RetrogeneDB ID: retro_oind_30

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 2:8696029..8697046(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA007855
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA021077
• Aliases: None
• Description: None

Sequence

>retro_oind_30
ATGGCGGCAATGTCTGCTTCGGGCCGGAGGGTCTTCTTGCTCGGTGCCCTTCTGCTCGTCGCCGTCTCCTGCCATGGCGG
CTTTGGCGGCGTCGGCGTGGCGGAGGGTTTGTCGACGAGGTACTATGCTAAGACGTGCCCCGCCGTGGAGTCCGTCGTTC
GGTCGGTGATGGCGCGGGTGGTGGCGGCGGACCGGCGCATGGGCGCGTCCGTGCTCAGGCTCTTCTTCCACGACTGCTTC
GTGAACGGCTGCGACGGGTCCGTCCTGCTCGACGACGCGCCGCCGGGGTTCACCGGGGAGAAGGGCGCCGGCGCGAACGC
CGGCTCCGCGCGCGGGTTCGAGGTGGTGGACGCGGCGAAGGCGCGGGTGGAGGCGGCGTGCCGCGCCACCGTGTCGTGCG
CCGACGTGCTCGCGCTCGCCGCGCGCGACGCCGTGGCGCTCCTCGGCGGGCCGACGTGGCCCGTGAGGCTGGGACGGAAG
GACGCCCGCACGGCGAGCCAGGCCGCGGCGAACGGCAACCTCCCCGGTCCGGTGTCAAGCCTCACCTCGCTGCTCGCCAC
GTTCGCCGCCAAGGGCCTTTCGGCGCGCGACATGACGGCGCTGTCGGGCGCGCACACGGTGGGGCGCGCCCGGTGCGCCA
CGTTCCGCGGCCGCGTCAACGGCGGCGACGCCAACGTGAACGCCACCTTCGCCGCCCAGCTCCGGCGCCTGTGCCCCGCG
GGCACCGGCGGCGACGGCAACCTCGCGCCGCTGGACGCCGAGACGCCCGACGTGTTCGACAACGGCTACTTCCGCGAGCT
GACGAAGCAGCGCGGGCTGCTGCACTCGGACCAGGAGCTGTTCGCCGGCGGCGGCGGCGGCAGGTCGTCGTCGCAGGACG
CGCTGGTGCGGAAGTACGCCGGCAACGGGGCGGAGTTCGCGAGGGACTTCGCCAAGGCGATGGTGAAGATGGGGAACCTC
GCGCCGGCCGCCGGGACGCCGGTGGAGGTCAGGCTCAACTGCCGGAAGCCCAACTAG

Alignment

ORF - retro_oind_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.49 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GLSTKFYAKTCPGVDTIVRSVVAQAVAKEPRMGASIIRLFFHDCFVNGCDASILLDDTPT-FTGEKNAGA
          GLST..YAKTCP.V...VRSV.A..VA...RMGAS..RLFFHDCFVNGCD.S.LLDD.P..FTGEK.AGA
Retrocopy GLSTRYYAKTCPAVESVVRSVMARVVAADRRMGASVLRLFFHDCFVNGCDGSVLLDDAPPGFTGEKGAGA

Parental  NINSVRGYEVIDAIKSQVEAACKGVVSCADIVALASRDAVNLLGGPTWNVQLGRKDSRTASGTAANANLP
          N..S.RG.EV.DA.K..VEAAC...VSCAD..ALA.RDAV.LLGGPTW.V.LGRKD.RTAS..AAN.NLP
Retrocopy NAGSARGFEVVDAAKARVEAACRATVSCADVLALAARDAVALLGGPTWPVRLGRKDARTASQAAANGNLP

Parental  GPASSGASLVAAFAGKGLSAREMTALSGAHTVGRARCLMFRGRIY-GEANINATFAAALRQTCPQSGGGD
          GP.SS..SL.A.FA.KGLSAR.MTALSGAHTVGRARC..FRGR...G.AN.NATFAA.LR..CP...GGD
Retrocopy GPVSSLTSLLATFAAKGLSARDMTALSGAHTVGRARCATFRGRVNGGDANVNATFAAQLRRLCPAGTGGD

Parental  GNLAPFDDQTPDAFDNAYFKNLVAQRGLLHSDQELFNGG
          GNLAP.D..TPD.FDN.YF..L..QRGLLHSDQELF.GG
Retrocopy GNLAPLDAETPDVFDNGYFRELTKQRGLLHSDQELFAGG

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_30 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 ,
Brachypodium distachyon	BRADI1G38297	1 retrocopy	retro_bdis_8,