RetrogeneDB ID: retro_oniv_6

Retrocopy location

• Organism: Indian wild rice (Oryza nivara)
• Coordinates: 1:42660770..42662111(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ONIVA01G51910
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ONIVA05G00830
• Aliases: None
• Description: None

Sequence

>retro_oniv_6
ATGGGGCACGGCCTGAGCTGCAGCCGCGACACCGACGAGTACGACCTGTTCCGCGCGGCGCAGCTGGGCGACATCCACGC
CCTCTCCGCCCTCCTCGCCGCCGACCCCGCGCTCGCCCGCCGCGCCACAGTCTACGACCGCTTCACCGCTCTTCACATCG
CCGCCGCCAACGGCCGCCTCCAGGTACTGTCCATGTTGCTGGATCGCGACGGCGACGTGGACGTCCTGAGCCGCAAGAAG
CAGACGCCGCTGATGGTGGCGGCCATGCGTGGCAACACCGAGTGCGTGGTCAGGCTCCTCCGCGGCGGCGCCAACGTCCT
GACCTTCGACTCGCCGCGCGCCAGGACGTGCCTCCACCACGCCGCCTACTACGGCCACGCCGAGTGCCTGCAGGCCATCC
TCGGCGCCGCGGCGCAGGCGCAGGGCCCCGTGGCCGCCTCCTGGGGCTTCGCGCGCTTCGTCAACGTGAGGGACGAGAGG
GGCGCCACGCCGCTGCACCTGGCTGCGAGGCACGCCCGCGCGTCCTGCGTGCGCCTGCTGCTCGACAAGGGCGCCATCGT
GTCGGCGCCAACCGCCGTCTACGGATTCCCCGGGAGCACGGCTCTGCACCTGGCGGCACGCGCCGGCAGCATGGAGTGCA
TCAGGGAGCTGCTGGCCTGGGGGGCGGACCGGCTCCAGAGGGACTCGGCGGGGCGGATCGCGTACGCGGTGGCGATGAGG
CGGGGGCACAGGGCGTGCGCGGCGCTGCTGAACCCGGCGGCGGCGGAGCCCATAGTGTGGCCGTCCCCGCTCAAGTTCAT
CGGCGAGCTGGAGGCGGACGCCAAGGCACTTCTGGAGGCGGCGCTGATGGAGGCCAACAGGGAGAGGGAGAAGAGGATCC
TGCTCGGCAGCGACATCAACATCAAGGGCGGCGACGAGGAGGAGGAGAGCGAGGATGAGGAGGAGGCGTGCAACATCTGC
TTCGAGCAGGCGTGCAGCATGGAGGTGAAGGAGTGCGGGCACCAGATGTGCGCGGCGTGCACGCTGGCCATCTGCTGCCA
CAGCAAGCCCAACCCCAAGACCCTCCTCCTCCACCCGCCCGCCTGCCCCTTCTGCCGCACCACCATCTCCCGCCTCGTCG
TCGCCACCACCAACTCCAACAAGACCAACAGCCGCCGCCGGTCGAGGAGCAGCAGCAGCAGCTTCAAGGGGGGGCTCTCG
TCGGCCATGGGGTCGTTTTCCAGGATAGGCCGCGGCTCCGGGAGATTGGTGGTGGACGGCAGCAGTGTAGGAGAGCTCGC
CGACAAGCCTGACCACGACTTCTCTTCTGTCGCCGCCGCTGCTGCTATTTGTGACACATGA

Alignment

ORF - retro_oniv_6 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.59 %
• Parental protein coverage: 77.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATLYDRLSVLHIAAANGRIEVLSMFLDRG
          MGHG.SC.R..DE.D.FRAAQLGD..AL.ALLAADP.LARRAT.YDR...LHIAAANGR..VLSM.LDR.
Retrocopy MGHGLSCSRDTDEYDLFRAAQLGDIHALSALLAADPALARRATVYDRFTALHIAAANGRLQVLSMLLDRD

Parental  APPDAVNRHKQTPLMLAAMHGKIDCVLKLLQADANILMFDSVHARTCLHHAAYYGHVDCLQAILAAAQTT
          ...D...R.KQTPLM.AAM.G...CV..LL...AN.L.FDS..ARTCLHHAAYYGH..CLQAIL.AA...
Retrocopy GDVDVLSRKKQTPLMVAAMRGNTECVVRLLRGGANVLTFDSPRARTCLHHAAYYGHAECLQAILGAAAQA

Parental  --PVADSWGFARFVNVRDDHGATPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGN
          ..PVA.SWGFARFVNVRD..GATPLHLAAR..R..CV..LL..GAIVSA.T..YGFPGST.LHLAAR.G.
Retrocopy QGPVAASWGFARFVNVRDERGATPLHLAARHARASCVRLLLDKGAIVSAPTAVYGFPGSTALHLAARAGS

Parental  LDCIRKLLAWGADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALLEA
          ..CIR.LLAWGADRLQRDSAGRI.Y.VA..R.H.ACAALLNP..AEP.VWPSPLKFI.ELE..AKALLEA
Retrocopy MECIRELLAWGADRLQRDSAGRIAYAVAMRRGHRACAALLNPAAAEPIVWPSPLKFIGELEADAKALLEA

Parental  ALMEANREREKKILNGTKYSLSSPSPGDDSADDDACSEVSDTELCCI----CFDQAC-TIEVQDCGHQMC
          ALMEANREREK.IL.G.............S.D............C......C..Q.C.......C.H...
Retrocopy ALMEANREREKRILLGSDINIKGGDEEEESEDEEEACNICFEQACSMEVKECGHQMCAACTLAICCHSKP

Parental  APCTLAL
          .P.TL.L
Retrocopy NPKTLLL

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_6 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018946	1 retrocopy	retro_oind_45,
Leersia perrieri	LPERR05G00860	1 retrocopy	retro_lper_10,
Oryza barthii	OBART05G00890	1 retrocopy	retro_obar_26,
Oryza glumaepatula	OGLUM05G00910	1 retrocopy	retro_oglu_21,
Oryza meridionalis	OMERI05G00950	1 retrocopy	retro_omer_12,
Oryza nivara	ONIVA05G00830	1 retrocopy	retro_oniv_6 ,
Oryza punctata	OPUNC05G00800	1 retrocopy	retro_opun_25,
Oryza glaberrima	ORGLA05G0009300	1 retrocopy	retro_ogla_12,
Oryza rufipogon	ORUFI05G00870	1 retrocopy	retro_oruf_36,
Oryza sativa japonica	OS05G0112000	1 retrocopy	retro_osat_41,