RetrogeneDB ID: retro_obra_27

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 4:8958966..8960298(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB04G18700
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB07G32920
• Aliases: None
• Description: None

Sequence

>retro_obra_27
ATGGCCACGGCGAGTTTGATCAAGGCGCCCGTGGGGCAGAGTCCTGGGACTGGGGGCAGGATGGTGGCGGGGAGGGGAGG
AGGAGGCGGCGTGGTCAGGTGCTCGCTGCAGGGCGCCGTGGTGGGGGGCCGGGCGGAGTGGCAGAGCAGCTGCGCCGTGC
TGTCCAGCAAGGTGGCCGGGCTGGGCCCCGCCGTCAACGGGCGCGCCGCGCCCAGCTTTGTTAATGGGCATGTCGCGCCG
CTGGTCCCGGAGCCGGCGGCGAAGGACGGGGCGGGGCTGGATTTGGTGCCGGTGAGCAGCGTCAATGGCGGGGGCGCCGC
CCGGAACCTGCCGCAGCCGCTGCGGATCTCGGACCTGTCGCCGGCGCCGATGCACGGGTCGCAGCTGCGCGTGGCGTACC
AGGGGGTCCCGGGGGCGTACAGCGAGAAGGCGGCCGGGAAGGCGTACCCGGGGTGCGACGCCATCCCCTGCGACCAGTTC
GAGGTGGCGTTCTCTGCCGTGGAGCTGTGGATCGCCGACCGGGCGGTGCTCCCCGTGGAGAATTCGCTGGGCGGCAGCAT
CCACCGCAACTACGACCTCCTGCTCAGGCACCGGCTCCACATCGTCGGCGAGGTGCAGCTCCCCGTGCACCACTGCCTCA
TGGCGCTCCCGGGCGTCCGCAAGGAGTGCCTCACCCGCGTCATCAGCCACCCGCAGGCGCTGGCGCAGTGCGAGCACACG
CTCACCGCCATGGGCCTCAACGTCGTCCGCGAGGCCTTCGACGACACCGCCGGCGCCGCCGAGTACGTCGCCGCCAACGG
CCTCCGCGACACGGCCGCCATCGCCTCCTCCCGCGCCGCCGAGCTGTACGGCATGGAGGTGCTCGCCGACGGCATCCAGG
ACGACTGCGGCAACGTCACCCGCTTCGTCATGCTCGCCCGCGAGCCCATCGTGCCCCGCACCGACCGCCCCTTCAAGACC
AGCATCGTCTTCGCCCACGACAAGGAGGGCACCTCCGTCCTCTTCAAGGTCCTCTCCGCCTTCGCCTTCCGCGACATCAC
CCTCACCAAGATCGAGAGCCGCCCGCACCGCCACCGCCCCATCCGCCTCGTCGACGACGCCAACGTCGGCACCGCCAAGC
ACTTCGAGTACATGTTCTACGTCGACTTCCAGGCCTCCCTCGCAGAGCCGCGGGCGCAGAACGCGCTCGCCGAGGTGCAG
GAGTACACCTCCTTCCTCCGTGTGCTCGGCAGCTACCCCATGGACATGACACCCATGACCGCCGGCTCCTCCTCCACCGT
CACGTCCTCCGATTCCTCCTCGCCGCCGCCGCCGTCGCCTTCCTCCACTTGA

Alignment

ORF - retro_obra_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.41 %
• Parental protein coverage: 97.97 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDGLKVAYQGCPGAYSEAAAKKAYPSCQTVPCEYFETAFQAVENWVADRAVLPLENSLGGSIHRNYDLLL
          G..L.VAYQG.PGAYSE.AA.KAYP.C...PC..FE.AF.AVE.W.ADRAVLP.ENSLGGSIHRNYDLLL
Retrocopy GSQLRVAYQGVPGAYSEKAAGKAYPGCDAIPCDQFEVAFSAVELWIADRAVLPVENSLGGSIHRNYDLLL

Parental  RHRLHIVGEVRLAVRHCLLANHGVKIENLRSAMSHPQALAQCEQTLTKLGIE-HREAVDDTAGAAKLIAE
          RHRLHIVGEV.L.V.HCL.A..GV..E.L....SHPQALAQCE.TLT..G....REA.DDTAGAA...A.
Retrocopy RHRLHIVGEVQLPVHHCLMALPGVRKECLTRVISHPQALAQCEHTLTAMGLNVVREAFDDTAGAAEYVAA

Parental  QRLQDTGAVASSLAAQLYGLDILAENIQDDTDNVTRFMMLAREPIIPRTDKPFKTSIVFSLE-EGPGQLF
          ..L.DT.A.ASS.AA.LYG...LA..IQDD..NVTRF.MLAREPI.PRTD.PFKTSIVF....EG...LF
Retrocopy NGLRDTAAIASSRAAELYGMEVLADGIQDDCGNVTRFVMLAREPIVPRTDRPFKTSIVFAHDKEGTSVLF

Parental  KALAVFALRKINLTKMESRPHKKKPLRIADDNSSAPLKHFDYLFYVDLEASMADPNAQNALANLKEFATF
          K.L..FA.R.I.LTK.ESRPH...P.R..DD......KHF.Y.FYVD..AS.A.P.AQNALA...E...F
Retrocopy KVLSAFAFRDITLTKIESRPHRHRPIRLVDDANVGTAKHFEYMFYVDFQASLAEPRAQNALAEVQEYTSF

Parental  LRVLGSYPTDVS
          LRVLGSYP.D..
Retrocopy LRVLGSYPMDMT

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza brachyantha was not studied using ChIP-Seq data.

EST

Oryza brachyantha was not studied using EST data.

TSS

Oryza brachyantha was not studied using FANTOM5 data.

Lab

retro_obra_27 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza brachyantha 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00093010	1 retrocopy	retro_atri_11,
Oryza brachyantha	OB07G32920	1 retrocopy	retro_obra_27 ,