RetrogeneDB ID: retro_obra_8

Retrocopy location

• Organism: Oryza brachyantha
• Coordinates: 1:33336662..33337739(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: OB01G54080
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: OB01G54100
• Aliases: None
• Description: None

Sequence

>retro_obra_8
ATGGCTTCCCGTGCTGCAGGTGCGCTGCTGCTCGCGGCGGCGCTGCTGGTATGCAGCAGCTCGTCGTCGTCGGCGGCGAG
GATGCCGCCGATTGCGAAGGGCCTGTCGCTGGGGTACTACGACGAGAGATGCCCGCAGGCGGAGGCCATCGTGTTCAGCT
TCCTGCAGGAGGCCATCGCCAAGGACGTCGGCCTCGCCGCCGCGCTGCTCCGCCTCCACTTCCACGACTGCTTCGTCCAG
GGCTGTGACGCCTCCATCCTGCTCGACGGCACGCCCGCCGGCGGGAAGAGCGAGAAGCAGGCACCGCCCAACCTCACGCT
CCGCTCCTCCGCGTTCAAGGCCGTCGACGACCTCCGCGCCCTCCTCGACAGGGAATGCGGCGGCACCGTCCTCTCCTGCC
CCGGCCTCGTCCCCCTCGCCGCTCGTGACTCCGTCCACCTCGCCGGAGGGCCGTGGTACCAGGTGCCGCTCGGCCGCCTC
GACGGCTTAAAGTTCGCGTCTCAGGAGGCCGTCCTCGACGCGCTCCCGCCGCCGAGCTCCAACGTCACCGAGCTCCTCCA
AGCGCTCGGCAAGCTCAAGCTCGACGACAACGACCTGGTGGCGCTCTCCGGCGGGCACACCGTCGGCATCGCGCACTGCC
CGTCGTTCGGCGACCGGCTGTACCCGAAGCAGGACGAGACGATGGACAAGTGGTTCGCCGGGCAGCTGAAGCTGACGTGC
CCCAAGAAGGACACCGACAACAGCACGGCGAACGACATCCGCACGCCGGACGTGTTCGACAACAAGTACTACGTCGACCT
GATGAACCGGCAGGGGCTGTTCACGTCGGACCAGGACCTGTACAGCGACGCGAGGACGAAGCCGATCGTCACCAAGTTCG
CCGTCGACCAGTCGGCGTTCTTCGACCAGTTCGCCTTCTCCATGGTGAAGATGGGGCAGATCGAGGTGCTGACGGGCAAG
CAGCAAGGGCAGATCCGCAAGCGCTGCTCGGTGCCCAACGCCGCCGTCGCCGCCGGTGACGGTGCCTGGTCCGTCGTGGA
GACCGTCGTTGATGCCGCCGAGAGCTTGGTGCTGTAG

Alignment

ORF - retro_obra_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.35 %
• Parental protein coverage: 87.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQPPVVSGLSFDFYRKSCPKAESVVRKFVKDAVRKDVGLAAGLLRLHFHDCFVQGCDASVLLDGS-ATGP
          ..PP...GLS...Y...CP.AE..V..F...A..KDVGLAA.LLRLHFHDCFVQGCDAS.LLDG..A.G.
Retrocopy RMPPIAKGLSLGYYDERCPQAEAIVFSFLQEAIAKDVGLAAALLRLHFHDCFVQGCDASILLDGTPAGGK

Parental  GEQQAPPNLTLRPSAFKAVNDIRDRLDKACGAAVVSCSDVLALAARDSVVVTGGPEYKVPLGRRDSTKFA
          .E.QAPPNLTLR.SAFKAV.D.R..LD..CG..V.SC.....LAARDSV...GGP.Y.VPLGR.D..KFA
Retrocopy SEKQAPPNLTLRSSAFKAVDDLRALLDRECGGTVLSCPGLVPLAARDSVHLAGGPWYQVPLGRLDGLKFA

Parental  SQQDVLSGLPPPSAAVPALLD----IKLDATDLVALSGGHTVGLAHCSSFEGRLFPRQDPAMNGTFARRL
          SQ..VL..LPPPS..V..LL......KLD..DLVALSGGHTVG.AHC.SF..RL.P.QD..M...FA..L
Retrocopy SQEAVLDALPPPSSNVTELLQALGKLKLDDNDLVALSGGHTVGIAHCPSFGDRLYPKQDETMDKWFAGQL

Parental  RRTCPAAGTDRRTVNDIRTPNVFDNMYYVNLVNREGLFTSDQDLFSNAGTKPIVAKFAADQKAFFDQFAV
          ..TCP...TD..T.NDIRTP.VFDN.YYV.L.NR.GLFTSDQDL.S.A.TKPIV.KFA.DQ.AFFDQFA.
Retrocopy KLTCPKKDTDNSTANDIRTPDVFDNKYYVDLMNRQGLFTSDQDLYSDARTKPIVTKFAVDQSAFFDQFAF

Parental  SMVKMGQISVLTG-SQGQVRRNCSARNPGTVGAGDLPLSILE
          SMVKMGQI.VLTG..QGQ.R..CS..N...V.AGD...S..E
Retrocopy SMVKMGQIEVLTGKQQGQIRKRCSVPN-AAVAAGDGAWSVVE

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_8 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza brachyantha	OB01G54100	1 retrocopy	retro_obra_8 ,