RetrogeneDB ID: retro_oind_77

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 2:14872180..14872420(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA037413
• Aliases: None
• Description: None

Sequence

>retro_oind_77
TCACCGGAGCCCAATAACCTCACCGCCTTGGGAAAGGAAGGGGATGAAAGAGACGTGGGGAGAAATGAAAAAGAAGGGCA
AGATGGCCATTTTGTCCTTAGATCGGGTGACATGGCCTCTTGCGGGCTCAAAAATGACACACGAGCAAGAAATCCTCTCT
ATCCGAAGTTATCCGAGATAGTGGCATTTGAGAACACGCCATCCGGGAGAGTGGCAAATAGTCCAAAACCCCCTCCCTCC

Alignment

ORF - retro_oind_77 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60. %
• Parental protein coverage: 52.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPEPNNLGALGKEGDERDRRRNEEEGQDGHFILRLGDLASCGLKNSTRLQDKKYPFFS-LKGTNNGNGLR
          SPEPNNL.ALGKEGDERD..RNE.EGQDGHF.LR.GD.ASCGLKN.TR.....YP..S......N....R
Retrocopy SPEPNNLTALGKEGDERDVGRNEKEGQDGHFVLRSGDMASCGLKNDTRARNPLYPKLSEIVAFENTPSGR

Parental  VLQESKATPT
          V....K..P.
Retrocopy VANSPKPPPS

Legend:

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

Expression

RNA-Seq

Oryza sativa indica was not studied using RNA-Seq expression data.

ChIP-Seq

Oryza sativa indica was not studied using ChIP-Seq data.

EST

Oryza sativa indica was not studied using EST data.

TSS

Oryza sativa indica was not studied using FANTOM5 data.

Lab

retro_oind_77 was not experimentally validated.

Homology

Retrocopy orthology:

Oryza sativa indica 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA037413	1 retrocopy	retro_oind_77 ,