RetrogeneDB ID: retro_olon_23

Retrocopy location

• Organism: Longstamen rice (Oryza longistaminata)
• Coordinates: KN538714.1:248644..249445(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: KN538714.1_FG044
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: KN540365.1_FG001
• Aliases: None
• Description: None

Sequence

>retro_olon_23
ATGAGAGGAGCTGTGGCCATCTTCAATGAGTTTAAGCGCCGTGGTTTGAACATTTCCATTACAGGGATCCCGAAAACTGT
GGACAATGATATCGGCATCATAGACAGGTCATTTGGGTTCCAAACCGCAGTGGAGATTGCTCAGCAGGCAATCGATGCAG
CACATGTCGAGGCTGTGAGTGCCGTGAATGGCATTGGACTTGTCAAACTTATGGGCAGGAGCACAGGCCACATTGCTCTT
CATGCCACCCTGAGCAGCCGCGATGTTGACTGCTGTTTGATTCCTGAGGTTGATTTCTATCTTGAAGGAAAGGGAGGCCT
GTTTGAGTTCTTGTATGAAAGGATAAAACAGAAGGGACATGCTGTTGTCGTTGTTGCTGAAGGTGCTGGTCAGGAATTGA
TTCCAAGGACTGACGATCAAAAGCGGGAGCAGGACGAGTCCGGCAACATTGTGTTCCTTGATGTGGGTCCCTGGTTAAAA
TCTGAGCTGGGTAAATGGTGGAAGAGAGAACACCCAAGCGAGTTGTTCACTGTGAAGTATATCGATCCCACTTACATGAT
ACGAGCTGTTCCAGCAAATGCCACTGACAATCTGTACTGTACATTGTTGGCACATTCGGCGATCCATGGGATCATGGCTG
GGTACACTGGCTTCGTCCCTGGCCCGATTAATGGAAACTATAGCTACATACCGCTGGAAGATGTTGCTGTGGCGAAGAAC
CCGGTGGATGTGAATGATCACAAATGGGCATGGGTTAGATCAGTCACAAACCAACCAGATTTCCTGAAGCCAAAATACTG
A

Alignment

ORF - retro_olon_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.23 %
• Parental protein coverage: 54.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGAGVIFEEIRRRGLKVAVAGIPKTIDNDIPVIDRSFGFDTAVEEAQRAINAAHVEAGSAENGIGLVKLM
          RGA..IF.E..RRGL.....GIPKT.DNDI..IDRSFGF.TAVE.AQ.AI.AAHVEA.SA.NGIGLVKLM
Retrocopy RGAVAIFNEFKRRGLNISITGIPKTVDNDIGIIDRSFGFQTAVEIAQQAIDAAHVEAVSAVNGIGLVKLM

Parental  GRHSGFIAHYATLASRDVDCCLIPESPFYLEGEGGLFRYLEKRLKENGHMVIVVAEGAGQKLINET-KES
          GR..G.IA..ATL.SRDVDCCLIPE..FYLEG.GGLF..L..R.K..GH.V.VVAEGAGQ.LI..T....
Retrocopy GRSTGHIALHATLSSRDVDCCLIPEVDFYLEGKGGLFEFLYERIKQKGHAVVVVAEGAGQELIPRTDDQK

Parental  MGKDASGNSILLDVGLWLSQKIKEHFKKIKTT--INLKYIDPTYMIRAIPSNASDNVYCTLLAHSVVHGA
          ...D.SGN...LDVG.WL........K..........KYIDPTYMIRA.P.NA.DN.YCTLLAHS..HG.
Retrocopy REQDESGNIVFLDVGPWLKSELGKWWKREHPSELFTVKYIDPTYMIRAVPANATDNLYCTLLAHSAIHGI

Parental  MAGYTGFTVGQVNGRHCYIPFYRITEKQNKVSITDRMWARLLSSTNQPSFLSKK
          MAGYTGF..G..NG...YIP........N.V...D..WA...S.TNQP.FL..K
Retrocopy MAGYTGFVPGPINGNYSYIPLEDVAVAKNPVDVNDHKWAWVRSVTNQPDFLKPK

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Oryza longistaminata was not studied using ChIP-Seq data.

EST

Oryza longistaminata was not studied using EST data.

TSS

Oryza longistaminata was not studied using FANTOM5 data.

Lab

retro_olon_23 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza longistaminata 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis lyrata	fgenesh2_kg.7__854__AT4G32840.1	1 retrocopy	retro_alyr_31,
Oryza longistaminata	KN540365.1_FG001	1 retrocopy	retro_olon_23 ,
Solanum lycopersicum	Solyc07g045160.2	1 retrocopy	retro_slyc_27,