RetrogeneDB ID: retro_oind_106

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: CH399501.1:4587..5313(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA015973
• Aliases: None
• Description: None

Sequence

>retro_oind_106
CAGCGCGTGGTGGACTACAACGTGAAGGTCCGCGTGAAGTCGGACAACACGGGTGTGGACATCGCGAACGTGAAGATGAG
CATGAATCCGTTCGACGAGATCGCGGTGGAAGAGGCGGTGCGGCTGAAGGAAAAGGGCGTGGTCACTGAAGTGATCGCCG
TTACCTGCGGCGTCACGCAATGCCAGGAGACGCTGCGCACGGCGATGGCGATCGGTGCGGACCGCGCGATCCTGGTGGAG
ACTGCCGAAGAGCTGCAGCCGCTGGCCGTGGCCAAGATCCTGAAGGCGCTGGTGGACAAGGAGCAGCCGCAACTGGTCAT
CCTGGGCAAGCAGGCGATCGACGACGACTCCAACCAGACCGGCCAGATGCTGGCGGCGCTCGCGGACCTGCCGCAGGCGA
CCTTCGCCTCGAAGGTGGAAGTGAATGGCGACAAGGTGAACGTGACGCGCGAGGTCGATGGCGGCCTGGAGACGCTGGCG
CTCACGCTGCCGGCGATCGTCACGACCGACCTGCGCCTGAACGAGCCGCGCTACGTGACGCTGCCCAACATCATGAAGGC
CAAGAAGAAGCAGCTGGACACCGTCAAGCCCGAGGACCTGGGCGTGGACGTGAAGCCGCGGCTGAAGACCCTCAAGGTGA
CGGAGCCGCCCAAGCGCGGCGCGGGCGTGAAGGTGCCGGACGTCGCCACGCTGGTCGAAAAGCTGAAGAACGAAGCCAAG
GTCATC

Alignment

ORF - retro_oind_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.01 %
• Parental protein coverage: 97.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KRVVDYAVKVRVRPDRTGVETASVKMSMNPFCEIAVEEALRLREAGAATEVVAATVGPSQSADTLRTALA
          .RVVDY.VKVRV..D.TGV..A.VKMSMNPF.EIAVEEA.RL.E.G..TEV.A.T.G..Q...TLRTA.A
Retrocopy QRVVDYNVKVRVKSDNTGVDIANVKMSMNPFDEIAVEEAVRLKEKGVVTEVIAVTCGVTQCQETLRTAMA

Parental  MGADRAVHVLHDPDPSRPLLPLAVAKILRALALQENPGLVILGKQAIDDDCNQTGQMLAGLLNWPQGTFA
          .GADRA..V.........L.PLAVAKIL.AL...E.P.LVILGKQAIDDD.NQTGQMLA.L...PQ.TFA
Retrocopy IGADRAILV----ETAEELQPLAVAKILKALVDKEQPQLVILGKQAIDDDSNQTGQMLAALADLPQATFA

Parental  SKVILNKEKATVEREVDGGIETISLDLPAVITTDLRLNQPRYATLPNIMKAKSKVIKKVTPEDLDVDIRS
          SKV..N..K..V.REVDGG.ET..L.LPA..TTDLRLN.PRY.TLPNIMKAK.K....V.PEDL.VD...
Retrocopy SKVEVNGDKVNVTREVDGGLETLALTLPAIVTTDLRLNEPRYVTLPNIMKAKKKQLDTVKPEDLGVDVKP

Parental  DMEVVEVTEPPKRKAGVILSSVDELIDRLKNEARVL
          ......VTEPPKR.AGV....V..L...LKNEA.V.
Retrocopy RLKTLKVTEPPKRGAGVKVPDVATLVEKLKNEAKVI

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_106 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	BGIOSGA015973	1 retrocopy	retro_oind_106 ,