RetrogeneDB ID: retro_bole_24

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C3:49522048..49522525(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo3g134640
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo3g134660
• Aliases: None
• Description: None

Sequence

>retro_bole_24
ATGGATTCATCTCCCAAGGGAAACTCAGCATGTGCGCAACAACAACAGAAGATGGAGATTCAGAACAGCCACAACGAGAA
GCTTGTTGGTCTGCTTCACGAAACTGGGTCAAGAGAAGTTGTGGTCTTATGCCACGGATTCAAATCTGACAAGAACAACA
CAATCCTCAAGAATGTGGCTGCTGCCATAGAGAAAGAAGGAATCAGCTCTTTTCGTTTTGATTTCTCTGGAAACGGAGAG
AGCGAAGGAGGTTTCAACTATGGTAACTACAAGTACGAAGCTGATGATCTACACTCCGTCATCCAACACTTCTCTAACAC
CAATCGCGTCGTTACTACGATTATCGGACACAGTAGAGGAGGTAACGTGGTGCTCCTCTACGCCTCCAAGTATTGCAATG
ATGGTAACGTCCGCAATATAATCAGTATATCTGGACGTTATGATCTGAAGAAAGGAATACGTCTTGGAGATGGGTAG

Alignment

ORF - retro_bole_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.16 %
• Parental protein coverage: 56.23 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSS-QGTSACAEEQQRIEILNSHNEKLVGLLHETGSTEVVVLCHGFRSNKNDTVMKSVAAAIEKEGISA
          MDSS..G.SACA..QQ..EI.NSHNEKLVGLLHETGS.EVVVLCHGF.S.KN.T..K.VAAAIEKEGIS.
Retrocopy MDSSPKGNSACAQQQQKMEIQNSHNEKLVGLLHETGSREVVVLCHGFKSDKNNTILKNVAAAIEKEGISS

Parental  FRFDFSGNGESEGSFYFGNYNHEADDLRSVIQHFSNFNRVVPLILGHSKGGDVVLLYASKY---HDISNV
          FRFDFSGNGESEG.F..GNY..EADDL.SVIQHFSN.NRVV..I.GHS.GG.VVLLYASKY.......N.
Retrocopy FRFDFSGNGESEGGFNYGNYKYEADDLHSVIQHFSNTNRVVTTIIGHSRGGNVVLLYASKYCNDGNVRNI

Parental  INLSGRYDLKKGI
          I..SGRYDLKKGI
Retrocopy ISISGRYDLKKGI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica oleracea was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica oleracea was not studied using ChIP-Seq data.

EST

Brassica oleracea was not studied using EST data.

TSS

Brassica oleracea was not studied using FANTOM5 data.

Lab

retro_bole_24 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica oleracea 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA001352	1 retrocopy	retro_oind_81,
Brassica oleracea	Bo3g134660	1 retrocopy	retro_bole_24 ,
Hordeum vulgare	MLOC_20645	1 retrocopy	retro_hvul_20,
Oryza sativa japonica	OS01G0579900	1 retrocopy	retro_osat_70,
Populus trichocarpa	POPTR_0018s06860	1 retrocopy	retro_ptri_17,