RetrogeneDB ID: retro_oind_33

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 10:347237..348230(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA032399
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA012189
• Aliases: None
• Description: None

Sequence

>retro_oind_33
ATGGCTGCACCAGCTTCCTCCACCTCGTCTCTTCTCCTAGTGTTGGTGATACTGCTCGCAGCAGCGCTGATCAGCCACTC
ATCAGCCAATGCCTGGCCTGCTAGTAGCTCCGGCTCCGGCGGCGGCGGCGGCGGCGGCCTCAGCGCCGGATTCTACGACG
AGACGTGCCCCAGCGCGCAGGACGTGGTGCGGCGCGTGATCCAGGACGCCCGCGTCGCCGACCCGCGCATCCCGGCCTCC
CTCATCCGCCTCCACTTCCACGACTGCTTCGTCAACGGCTGCGACGCCTCCATCCTCCTCGACGACGACCTGCCGTCCGG
GATCCACACCGAGAAGCGCGTCCCGGCCAACGACAACTCCGCCCGGGGGTTCGACGTCGTCGACGACATCAAGTGCGAGC
TCGACAAGGCATGCCCGGGCGTCGTCTCCTGCGCCGACATCCTCGCCATCGCCGCCCAGGTCTCCGTCGACCTCGCCGGC
GGCCCGCGCTGGCGCGTCCAGCTCGGCCGCCGCGACGCCACCGCCACCAACATCCCCAAAGCCGACAACCTCCCCGGCTT
CACCGACACGCTCGAGGACCTCGTCGCCAAGTTCGACGCCGTCGGCCTCGACCACGGCGACCTCGTGGCGCTCCAGGGCG
CCCACACGTTCGGGCGGGCGCAGTGCCTGTTCACGCGGGAGAACTGCACGGCGGGGCAGCCGGACGACGCGCTGGAGAAC
CTGGACCCGGTCACCCCCGACGTGTTCGACAACAACTACTACGGCAGCCTCCTCCGCGGCACCGCCAAGCTCCCCTCCGA
CCAGGTCATGCTCTCCGACGACCCCTACGCCGCCGCCACCACCGCGCCCTTCGTCCGCCGCTTCGCTGGCAGCCAGAAGA
GCTTCTTCAGGAGCTTCGCGGCGTCGATGATCAAGATGGGGAACATCAGCCCGCTCACCGGGATGGACGGACAGATCAGG
CAAAACTGCCGCAGGATCAACACCTATTACTAG

Alignment

ORF - retro_oind_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.79 %
• Parental protein coverage: 55.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  AAAGGASAWPVMSPSYYEASCPSVYDIVRRVVQEARCTDPRAPASLLRLHFHDCFVNGCDGSLLLDDF--
          ....G.......S...Y...CPS..D.VRRV.Q.AR..DPR.PASL.RLHFHDCFVNGCD.S.LLDD...
Retrocopy SSGSGGGGGGGLSAGFYDETCPSAQDVVRRVIQDARVADPRIPASLIRLHFHDCFVNGCDASILLDDDLP

Parental  GAMQSEKNAPPNKGSARGFDVVDGIKAALENACPGVVSCADILALAAEISVELSGGPSWNVMLGRRDGTA
          .....EK..P.N..SARGFDVVD.IK..L..ACPGVVSCADILA.AA..SV.L.GGP.W.V.LGRRD.TA
Retrocopy SGIHTEKRVPANDNSARGFDVVDDIKCELDKACPGVVSCADILAIAAQVSVDLAGGPRWRVQLGRRDATA

Parental  ANFEGARDLPGPTDDLDLLRRKFSEFNLDDTDFVALQGAHTIGRAQCRF
          .N...A..LPG.TD.L..L..KF....LD..D.VALQGAHT.GRAQC.F
Retrocopy TNIPKADNLPGFTDTLEDLVAKFDAVGLDHGDLVALQGAHTFGRAQCLF

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_33 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA003712	1 retrocopy	retro_oind_39,
Oryza sativa indica	BGIOSGA012189	1 retrocopy	retro_oind_33 ,
Oryza sativa indica	BGIOSGA021077	1 retrocopy	retro_oind_30,
Oryza glaberrima	ORGLA03G0092500	1 retrocopy	retro_ogla_52,