RetrogeneDB ID: retro_osat_9

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 5:29579147..29580572(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS05G0593900
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS01G0559600
• Aliases: None
• Description: None

Sequence

>retro_osat_9
ATGGGGCGCGGTCTCCTCTGCCTGCTGCTGCTGCAGCTCGTCGGCCTCGTCGTCGCCGGCGGTGGGCGGTGGCGGTGGCA
GGAGGAGTTCCTCCGGCTGCCGTCGTCGGATGAGACGACGAGGTGGGCGGTGCTGATCGCGGGGTCGAATGGGTTCTATA
ACTACCGGCACCAGGCGGACGTGTGCCACGCGTACCAGATCATGAGGAAGGGAGGCGTGGAGGAGCAAAACATCGTGGTG
ATGATGTACGACGACATCGCCCACAACCCCGACAACCCCAGGCCTGGGCTCATCTTCAACCACCCTTCCGGCCCCGACGT
CTACGCCGGCGTCCCCAAGGATTACACCGGCGACGACGTCAACGTCAACAACTTCCTCGCCGTCCTCCTCGGCAACCGCT
CCGCCCTCACCGGCTCCGGCAGCGGCAAGGTCGTCGCCAGCGGCCCCAACGACCACGTCTTCGTCTACTACGCCGACCAC
GGCGGCCCCGGCGTCCTGAGCATGCCAGCCGACGGCGAGTACCTGTACGCCGACGACCTGGTCAAGGCGCTCAAGAAGAA
GCACGCCGGCGGCGGGTACAAGAGCCTGGTCGTGTACGTGGAGGCGTGCGAGTCCGGCAGCATCTTCGAGGGCCTCCTGC
CTTCCGACATCTCCGTGTACGCCACCACGGCCTCCAACGCGGAGGAGAGCAGCTGGGGCACCTACTGCCCCGGCGACGAC
CACGACGCCCCGGCGGCGGAGTTCGACACCTGCCTCGGGGACCTCTACAGCGTGGCGTGGATGGAGGACGCGGAGGCGCA
CCAGGAGGGGCGCCTCGCCGAGACGCTGCGGCAGCAGTACAGGACGGTGAAGAACCGGACGTCCGACGAGGGCACCTACA
CGCTCGGCTCCCACGTCATGCAGTACGGCGACATGGCGCTCGCACCGCAGAGCCTGGACCTCTACTACATGGATACATCA
CCTGCGACGGCGAACGACCACAAATTAGCTGCTGCTGGCGCCAAAGGCAGCCACTCCTACACTGTGTCTGTGAATCAGCG
CGACGCCGATCTGCTCTACTTGTGGCGCAAGTACCGGAGAGCCGGCGAGGGGACGGCAGAGAAGGTGGAGGCTCGGGAGC
GGCTTGTGCAGGAGATGGGACGGCGATCGCGCGTGGACAGAAGCGTGGAGATGATCGGGGGCCTCCTCTTGGGCGGCGCC
AAGCACAAGCAGCAGGTTGTGCGGGAGCGGGCTGCGCTGGTTGAGGACTGGGAGTGCCTCAGGTCGATGGTGCGGACGTT
CGAGGATCAGTGTGGGTCGCTGGGACAGTACGGGATAAAGCACATGCGCTCCTTCGCCAACATCTGCAACGCCGGCGTCC
CCCACCACGCCATGGCCAAGGCCGCCTCCCTGGCCTGTCCATCCCCTCCTCCGTTACACTTATGA

Alignment

ORF - retro_osat_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.4 %
• Parental protein coverage: 56.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGTRWAVLIAGSNGYYNYRHQADVCHAYQIMKRGGLKDENIIVFMYDDIAHNPENPRPGVIINHPQGGDV
          E.TRWAVLIAGSNG.YNYRHQADVCHAYQIM..GG....NI.V.MYDDIAHNP.NPRPG.I.NHP.G.DV
Retrocopy ETTRWAVLIAGSNGFYNYRHQADVCHAYQIMRKGGVEEQNIVVMMYDDIAHNPDNPRPGLIFNHPSGPDV

Parental  YAGVPKDYTGKEVNVKNLFAVLLGNKTAVKG-GSGKVLDSGPNDHIFIFYSDHGGPGVLGMPT-YPYLYG
          YAGVPKDYTG..VNV.N..AVLLGN..A..G.GSGKV..SGPNDH.F..Y.DHGGPGVL.MP....YLY.
Retrocopy YAGVPKDYTGDDVNVNNFLAVLLGNRSALTGSGSGKVVASGPNDHVFVYYADHGGPGVLSMPADGEYLYA

Parental  DDLVDVLKKKHAAGTYKSLVFYLEACESGSIFEGLLPNGINVYATTASNADESSWGTYCPG-EYPSPPPE
          DDLV..LKKKHA.G.YKSLV.Y.EACESGSIFEGLLP..I.VYATTASNA.ESSWGTYCPG.....P..E
Retrocopy DDLVKALKKKHAGGGYKSLVVYVEACESGSIFEGLLPSDISVYATTASNAEESSWGTYCPGDDHDAPAAE

Parental  YDTCLGDLYSVAWMEDSDVH--NLRTESLKQQYNLVKERTSVQHTYYSGSHVMEYGSLELNAHHV-FMYM
          .DTCLGDLYSVAWMED...H......E.L.QQY..VK.RTS...TY..GSHVM.YG...L........YM
Retrocopy FDTCLGDLYSVAWMEDAEAHQEGRLAETLRQQYRTVKNRTSDEGTYTLGSHVMQYGDMALAPQSLDLYYM

Parental  GSNPANDN
          ...PA..N
Retrocopy DTSPATAN

Legend:

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

Expression

RNA-Seq

Oryza sativa japonica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa japonica was not studied using ChIP-Seq data.

EST

Oryza sativa japonica was not studied using EST data.

TSS

Oryza sativa japonica was not studied using FANTOM5 data.

Lab

retro_osat_9 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa japonica 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 ,