RetrogeneDB ID: retro_omer_20

Retrocopy location

• Organism: Oryza meridionalis
• Coordinates: 3:23155968..23157009(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OMERI03G22780
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OMERI06G22050
• Aliases: None
• Description: None

Sequence

>retro_omer_20
ATGGACCACAGCGCGTGGCTTAAGCTGCTCCTCGGGCCCAAGAAGCCGGCGAGGTCGGCGGCGATCGTCGAGACGTGGGC
GGCGGACCGGTCGAAGCTGCTCCTCGGGCCCAAGATCGCGTCGGGGTCCAACAGCCGCATCCACCGCGGCATGTACGGGG
AGCAACCAGTGGCCGTGAAGATCATGCACGCGCCGGTGGGCGACGACGACGACGACGACGTGCAGGTCCGGCGTGAGATG
GAGGCGCAGTTCGACGCCGAGGTGTCCCTCCTGTCGCGGCTGCGCCACCCCAACGTCGTGCGGCTCGTCGCCGTGTGCCG
GGAGCCGGAGGTGTACTGGATCATCACCGAGCTCATGCGACGCGGCACGCTCAGCGCGTACCTGCACGGGCGGGAGCCCT
ACTCGCTGCCGCCGGAGACCGTCGTCCGCCTCGCGCTTGACGTCGCCCGTGGCATGGAGTACCTCCACGCGCGTGGCGTC
GTCCACCGCGACCTCAAGCCGGAGAACCTGCTGCTCGACGGCGGCGGGCGCGTCAAGGTCGCCGACCTGGGCACGTCCTG
CCTCGAGGCCACCTGCCGCCGCGACAAGTGCTCCTCCAAGGCGGGCACGTTCCGGTGGATGGCGCCGGAGATGATCCACG
ACAAGCGCTGCAACCGCAAGGTGGACGTGTACAGCTTCGGCCTCGTGCTGTGGGAGCTCACCACCTGCCTCGTGCCGTTC
CAGAACTTGAGCCCCGTGCAGGTCGCCTACTCCGTCTGCGACAGGGACGCCAGGCCGCCGCTCTCGCCGTCGTGCCCGCC
GGCCATCAACAGCCTCATCGAGAGGTGCTGGTCCACCGAACCAGCGAGGCGTCCCGAGTTCAAACAGATCGTGTCCGTGC
TGGAGAGCTACGACCGCTGCCTCCGGCAAGGCTTGCCAGTGGTGGCGCTGCCGGAGCCGTCGCCATCGCCGCTGGCCTCG
TTGCTCGGCGCCTTCAAGATCCGATCCTGCACGAGCACAACGCGTTCCTCCATAACCGATCATAGAAGAGTTCATCCTTA
G

Alignment

ORF - retro_omer_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.59 %
• Parental protein coverage: 58.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RAVLEDQFNSEVAFLSRLYHPNIVQFIAACKKPPVYCIITEYMSQGTLRMYLNKKDPYSLSSETILKLAL
          R...E.QF..EV..LSRL.HPN.V...A.C..P.VY.IITE.M..GTL..YL....PYSL..ET...LAL
Retrocopy RREMEAQFDAEVSLLSRLRHPNVVRLVAVCREPEVYWIITELMRRGTLSAYLHGREPYSLPPETVVRLAL

Parental  DISRGMEYLHAQGVIHRDLKSQNLLLNDEMRVKVADFGTSCLETACQATK--GNKGTYRWMAPEMTKEKP
          D..RGMEYLHA.GV.HRDLK..NLLL....RVKVAD.GTSCLE..C...K.....GT.RWMAPEM...K.
Retrocopy DVARGMEYLHARGVVHRDLKPENLLLDGGGRVKVADLGTSCLEATCRRDKCSSKAGTFRWMAPEMIHDKR

Parental  YTRKVDVYSFGIVLWELTTCLLPFQGMTPVQAAYAASEKNLRPPLSSSCSPVLNNLIKRCWSANPARRPE
          ..RKVDVYSFG.VLWELTTCL.PFQ...PVQ.AY.......RPPLS.SC.P..N.LI.RCWS..PARRPE
Retrocopy CNRKVDVYSFGLVLWELTTCLVPFQNLSPVQVAYSVCDRDARPPLSPSCPPAINSLIERCWSTEPARRPE

Parental  FSYIVSVLEKYDHCVKEGMPIMAHQE
          F..IVSVLE.YD.C...G.P..A..E
Retrocopy FKQIVSVLESYDRCLRQGLPVVALPE

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza meridionalis was not studied using ChIP-Seq data.

EST

Oryza meridionalis was not studied using EST data.

TSS

Oryza meridionalis was not studied using FANTOM5 data.

Lab

retro_omer_20 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza meridionalis 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.

---

Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA023324	1 retrocopy	retro_oind_40,
Oryza glumaepatula	OGLUM06G23210	1 retrocopy	retro_oglu_33,
Oryza meridionalis	OMERI06G22050	1 retrocopy	retro_omer_20 ,
Oryza nivara	ONIVA06G26030	1 retrocopy	retro_oniv_29,
Oryza glaberrima	ORGLA06G0183600	1 retrocopy	retro_ogla_6,
Oryza rufipogon	ORUFI06G23740	1 retrocopy	retro_oruf_15,
Oryza sativa japonica	OS06G0636600	1 retrocopy	retro_osat_5,