RetrogeneDB ID: retro_oruf_28

Retrocopy location

• Organism: Brownbeard rice (Oryza rufipogon)
• Coordinates: 3:34249172..34249907(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ORUFI03G43450
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ORUFI02G26160
• Aliases: None
• Description: None

Sequence

>retro_oruf_28
ATGGAGAATAGCAGGGAGCAGCAGCCGGAGTCGTCGCCGGCGAACAACAATAGCAAGAAGAAGAAGAAGAAGAAGACGGC
GTCGCGGTTCCGGCGTGTGTGCGTGTTCTGCGGCAGCAGCCCCGGGAAGAAGGCGTCGTACCAGGTGGCCGCCGTGCAGC
TGGGGCAGCAGCTGGTGGAGCGCGGCATCGACCTGGTGTACGGCGGCGGCAGCGTTGGGCTGATGGGGCTGGTGTCCCGC
GCCGTCCACGGAGGCGGCGGGCACGTGGTGGGCGTGGTGCCCAATGGCGTGCTGCCACGCGAGCTGATCGGCGAGACGCT
GGGGGAGGTGAGGGCGGTGGGAAGCATGCACCAGCGGAAGGCGGAGATGGCGCGGGAGTCGGACGCCTTCATCGCCCTCC
CCGGCGGCTACGGCACGCTGGAGGAGCTCCTCGAGGTCATCACCTGGGCTCAGCTCCGCATCCACCACAAGCCCGTCGGC
CTCCTCAACGTCGACGGCTACTACGACTCCCTGCTCGCCTTCATCGACAAGGCCGTCCACGAAGGCTTCGTCTCGCCGCC
CGCCCGCCGCATCATCGTCGCCGCACCCACCGCCTCCGACCTGCTCTGCAAGCTCGAGGAATACGTGCCGCCGCCGCACG
ACGCCACCGCCCTGAAGCTCACCTGGGAGATGTCCACCGTATCGGAGCAGCACGCCGGAAGCATCTACTCCCCCAAGCCC
GACATGGCACGCTAG

Alignment

ORF - retro_oruf_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 86.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRFRRVCVFCGSSHGKKKIYQDAAIELGKELVARNIDLVYGGGSVGLMGLVSQAVHNGGRHVIGVIPKTL
          SRFRRVCVFCGSS.GKK..YQ.AA..LG..LV.R.IDLVYGGGSVGLMGLVS.AVH.GG.HV.GV.P...
Retrocopy SRFRRVCVFCGSSPGKKASYQVAAVQLGQQLVERGIDLVYGGGSVGLMGLVSRAVHGGGGHVVGVVPNGV

Parental  MPREISGETVGEVKAVSDMHQRKAEMARQSDAFIALPGGYGTLEELLEVIAWAQLGIHDKPVGLLNVDGY
          .PRE..GET.GEV.AV..MHQRKAEMAR.SDAFIALPGGYGTLEELLEVI.WAQL.IH.KPVGLLNVDGY
Retrocopy LPRELIGETLGEVRAVGSMHQRKAEMARESDAFIALPGGYGTLEELLEVITWAQLRIHHKPVGLLNVDGY

Parental  YNPLLSFIDKAVEEGFIRPSARHIIVLAPTPKELIEKLEEY-SPQHEKVVSKMKWEMEQMSYPQNYDIPR
          Y..LL.FIDKAV.EGF..P.AR.IIV.APT...L..KLEEY..P.H.....K..WEM...S......I..
Retrocopy YDSLLAFIDKAVHEGFVSPPARRIIVAAPTASDLLCKLEEYVPPPHDATALKLTWEMSTVSEQHAGSIYS

Parental  PK
          PK
Retrocopy PK

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza rufipogon was not studied using ChIP-Seq data.

EST

Oryza rufipogon was not studied using EST data.

TSS

Oryza rufipogon was not studied using FANTOM5 data.

Lab

retro_oruf_28 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza rufipogon 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA008655	1 retrocopy	retro_oind_31,
Oryza longistaminata	KN538764.1_FG025	1 retrocopy	retro_olon_22,
Hordeum vulgare	MLOC_6463	1 retrocopy	retro_hvul_10,
Oryza barthii	OBART02G24840	1 retrocopy	retro_obar_25,
Oryza nivara	ONIVA02G27160	1 retrocopy	retro_oniv_19,
Oryza rufipogon	ORUFI02G26160	1 retrocopy	retro_oruf_28 ,