RetrogeneDB ID: retro_oind_46

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02043684.1:2463..3351(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039618
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA018388
• Aliases: None
• Description: None

Sequence

>retro_oind_46
ATGATGCTGGACGATCCGGAGATGCGCGAGATGGCGCAGGAAGAGCTGAAACAGGCGCGGGCGAGCAGCGAAGAGCTGGA
ACAGCAGCTGCAGGTGTTGCTGCTGCCGAAAGATCCGGATGATGAGCGCAGCTGCTTCCTCGAAGTGCGCGCTGGCACCG
GCGGCGATGAGGCGGCGATCTTCGCCGGCGATCTGTTCCGCATGTACAGCCGTTACGCCGAAGGCCGCCGCTGGCGCGTC
GAGGTGATGAGCGCCAACGAAGGCGAGCACGGCGGCTTCAAAGAAGTGATCGCCAAAGTTTCCGGCGACGGCGTGTACGG
CCAGCTGAAGTTTGAATCCGGCGGCCATCGCGTGCAGCGCGTGCCGGAAACCGAATCCCAGGGGCGCATCCACACCTCCG
CCTGCACCGTGGCGGTGATGCCGGAAGTGCCGGAAGCCGAGCTGCCGGACATCAACCCGGGCGATCTGAAAATCGACACC
TTCCGCTCCTCCGGCGCCGGCGGCCAGCACGTTAACACCACCGACTCGGCGATCCGCATTACCCACCTGCCGACCGGCAT
CGTGGTGGAGTGTCAGGACGAACGTTCTCAACACAAAAACAAAGCCAAGGCGATGTCGGTGCTGGGCGCGCGCATTCGCG
CCGCCGAGATGGCCAAGCGCCAGCAGGCCGAGGCGTCCACTCGCCGCAACCTGCTGGGCAGCGGCGATCGTTCCGATCGC
AACCGCACCTACAACTTCCCGCAGGGGCGGGTGACCGACCACCGCATCAACCTGACGCTTTACCGCCTGGACGAAGTGAT
GGAAGGCAAACTGGACATGCTGATCCAGCCGATCGTGCAGGAGTATCAGGCCGATCAGCTGGCTGCGCTGTCCGCCGAGC
AAGAGTGA

Alignment

ORF - retro_oind_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.2 %
• Parental protein coverage: 78.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEEKDFREMAAQELLQALEEEKQLQHKLFRSLLPKDEADERDCILEVRAGTGGEEASLFAMDIFKMYEKY
          ......REMA..EL.QA......L...L...LLPKD..DER.C.LEVRAGTGG.EA..FA.D.F.MY..Y
Retrocopy LDDPEMREMAQEELKQARASSEELEQQLQVLLLPKDPDDERSCFLEVRAGTGGDEAAIFAGDLFRMYSRY

Parental  SQKNGWKFDAIDIMESALKGYKEASGTISGPGAYGKLKFESGIHRVQRVPVTEKSGRVHTSAVSVAILPQ
          .....W........E....G.KE.....SG.G.YG.LKFESG.HRVQRVP.TE..GR.HTSA..VA..P.
Retrocopy AEGRRWRVEVMSANEGEHGGFKEVIAKVSGDGVYGQLKFESGGHRVQRVPETESQGRIHTSACTVAVMPE

Parental  ADEVDV-QLRNEDLRIDTYRSGGSGGQSVNTTDSAVRITHVPTGTVVAIQDERSQHQNKAKALKVLRARL
          ..E.........DL.IDT.RS.G.GGQ.VNTTDSA.RITH.PTG.VV..QDERSQH.NKAKA..VL.AR.
Retrocopy VPEAELPDINPGDLKIDTFRSSGAGGQHVNTTDSAIRITHLPTGIVVECQDERSQHKNKAKAMSVLGARI

Parental  YEIERHRLHMDRSKLRSEQIGSGDRSERIRTYNFPQGRVTDHRVGITHHSIEDVMEGESLDIFIDALLLR
          ...E...........R....GSGDRS.R.RTYNFPQGRVTDHR...T......VMEG..LD..I......
Retrocopy RAAEMAKRQQAEASTRRNLLGSGDRSDRNRTYNFPQGRVTDHRINLTLYRLDEVMEGK-LDMLIQPIVQE

Parental  YEMDAIASFAS
          Y..D..A....
Retrocopy YQADQLAALSA

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_46 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.

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA018388	1 retrocopy	retro_oind_46 ,