
ATCGGCGGCGCCACGGGGCGGTGCTCCGACGGGTACCTCATGATCGACTACCTCGCCAAGGACCTCGGGCTGCCGCTGCT
CAACCCGTACCTCGACAAGGGCGCCGACTTCACCCACGGTGTCAACTTCGCCGTCACCGGCGCCACCGCCCTCGACGCGG
CGGCCCTCGCGAGGATCGGCGTCGCCGCGCCGCACACCAACAGCTCCCTGAGCGTCCAGCTCCAGTGGTTCAGGGACTTC
ATGAGCGCCACCACCAAGTCGCCCGCCGAGGTGCGCGACAAGCTGGCGAGCTCGCTGGTGATAGTGGGCGAGATCGGCGG
GAACGACTACAACTACGCCTTCGCCGCGAACCGGCCGCGGCCGGGAGGGCGCAGCGCCGCGGACGTCGGGCGCATGGTGA
CCGGCGTGGTGGAGTCGGTGGTGCTCGTCCCGGAGGTGGTGCGGTCCGTGGTGGGCGCGGCGAGGGAGGTGCTCGAGATG
GGCGCGACGCGGGTGGTGATCCCGGGCAACTTCCCGCTGGGTTGCGCGCCGAGCTACCTGGCGGCGGTGGACGAGACGGA
GCGCGCGGCGTACGACGGGAACGGGTGCCTCGTGGGTCTCAACCTGTTCGCGCAGATGCACAACGTGCTGCTGCAGCAGG
GGATCCGGGAGCTGAGGCGGTCGTACCCGGAGGCCACGGTCGCGTACGCCGACTACTTCGGCGCGTACGTGCGGATGCTG
GAGCGCGCGCGCGAGATGGGGTTCGACGGCACGGCGCTGACCAACGCGTGCTGCGGCGCGGGCGGCGGCAAGTACAACTT
CGAGATGGAGCGGATGTGCGGCGCGGGCGGGACGGCGGTGTGCGCGAGGCCCGAGGAGCGGATCAGCTGGGATGGCGTCC
ACCTGACGCAGCGCGCGTACAGCGTCATGGCCGAGCTTCTGTACCACAAGGGCTTCGCGTCCCCTGCACCCGTCAAGTTC
CCGCATCAGTAG

Alignment

ORF - retro_oniv_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.19 %
• Parental protein coverage: 77.13 %
• 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  IDFLARDLGLPLLNPYHDEGADFAHGVNFAVAGATALNTTALAARRITVPHTNSPSD--LRWFKEFMNST
          ID.LA.DLGLPLLNPY.D.GADF.HGVNFAV.GATAL...ALA......PHTNS.....L.WF..FM..T
Retrocopy IDYLAKDLGLPLLNPYLDKGADFTHGVNFAVTGATALDAAALARIGVAAPHTNSSLSVQLQWFRDFMSAT

Parental  TSSPQEIREKLSKSLVMLGEIGGNDYNYAFLQTWPMDGGYSLGNVTRMIESVATAVDLVPEVVQSIASAA
          T.SP.E.R.KL..SLV..GEIGGNDYNYAF....P..GG.S...V.RM...V...V.LVPEVV.S...AA
Retrocopy TKSPAEVRDKLASSLVIVGEIGGNDYNYAFAANRPRPGGRSAADVGRMVTGVVESVVLVPEVVRSVVGAA

Parental  KEVLDMGATRVVIPGNLPLGCVPSYMSAVNATDRAAYDARGCLVALNLFAALHNAWLRRAVGELRRAYRG
          .EVL.MGATRVVIPGN.PLGC.PSY..AV..T.RAAYD..GCLV.LNLFA..HN..L.....ELRR.Y..
Retrocopy REVLEMGATRVVIPGNFPLGCAPSYLAAVDETERAAYDGNGCLVGLNLFAQMHNVLLQQGIRELRRSY-P

Parental  AAVVAYADYSAEYAATLDGAAALGFDERRVFRACCGAGAG
          .A.VAYADY...Y...L..A...GFD......ACCGAG.G
Retrocopy EATVAYADYFGAYVRMLERAREMGFDGTALTNACCGAGGG

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza nivara was not studied using ChIP-Seq data.

EST

Oryza nivara was not studied using EST data.

TSS

Oryza nivara was not studied using FANTOM5 data.

Lab

retro_oniv_13 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza nivara 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,