RetrogeneDB ID: retro_osat_39

Retrocopy location

• Organism: Rice subsp. japonica (Oryza sativa japonica)
• Coordinates: 8:96144..96861(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OS08G0101700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OS04G0533500
• Aliases: None
• Description: None

Sequence

>retro_osat_39
ATGGCGATGAAGGCGGTGATCAAGGGCGGCGATGGCGGAGGCGGGTGCATGGTGGTGGTGGCGCACGTGCTAGCGGTGGC
GGCGACGGCGATGGTGTTGGTGTGGTGCGTTCACTTCCGCGGCGGACTCGCCCTGCGCTCCCACAACAAGCAGCTCATCT
TCAACACCCACCCGGTGCTCATGGTGCTTGGCCTCGTCGTCCTCGCCGCCGAGGCCATCCTCTCCTACCGCTCCCTCTCC
ATCATCGTCAGCAGCAGGGACGCCAGAAAGAAGGTGCACCTGGGGCTGCACGCCGTGGGGCTCGCCCTCGGCGGCGTCGG
CATCTACGCGGTGTTCAAGTACCACGCCGAGGCCGACATCCCCAACCTCTACTCCCTCCACTCCTGGATCGGCATCGCCA
CCATCTCCCTCTACGCGCTCCACTGGCTCCTCGCCTTCCTCACCTTCTTCTTCCCCGGCGCCTCCCACGACACCAGGCGC
TCCGCCGTCCCGTGGCACGCGCTCCTCGGCCTCCTCGTCTTCGCGCTCGCCGTGGGCAACGCCCAGCTCGGCTTCCTCGA
GAAGCTCACCTTCCTGCAGGCCCCGCCGCTGCGCCTGTCCAGGTACGGGGCGGAGGCGCTACTCGTCAACTTCACGGCGC
TGGTGGTCCTCCTCCTCGGCGTCGCCGTCGTCCTCGCCACCGCCAACGTCGACTCCACTAAATACACCGCCATGTAA

Alignment

ORF - retro_osat_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.49 %
• Parental protein coverage: 86.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VAHALAVAAAVMVLVWCISFRGGLAFEADNKNLIFNVHPVLMLIGYIILGSEAIMIYKIFPKL--NHDTT
          VAH.LAVAA..MVLVWC..FRGGLA....NK.LIFN.HPVLM..G...L..EAI..Y..........D..
Retrocopy VAHVLAVAATAMVLVWCVHFRGGLALRSHNKQLIFNTHPVLMVLGLVVLAAEAILSYRSLSIIVSSRDAR

Parental  KLIHLILHAIAIVLGAVGIYCAFKFHNESGIANLYSLHSWLGIGTISLYGIQWIFGFVAFFYPGAAPHVR
          K..HL.LHA....LG.VGIY..FK.H.E..I.NLYSLHSW.GI.TISLY...W...F..FF.PGA....R
Retrocopy KKVHLGLHAVGLALGGVGIYAVFKYHAEADIPNLYSLHSWIGIATISLYALHWLLAFLTFFFPGASHDTR

Parental  RGALPWHVLFGLFVYVLTLATAELGLLEKLTFLQSS--GLDKYGAEAFLVNFTGLVVALFGAAVVVA
          R.A.PWH.L.GL.V..L....A.LG.LEKLTFLQ.....L..YGAEA.LVNFT.LVV.L.G.AVV.A
Retrocopy RSAVPWHALLGLLVFALAVGNAQLGFLEKLTFLQAPPLRLSRYGAEALLVNFTALVVLLLGVAVVLA

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_39 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Zea mays	GRMZM2G034668	1 retrocopy	retro_zmay_23,
Leersia perrieri	LPERR04G16060	1 retrocopy	retro_lper_17,
Hordeum vulgare	MLOC_12641	1 retrocopy	retro_hvul_22,
Oryza sativa japonica	OS04G0533500	1 retrocopy	retro_osat_39 ,
Physcomitrella patens	PP1S194_18V6	1 retrocopy	retro_ppat_14,
Sorghum bicolor	Sb06g023650	1 retrocopy	retro_sbic_21,
Setaria italica	Si010957m.g	1 retrocopy	retro_sita_34,