RetrogeneDB ID: retro_oind_9

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02040097.1:1480..2143(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA038864
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA005240
• Aliases: None
• Description: None

Sequence

>retro_oind_9
ATGGGTGATTTACAATACGGAATTGACCCTAAAAGATTGGGGGAATATGCAGACGAAATTAAGCAGATTCACGACAAAGG
AGTAGAAATTGCGATCGTTATTGGAGGAGGAAATATTTTTAGAGGCGTTGCCGGTGCAAGCGCAGGAATGGACAGAGTGC
AAGGTGACTATATGGGAATGCTTGCTACTGTTATTAACGGAATGGCTTTGCAGGGCGCACTTGAAGATAAAGGAATGAAA
ACGCGTTTGCAGACTGCTTTAAAAATGGAATCTATCGCAGAACCATACATTAAAAGAAGAGCTGACCGCCACCTTGAAAA
AGGAAGAATTGTAATTTTTGGTGCCGGAACCGGAAACCCATATTTTACAACTGATACTGCAGCTGTTTTAAGAGGAATCG
AAATTAATGCTGATGTAATCTTAAAAGGAACCCGCGTTGATGGTGTTTACGATTCTGATCCTGAAAAAAATGCTTCGGCT
GTAAAATTTGATTTCATCTCGTTTGATGATGTCCTTAAAAAAGGATTAAACGTAATGGATACAACCGCTTTTACTTTAAG
CCAGGAAAACAAACTGCCAATTGTTGTTTTTGACATGAACAAAATTGGAAACCTGTTAAAAATCTGCGAAGGCGAAAACA
TCGGAACTGTAGTAAATATTTAG

Alignment

ORF - retro_oind_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.5 %
• Parental protein coverage: 60.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GDHTENIDPKITMAIAREVASVTRLGVEVAIVVGGGNIFRGASWAGCSGLDRSSADYIGMLATVMNAIFL
          GD....IDPK.....A.E.......GVE.AIV.GGGNIFRG...A...G.DR...DY.GMLATV.N...L
Retrocopy GDLQYGIDPKRLGEYADEIKQIHDKGVEIAIVIGGGNIFRGVAGAS-AGMDRVQGDYMGMLATVINGMAL

Parental  QATMESIGIPTRVQTAFRMSEVAEPYIRRRAVRHLEKGRVVIFAAGTGNPFFTTDTAAALRCAEINAEVV
          Q...E..G..TR.QTA..M...AEPYI.RRA.RHLEKGR.VIF.AGTGNP.FTTDTAA.LR..EINA.V.
Retrocopy QGALEDKGMKTRLQTALKMESIAEPYIKRRADRHLEKGRIVIFGAGTGNPYFTTDTAAVLRGIEINADVI

Parental  LKATNVDGVYDADPKRNPNARLLEAVSYHEVQTRDLSVMDMTAITLCQENNIPVVVFNLQKPGNIAKAIV
          LK.T.VDGVYD.DP..N..A......S...V....L.VMD.TA.TL.QEN..P.VVF...K.GN..K...
Retrocopy LKGTRVDGVYDSDPEKNASAVKFDFISFDDVLKKGLNVMDTTAFTLSQENKLPIVVFDMNKIGNLLKICE

Parental  GEKVGTFI
          GE..GT..
Retrocopy GENIGTVV

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_9 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	BGIOSGA005240	1 retrocopy	retro_oind_9 ,