RetrogeneDB ID: retro_opun_12

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 5:30848128..30849514(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC05G25630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC01G20010
• Aliases: None
• Description: None

Sequence

>retro_opun_12
ATGGGGCGCGGTCTCCTCAGCTGCCTCCTGCTGCTGCAACTCGTCCTCCTCGCCGGCGGTTGGCAGGAGGAGTTCCTCCG
GCTGCCGTCCGATGGCGGGACGAGGTGGGCGTTGCTGGTGGCGGGGTCGAGTGGGTTCTACAACTACCGGCATCAGGCGG
ACGTGTGCCACGCGTACCAGGTAATGAGGAAGGGAGGAGTGAAGGAGGAGAACATCGTGGTGATGATGTACGACGACATC
GCCCACCACCCCGACAACCCCAGGCCTGGACTCATCATCAACCACCCCACCGGCCCCGACGTCTACTCCGGCGTCCCCAA
GGATTACACCGCCAACGACGTCAACGTCAACAACTTCCTCGCCGTCCTCCTCGGCAACCAGTCCGCCCTCACCGGCGCCG
GCAGCGGCAAGGTCGTCGCCAGCGGCCCCAACGACCACGTCTTCGTCTACTACGCCGACCACGGCGGCCCCGGTGTCCTG
AGCATGCCAGCCGACGGCGAGTACCTGTACGCCGACGACCTTGTCAAGGCGCTCAAGAAGAAGCACGCCGCCGGCGCCTA
CAAGAGCCTCGTCGTCTACGTGGAGGCCTGCGAGTCCGGCAGCATCTTCCAGGGCCTCCTGCCGGCCAACATCTCCGTCT
ACGCCACCACGGCTTCCAACGCCGACGAGAGCAGCTGGGGCACCTACTGCCCCGGCGACGACCATGGTGCCCCGCCGGCG
GAGTTCGACACCTGCCTCGGCGACCTCTACAGCGTGGCCTGGATGGAGGACGCCGACGCGCACCAGGACGGCCGCCGCGC
CGAGACGCTGCTGCAGCAGTACAAGACGGTCAAGAACCGGACGTCCGATGAGGGCACCTACACGCTCGGCTCCCACGTCA
TGCAGTACGGCGACATGGCGCTCGCACCGCAGAGCCTCGACCTCTACTACATGGACACAACATCAGCGGCGACTGCGAAC
GACGACAAATTAGCTGCTGCTGGCGCCGTGAAAGGCACTGTGTCCGTGAAGCAGCGCGACGCCGATCTGTTCTACTTGTG
GCGCAAGTACCGGAGAGCCGGCGAGGGGACGGCTGAGAAGGTGGAGGCTCGGGAACGGCTTCTCCAGGAGATGGGGCGGC
GATCGCGCGTGGACAGAAGCGTGGAGCTGATCGAAGGCCTCCTTCTCGACGGCGGCAAGGTCGACGTCGGCGTGCGGGCG
GCGGTGGTTGACGACTGGGAGTGCCTCAAGTCGATGGTGCGGACGTTCGAGGACAAGTGTGGGTGGCTGGGGCAGTACGG
GATAAAGCACATGCGCTCCTTCGCCAACATTTGCAACGCCGGCGTCTCTCACCACGCCATGCCCAACGCCGCGTCCCTCG
CCTGCCCCTCCCCTCCCCTTAGTTGA

Alignment

ORF - retro_opun_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.85 %
• Parental protein coverage: 73.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GTRWAVLIAGSNGYYNYRHQADVCHAYQIMKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDVY
          GTRWA.L.AGS.G.YNYRHQADVCHAYQ.M..GG.K.ENI.V.MYDDIAH.P.NPRPG.IINHP.G.DVY
Retrocopy GTRWALLVAGSSGFYNYRHQADVCHAYQVMRKGGVKEENIVVMMYDDIAHHPDNPRPGLIINHPTGPDVY

Parental  AGVPKDYTGKEVNVKNLFAVLLGNKTAVKG-GSGKVLDSGPNDHIFIFYSDHGGPGVLGMPT-YPYLYGD
          .GVPKDYT...VNV.N..AVLLGN..A..G.GSGKV..SGPNDH.F..Y.DHGGPGVL.MP....YLY.D
Retrocopy SGVPKDYTANDVNVNNFLAVLLGNQSALTGAGSGKVVASGPNDHVFVYYADHGGPGVLSMPADGEYLYAD

Parental  DLVDVLKKKHAAGTYKSLVFYLEACESGSIFEGLLPNDINVYATTASNADESSWGTYCPG-EYPSPPPEY
          DLV..LKKKHAAG.YKSLV.Y.EACESGSIF.GLLP..I.VYATTASNADESSWGTYCPG.....PP.E.
Retrocopy DLVKALKKKHAAGAYKSLVVYVEACESGSIFQGLLPANISVYATTASNADESSWGTYCPGDDHGAPPAEF

Parental  DTCLGDLYSVAWMEDSDVH--NLRTESLKQQYNLVKERTSVQHTYYSGSHVMEYGSLELNAHHVFMYMGS
          DTCLGDLYSVAWMED.D.H....R.E.L.QQY..VK.RTS...TY..GSHVM.YG...L.......Y...
Retrocopy DTCLGDLYSVAWMEDADAHQDGRRAETLLQQYKTVKNRTSDEGTYTLGSHVMQYGDMALAPQSLDLYYMD

Parental  NPANDNATFVEDNSLPSFSRSVNQRDADLVYFW--QKYRKLAESSPEKNEARKQLLEMMTHRSHVDNSVE
          ......A..............V.....D...F....KYR...E...EK.EAR..LL..M..RS.VD.SVE
Retrocopy TTSAATANDDKLAAAGAVKGTVSVKQRDADLFYLWRKYRRAGEGTAEKVEARERLLQEMGRRSRVDRSVE

Parental  LIGNLLFGSEEGPRVLKAVRATGEPLVDDWSCLKSMTLVWD
          LI..LL.....G..V...VRA.....VDDW.CLKSM.....
Retrocopy LIEGLLL---DGGKVDVGVRAA---VVDDWECLKSMVRTFE

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_12 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G093032	1 retrocopy	retro_zmay_6,
Oryza longistaminata	KN538817.1_FG009	1 retrocopy	retro_olon_1,
Oryza brachyantha	OB01G29280	1 retrocopy	retro_obra_23,
Oryza barthii	OBART01G19640	1 retrocopy	retro_obar_1,
Oryza glumaepatula	OGLUM01G23260	1 retrocopy	retro_oglu_32,
Oryza meridionalis	OMERI01G18100	1 retrocopy	retro_omer_24,
Oryza punctata	OPUNC01G20010	1 retrocopy	retro_opun_12 ,
Oryza glaberrima	ORGLA01G0161200	1 retrocopy	retro_ogla_9,
Oryza sativa japonica	OS01G0559600	1 retrocopy	retro_osat_9,