RetrogeneDB ID: retro_oind_105

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: AAAA02049842.1:1540..2059(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA011944
• Aliases: None
• Description: None

Sequence

>retro_oind_105
ATCGCCCCCTCGATCCTGTCCGCCGACTTCGCCCGGCTGGGTGAGGAAGTCCGCGCCATCGACGCCGCCGGCGCCGACTG
GATCCATATCGATGTGATGGACGGGCATTTCGTGCCCAACATCACCATCGGCCCGGCGGTGGTGAAGGCGCTGCGCCCGC
ATACGACCAAGCCGTTCGACGTGCATCTGATGATTTCCCCCATCGACGCCTATCTCGATGCGTTCGCCGCGGCGGGCGCG
GACACGATCACCGTCCATCCCGAGGCGGGCCCGCACATCCACCGCACGATCCAGCACATCAAGGGGCTGGGCAAGCGCGC
CGGCGTCGTCCTGAACCCCGCCACGCCCGCCAAGATGCTGGATTATCTGATCGACATGGTCGACCTGGTCCTCGTCATGA
GCGTGAACCCCGGCTTCGGTGGCCAGAGCTTCATCGAGAGCCAGCTCAAGAAGATTGCGGCGATCCGCAAGATGATCGAG
CATTCGGGCCGCGCCATCGATCTGGAGGTCGACGGCGGC

Alignment

ORF - retro_oind_105 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.14 %
• Parental protein coverage: 63.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VSPSILSANFSKLGEQVKAVEVAGCDWIHVDVMDGRFVPNITIGPLVVDALRPVTDLPLDVHLMIVEPEQ
          ..PSILSA.F..LGE.V.A...AG.DWIH.DVMDG.FVPNITIGP.VV.ALRP.T..P.DVHLMI.....
Retrocopy IAPSILSADFARLGEEVRAIDAAGADWIHIDVMDGHFVPNITIGPAVVKALRPHTTKPFDVHLMISPIDA

Parental  RVPDFIKAGADIVSVHCEQSSTIHLHRTVNQIKSLGAKAGVVLNPATPLTAIDYVLDVVDLVLIMSVNPG
          ....F..AGAD...VH.E.....H.HRT...IK.LG..AGVVLNPATP....DY..D.VDLVL.MSVNPG
Retrocopy YLDAFAAAGADTITVHPEAGP--HIHRTIQHIKGLGKRAGVVLNPATPAKMLDYLIDMVDLVLVMSVNPG

Parental  FGGQSFIESQVKKIAELRRLCAEKGVNPWIEVDGG
          FGGQSFIESQ.KKIA..R......G.....EVDGG
Retrocopy FGGQSFIESQLKKIAAIRKMIEHSGRAIDLEVDGG

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_105 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	BGIOSGA011944	1 retrocopy	retro_oind_105 ,