RetrogeneDB ID: retro_oind_22

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02042308.1:296..1388(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA039343
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA013168
• Aliases: None
• Description: None

Sequence

>retro_oind_22
ATGGCAGTGACTGAACAGGCGCTACTCGCGGCGCTCGCGAGCGTACGCGATCCGCACACGGGCAAGGATTTCGTTTCCAC
GCGCGCCCTGCGCGACCTGCGCATCGACGGCGGCGCCGTGTCCTTCACCGTGGAGCTGGGCTACCCGGCCCGCAGCCTGG
AAGCCGCCCTGGCGGGCGAGCTGGAGGCCGCGGCGCGTACCGTGGCGGGCGTGGGGCGGGTGTCCGCCACCATCGCCACG
CGCATCGTCGCGCACGCGGTCCAGCGCGGCGTGCAGGTGCTGCCGCAGGTGCGCAACATCATCGCCGTCGCCTCGGGCAA
GGCCGGGGTGGGCAAGAGCACCACGGCCGCCAACCTCGCCCTCGCGCTGGCCTCCGAGGGCGCGCGCGTGGGCGTGCTCG
ATGCCGACATCTACGGCCCCAGCCAACCGATGATGCTGGGCATCGCGGACCGGCCCGAGAGCGCCGACGGCAAGACCATG
GAGCCGCTGCGCAACCATGGCGTGCAGGTGATGTCCATCGGCTTCCTGGTGGAGCCCGACCAGGCCATGATCTGGCGCGG
GCCCATGGCCACCCAGGCGCTGGAGCAGCTGCTGCGCCAGACGAACTGGCAGGACCTGGACTACCTGGTCGTGGACATGC
CGCCCGGCACCGGCGACATCCAGCTCACCCTCTCGCAGCGCGTGCCCCTCACGGGTGCCGTGATCGTGACCACGCCGCAG
GACATCGCGCTGCTCGATGCGCGCAAGGGCATCAGGATGTTCGAGAAGGTGGGCGTGCCCATCCTGGGGGTGGTGGAGAA
CATGGCCGCCCACGTGTGCAGCCAGTGCGGGCATGTCGAGCACATCTTCGGCGAGGGCGGCGGCCGCCGCATGGCCGAGG
AGAACGGCATGGCCTACCTGGGCGCCCTGCCGCTGGATTTGCAGATCCGCCTGCAGGCCGACAGCGGCACCCCCACCGTG
GTGGCCGAACCCGACGGCGAGGTGGCCAACATCTACCGCCGGGTGGCGCGCGAGGTGGCCGCGAAGGTCGCGACCCAGGC
CAGGGATTTTTCCTCGAAGTTCCCCACCATCTCCGTCAGCAAGGACACCTGA

Alignment

ORF - retro_oind_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.51 %
• Parental protein coverage: 88.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSDIIAVASGKGGVGKSTTAVNIAVALAKKFQLKVGLLDADIYGPSIPTMMNLHAKPEVSEDMRMIPVDN
          V..IIAVASGK.GVGKSTTA.N.A.ALA......VG.LDADIYGPS.P.M......PE......M.P..N
Retrocopy VRNIIAVASGKAGVGKSTTAANLALALASE-GARVGVLDADIYGPSQPMMLGIADRPESADGKTMEPLRN

Parental  YGVQCMSIGFLVDKDAPIVWRGPMVMSALEKITRGVAWGNLDILVVDMPPGTGDAQLSMSQRLRLSGALI
          .GVQ.MSIGFLV..D....WRGPM...ALE...R...W..LD.LVVDMPPGTGD.QL..SQR..L.GA.I
Retrocopy HGVQVMSIGFLVEPDQAMIWRGPMATQALEQLLRQTNWQDLDYLVVDMPPGTGDIQLTLSQRVPLTGAVI

Parental  VSTPQDIALIDARRGANMFRKVQVPILGLVENMSCFKCPKCGEKSYIFGEGGGQRTAEEMDMKLIGEIPL
          V.TPQDIAL.DAR.G..MF.KV.VPILG.VENM....C..CG....IFGEGGG.R.AEE..M...G..PL
Retrocopy VTTPQDIALLDARKGIRMFEKVGVPILGVVENMAAHVCSQCGHVEHIFGEGGGRRMAEENGMAYLGALPL

Parental  EIDIRTGSDEGTPIVISSPDSASAQAYIQVAEKVIHRLKELAEE
          ...IR...D.GTP.V...PD...A..Y..VA..V.......A..
Retrocopy DLQIRLQADSGTPTVVAEPDGEVANIYRRVAREVAAKVATQARD

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_22 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	BGIOSGA013168	1 retrocopy	retro_oind_22 ,