RetrogeneDB ID: retro_opun_25

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:45889919..45891284(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G44590
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC05G00800
• Aliases: None
• Description: None

Sequence

>retro_opun_25
ATGGAGTCGTTCCGAGCTGCTCTGCCCACCGCCGCCTATACTCCTATGGGGCACGGCCTGAGCTGCAGCCGCGACACCGA
CGAGTACGACTTGTTCCGCGCGGCGCAGCTTGGCGACACCCACGCCCTCTCCGCCCTCCTCACCGCCGACCCCGCGCTCG
CCCGCCGCGCCACCATCTACGACCGCTCCACCGCTCTCCACATCACCGCCGCCAATGGCCGCCTCCAGGCTCTGTCCATG
TTGCTGGATCGCGACGGCGTGCGGCCGGACGTCGTCAACCGCAAGAAGCAGACGCCGCTGATGGTGGCGGCCATGCGTGG
CAACACCGACTGCGTGCTCAAGCTCCTCCACGCCGGCGCCAACATCCTCACCTTCGACTCGCCGCGCGCCAGGACGTGCC
TCCACCACGCCGCCTACTACGGCCACGCCGACTGCCTGCAGGCCATCCTCGCCGCCGCGCAGGCGCAGGGCCCCGTGGCC
GCCTCCTGGGGCTTCGCGCGCTTCGTCAACGTCAGGGACGAGCGGGGCGCCACGCCGCTGCACCTGGCGGCAAGGCACGG
CCGCGCGGCCTGCGTGCGGCTGCTGCTCGACAAGGGCGCCATCGTCTCCGCGCCAACCGCCGTCTACGGCTTCCCAGGGA
GCACGGCGCTGCACCTGGCCGCACGCGCCGGCAACCTGGACTGCATCCGAGAGCTGCTCGCCTGGGGGGCGGACCGGCTG
CAGAGGGACTCGGCCGGGCGGATCGCGTACGCGGTGGCGGTGAGGCGGGGCCACAGAGCGTGCGCGGCGCTGCTGAACCC
AGCGGCGGCGGAGCCCATAGTGTGGCCGTCCCCGCTCAAGTTCATCGGCGAGCTGGAGGCGGACGCCAAGGCACTTCTGG
AGGCGGCGCTGATGGAGGCGAACAGGGAGAGGGAGAAGAGGATCCTCGTCAACCTCAGCATCAAGGGCGGCGGCGGCGAG
GAGAGCGAGGAGGAGGAGGAGGAGGAGGCGTGCAACATCTGCTTCGAGCAGGCGTGCAGCATGGAGGTGAAGGAGTGCGG
GCACCAGATGTGCGCGGCGTGCACGCTGGCGATCTGCTGCCACAGCAAGCCCAACCCCAAGACCCTCCTCCTCCACCCGC
CGGCCTGCCCCTTCTGCCGCACCACCATCTCCCGCCTCGTCGTCGCAACCACCAAGACCAACGCCGCGGCGCTAAGCCGC
CGGCGGTCGAGGAGATCTCGCGATGGAAGCAGCAGCTTCAAGGGGCTCTCCTCGGCCATCGGGTCGTTTTCCAGGATGGG
GCGAGGCTCCGGGAGATTGGTGGTCGCCGACAAGCCTGACCACGACTTCTCCTCTCTCGCCGCTGCTGCTAATTGTGTCG
TGTGA

Alignment

ORF - retro_opun_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.61 %
• Parental protein coverage: 70. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGHGVSCARTGDEHDFFRAAQLGDLDALAALLAADPSLARRATLYDRLSVLHIAAANGRIEVLSMFLDR-
          MGHG.SC.R..DE.D.FRAAQLGD..AL.ALL.ADP.LARRAT.YDR...LHI.AANGR...LSM.LDR.
Retrocopy MGHGLSCSRDTDEYDLFRAAQLGDTHALSALLTADPALARRATIYDRSTALHITAANGRLQALSMLLDRD

Parental  GAPPDAVNRHKQTPLMLAAMHGKIECVLKLLQAGANILMFDSVHARTCLHHAAYYGHVDCLQAIISAAQT
          G..PD.VNR.KQTPLM.AAM.G...CVLKLL.AGANIL.FDS..ARTCLHHAAYYGH.DCLQAI..AAQ.
Retrocopy GVRPDVVNRKKQTPLMVAAMRGNTDCVLKLLHAGANILTFDSPRARTCLHHAAYYGHADCLQAILAAAQA

Parental  T-PVADSWGFARFVNVRDDHGATPLHLAARQGRPGCVQVLLENGAIVSALTGSYGFPGSTSLHLAARSGN
          ..PVA.SWGFARFVNVRD..GATPLHLAAR.GR..CV..LL..GAIVSA.T..YGFPGST.LHLAAR.GN
Retrocopy QGPVAASWGFARFVNVRDERGATPLHLAARHGRAACVRLLLDKGAIVSAPTAVYGFPGSTALHLAARAGN

Parental  LDCIRKLLAWGADRLQRDSAGRIPYSVALKRNHGACAALLNPTSAEPMVWPSPLKFISELEPEAKALLEA
          LDCIR.LLAWGADRLQRDSAGRI.Y.VA..R.H.ACAALLNP..AEP.VWPSPLKFI.ELE..AKALLEA
Retrocopy LDCIRELLAWGADRLQRDSAGRIAYAVAVRRGHRACAALLNPAAAEPIVWPSPLKFIGELEADAKALLEA

Parental  ALMEANREREKKILNGTKYSLPSPSPGDDSADDDACS
          ALMEANREREK.IL....................AC.
Retrocopy ALMEANREREKRILVNLSIKGGGGEESEEEEEEEACN

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza punctata was not studied using ChIP-Seq data.

EST

Oryza punctata was not studied using EST data.

TSS

Oryza punctata was not studied using FANTOM5 data.

Lab

retro_opun_25 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza punctata 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,