RetrogeneDB ID: retro_oind_66

Retrocopy location

• Organism: Rice subsp. indica (Oryza sativa indica)
• Coordinates: 6:31561340..31562291(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: BGIOSGA020576
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: BGIOSGA003218
• Aliases: None
• Description: None

Sequence

>retro_oind_66
ATGGACGCCAACATGCTGAGCGCGATGATGGCCGCCGTCGGCGGCGACAGGGCGGCGGCGCCGGGCGGCGACAAGCCGCA
GCCGGACACGTCGGAGCAGATCAACGTGTCCCCCCTCGCCCTCCTCAAGATGCTCAAGCACGGGCGAGCCGGCGTGCCGA
TGGAGGTGATGGGGCTGATGCTGGGCGAGTTCGTCGACGAGTACACGGTGACGGTCGCCGACGTGTTCGCCATGCCGCAG
AGCGGCACCGGCGTGAGCGTGGAGGCGGTGGACCACGCGTTCCAGAGCGAGATGCTGGAGATGCTCCGGCAGACGGGGCG
GCCGGAGATGGTGGTGGGGTGGTACCACTCCCACCCCGGCTTCGGCTGCTGGCTCTCCGGCACCGACATGGCCACGCAGC
AGAGCTTCGAGCAGCTGCACCCGCGCGCCGTCGCCGTGGTGATCGACCCGGTGCAGAGCGTCAAGGGGAAGGTGGTCATG
GACGCGTTCCGCCTCGTCGACCACATGGCGATGGTGCTCGGCGGCGCCGCGGGCGGCGAGGCGCGGCAGACCACGTCGAA
CGTCGGCGCCGTCGCGCGGCCGTCGGCGGTGGCGCTCGTCCACGGCCTCGGGCGGCACTACTACTCGCTCGCCATCAGCT
ACCGGATGAAGGAGGGGGAGGAGCGGATGCTGGCGTGCCTCAGCCGGAGCGGGTGGTCCGACGGGTTCGCGCTGCGGCGG
TTCGGCGCGCACGACGCCGGCAACGAGGCGGCGGTGCGCGGGATGCGGGACCTCGCCGTGGGCTACGGGGCGCAGGTGAG
GGAGGAGGACGAGACGCCGCCGGAGAGGCTCGCCGTGGTGAGGGCGGGCAAGGTGGACGCCAAGGGGAAGCTGGAGGAGA
AGGCCATGGACGCCATGTCCGCCAACATCGTGCAGACGCTCGGCATGATGCTCGACACCGTCACCTTCTAG

Alignment

ORF - retro_oind_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.01 %
• Parental protein coverage: 97.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GASGMGQPPTDSPLLDSSEQVYISSLALLKMLKHGRAGVPMEVMGLMLGEFVDDYTVRVVDVFAMPQSGT
          G......P..D.P..D.SEQ...S.LALLKMLKHGRAGVPMEVMGLMLGEFVD.YTV.V.DVFAMPQSGT
Retrocopy GGDRAAAPGGDKPQPDTSEQINVSPLALLKMLKHGRAGVPMEVMGLMLGEFVDEYTVTVADVFAMPQSGT

Parental  GVSVEAVDHVFQTNMLDMLKQTGRPEMVVGWYHSHPGFGCWLSGVDINTQQSFEALNPRAVAVVIDPIQS
          GVSVEAVDH.FQ..ML.ML.QTGRPEMVVGWYHSHPGFGCWLSG.D..TQQSFE.L.PRAVAVVIDP.QS
Retrocopy GVSVEAVDHAFQSEMLEMLRQTGRPEMVVGWYHSHPGFGCWLSGTDMATQQSFEQLHPRAVAVVIDPVQS

Parental  VKGKVVIDAFRLINPQTMML----GQEPRQTTSNVGHLNKPSIQALIHGLNRHYYSIAINYRKNELEEKM
          VKGKVV.DAFRL.....M.L....G.E.RQTTSNVG....PS..AL.HGL.RHYYS.AI.YR..E.EE.M
Retrocopy VKGKVVMDAFRLVDHMAMVLGGAAGGEARQTTSNVGAVARPSAVALVHGLGRHYYSLAISYRMKEGEERM

Parental  LLNLHKKKWTDGLILKSFDTHSKTNEQTVQEMLNLAIKYNKAVQEEDELPPEKLAIANVGRQDAKKHLEE
          L..L....W.DG..L..F..H...NE..V..M..LA..Y...V.EEDE.PPE.LA....G..DAK..LEE
Retrocopy LACLSRSGWSDGFALRRFGAHDAGNEAAVRGMRDLAVGYGAQVREEDETPPERLAVVRAGKVDAKGKLEE

Parental  HVSNLMSSNIVQTLGTMLDTVVF
          .....MS.NIVQTLG.MLDTV.F
Retrocopy KAMDAMSANIVQTLGMMLDTVTF

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_66 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	BGIOSGA003218	1 retrocopy	retro_oind_66 ,