RetrogeneDB ID: retro_oind_13

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02036315.1:11272..12256(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA038093
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA013825
• Aliases: None
• Description: None

Sequence

>retro_oind_13
ATGGAGGAGGAGCGGCGCGTGCTCGTGACCGGCGGCAATGGTTTCATCGGATCCTGGATCGTGCGGATCCTTCTCGCACG
CGGGTACGCCGTGACCGCAACCTACCAGCCGGGCACGGACGCTGCGCACCTCCTCGCCCTCGACGACGAAAGGCTCCTCC
TGCTCCCCGCCGACCTGCTTGATGCGGGCGCCATCTCCGCGGCGGCGGCAGCGGGCGGGGGCTGCCGGGCGGGCGTGCTG
CACGTGGCCTCCCCGTGCACGCTGGCTGACCCGCGGGATCCGCAGGCCGAACTGGTGGAGCCGGCGGTGCGGGGCACGCT
GCACGTGCTGGAGGCGGCGCGGGGCGCGGGAGCGCGGCGCGTGGTGGTGACGTCCTCCATCTCAGCCATGGTGCCCAACC
CGGGGTTGGCGGCGGGAGAGCTCGTCGACGAGCGAAGCTGGACGGACATGGAATTCTGCAAGGCCCGGGGCAAGTGGTAC
CCGGTGTCCAAGACGCTGGCCGAGAGGGCGGCGTGGGAGTACGCGGCGCGGTGGCCCGGCTTCGAGTTGGCCACCATCCT
GCCGTCGACATGCCTCGGCCCGCTCCTGCAGCCCACCCTGAACGCCAGCTCTGTCGTGCTGCAGCGCCTCTTGCAGGGCT
CCACGGACGACCAGGCGGACTACTGGCTCGGCGCCGTCCACGTCCGCGACGTCGCCGCCGCCCACCTCCTGCTGCTCGAG
GCTCCCACCGTCTCCGGGAGGTACCTCTGCACCAACGGCATCTACCAGTTCAGCGACTTCGCACGGCTAGCTGCCAGGAT
CTGCCCCGCGTACGCCCACGCCATCCACCGCTTCGAGGAGGGGACTACACAACCGTGGCTCGTGCCGCGCGACGCCCGTG
ACGCAGCACGCCGGCTCCTCGACCTCGGCCTCGTCCTCACTCCCCTCGAGGAGGCAATCAAGGACGCGGAGAAGAGTCTC
ACCGATAAATGCTTCCTTCCTTGA

Alignment

ORF - retro_oind_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.1 %
• Parental protein coverage: 69.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TDHLHALAAAGGGEGRRLRVFPGDLLDGAALLAAAR---GC-SGVFHLASPCIVDRVLDPQAQLMVPAVE
          TD..H.LA........RL...P.DLLD..A..AAA....GC..GV.H.ASPC......DPQA.L..PAV.
Retrocopy TDAAHLLAL----DDERLLLLPADLLDAGAISAAAAAGGGCRAGVLHVASPCTLADPRDPQAELVEPAVR

Parental  GTLNVLRAAKDAGGVRRVVVTSSISAIVPSPGWPAGEVRDERCWTDLDYCEKNGVWYPASKTLAEKAAWK
          GTL.VL.AA..AG..RRVVVTSSISA.VP.PG..AGE..DER.WTD...C...G.WYP.SKTLAE.AAW.
Retrocopy GTLHVLEAARGAGA-RRVVVTSSISAMVPNPGLAAGELVDERSWTDMEFCKARGKWYPVSKTLAERAAWE

Parental  FAEE-NGLDVVVVNPGTVMGLVIPPTINASMAMLVRLLEGCTEEYADFYMGPVHVEDVALAHILLYENPS
          .A....G.......P.T..G....PT.NAS...L.RLL.G.T...AD...G.VHV.DVA.AH.LL.E.P.
Retrocopy YAARWPGFELATILPSTCLGPLLQPTLNASSVVLQRLLQGSTDDQADYWLGAVHVRDVAAAHLLLLEAPT

Parental  ASGRHLCVQSIAHWSDFASRVAELYPEY
          .SGR.LC...I...SDFA...A...P.Y
Retrocopy VSGRYLCTNGIYQFSDFARLAARICPAY

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_13 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA013825	1 retrocopy	retro_oind_13 ,
Oryza punctata	OPUNC03G36000	1 retrocopy	retro_opun_40,
Oryza sativa japonica	OS03G0818200	1 retrocopy	retro_osat_21,