RetrogeneDB ID: retro_opun_22

Retrocopy location

• Organism: Red rice (Oryza punctata)
• Coordinates: 1:8580998..8582144(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OPUNC01G10280
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OPUNC02G29860
• Aliases: None
• Description: None

Sequence

>retro_opun_22
ATGCTCGACGAGTTCGCCATCCCGCGTGACCTCGTCGACCGCCGCGTCACACGCATGCGCGTCCTCTCGCCGTCCAACCT
CGCCGCCGACTTCTCCCGCGCGCTGCCCCCCGGCGCCCACATCCCCATGCTCCGACGCGAGGTGCTCGACTCCTTCCTCC
GCCGCCGCGCCGCCGACGCCGGCGCCACCCTCGTCCCGGGTCTCGTCACCTCGCTCTCCCTCCCCGCCGACCCCACCGCC
GACCCTTACCTCGTCCACTACATCTCCTCCGACTCCGGTAGCCCCTCCTCCTCCTCCTCCCGGAGCGTCCTCGAGGTAGA
CGCCGTCGTCGGCGCGGACGGCGCGAACAGCCGTGTCGCCCGCGAGGTAGGCGCCGGCGACTACACTACGGCCATCGCGT
TCCAGGAGCGCATCCGCCTCCCCGACGAGGCCATGTCCTACTACGACGACCTCGCCGAGATGTACGTCGGCGGCGACGTC
TCCCCGGACTTCTACGCCTGGGTCTTCCCCAAGTGCGACCACGTCGCCGTCGGGACGGGCACGGTCGCCGCCAAGCCGGA
TATCAAGAAGCTCCAGTCCGGCATCCGCGCGCGCGCGGGCGGCAAGATCGCCGGTGGCCGCGTGATCAAGGTGGAGGCGC
ACCCGATCCCGGAGCACCCGCGCCCTCGCCGCGTGGTCGGACGCGTGGCGCTCGTCGGCGACGCGGCGGGCTACGTCACC
CGGTGCTCCGGCGAGGGAATCTACTTCGCGGCCAAGTCCGGCCGCCTCTGCGGCCAGGCCATGGCCGACGAGTGGAAGCT
CACCGGCGCGGTGACGGAGGCCGGGATACGGGCGGGTTACCTCCGGCGATGGGACGACGAGTTCCGGCTGACGTTCCGGT
TCCTGGACATGCTGCAGCGGGTGTTCTACGGCGGGAACGCCGGGAGGGAGGCGCTGGTGGAGATGTGCGCCGACGAGCAC
GTGCAGCGGCGGACGTTCGAGAGTTACCTGCACAAGAGGATGGCGGCCGTCGAGCCGTGGGGGGATCTCCGGCTGCTGTG
GCGCACGGCGGCGACCATGGTGCGCTGCGGCGTGCTCGGCAGGGAGGTCGAACGCCTCCGCCGTCTCGAGCAGCAAGCCG
CCGACCAGGTGCTCCTCCGGCATTGA

Alignment

ORF - retro_opun_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.22 %
• Parental protein coverage: 79.18 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVSEFDLPLDLVDRKVRKMKMISPSNVAVDIGGTLAPHEYIGMVRREVLDAYLRSRAEGAGAEVVNGLFL
          M..EF..P.DLVDR.V..M...SPSN.A.D....L.P...I.M.RREVLD..LR.RA..AGA..V.GL..
Retrocopy MLDEFAIPRDLVDRRVTRMRVLSPSNLAADFSRALPPGAHIPMLRREVLDSFLRRRAADAGATLVPGLVT

Parental  RYEAPKEPNGS-YVVHYNHYDSSNGKAGGEKRTFEVDAIVGADGANSRVAKDMGAGDYEYAIAFQERVKI
          ....P..P....Y.VHY...DS............EVDA.VGADGANSRVA...GAGDY..AIAFQER...
Retrocopy SLSLPADPTADPYLVHYISSDSGSPSSSSSRSVLEVDAVVGADGANSRVAREVGAGDYTTAIAFQERIRL

Parental  PDDKMKYYEERAEMYVGDDVSPDFYGWVFPKCDHVAVGTGTVTHKPDIKKFQAATRLRAKDRIEGGKIIR
          PD..M.YY...AEMYVG.DVSPDFY.WVFPKCDHVAVGTGTV..KPDIKK.Q...R.RA...I.GG..I.
Retrocopy PDEAMSYYDDLAEMYVGGDVSPDFYAWVFPKCDHVAVGTGTVAAKPDIKKLQSGIRARAGGKIAGGRVIK

Parental  VEAHPIPEHPRPKRVAGRVTLVGDAAGYVTKCSGEGIYFAAKSGRMCAEAIVAGSANGTRMVEESDLRK-
          VEAHPIPEHPRP.RV.GRV.LVGDAAGYVT.CSGEGIYFAAKSGR.C..A..A.....T..V.E...R..
Retrocopy VEAHPIPEHPRPRRVVGRVALVGDAAGYVTRCSGEGIYFAAKSGRLCGQA-MADEWKLTGAVTEAGIRAG

Parental  YLAEFDRLYWPTYKVLDVLQKVFYRSNAAREAFVEMCADDYVQRMTFDSYLYKRVVPGNPLDDIKLAVNT
          YL...D.....T...LD.LQ.VFY..NA.REA.VEMCAD..VQR.TF.SYL.KR.....P..D..L...T
Retrocopy YLRRWDDEFRLTFRFLDMLQRVFYGGNAGREALVEMCADEHVQRRTFESYLHKRMAAVEPWGDLRLLWRT

Parental  IGSLVRATALRREMEKV
          ....VR...L.RE.E..
Retrocopy AATMVRCGVLGREVERL

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_22 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
Brachypodium distachyon	BRADI3G59430	1 retrocopy	retro_bdis_46,
Zea mays	GRMZM2G105644	1 retrocopy	retro_zmay_29,
Oryza meridionalis	OMERI02G30980	1 retrocopy	retro_omer_17,
Oryza nivara	ONIVA06G04710	1 retrocopy	retro_oniv_24,
Oryza punctata	OPUNC02G29860	1 retrocopy	retro_opun_22 ,
Oryza rufipogon	ORUFI02G34000	1 retrocopy	retro_oruf_42,
Oryza sativa japonica	OS02G0744900	1 retrocopy	retro_osat_44,
Sorghum bicolor	Sb04g028050	1 retrocopy	retro_sbic_27,
Triticum aestivum	Traes_6DL_0FF72D765	1 retrocopy	retro_taes_28,