RetrogeneDB ID: retro_brap_33

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A03:21014780..21015398(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra013014
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra001266
• Aliases: None
• Description: None

Sequence

>retro_brap_33
ATGTTCTCCGGGAAAACCACAACGCTTCTCCGCCGAATCCTCTCGGAGAGGGAGAGCGGGAAGAAGGTAGCCGTCATCAA
ATCGGATAAAGACGACAGGTACTGTGCGGAATCGATCGTTACTCACGACGGAGAGAAGTTCCCTTGCTGGGCTCTCCCTG
ATCTGAACTCTTTCAAGGAGAGATTCGGTTTCGATGCGTATAGGAATCAGTTGGACGTGATTGGGATCGACGAGGCGCAG
TTCTTCGGGGACCTCTACGAGTTTTGCCGCGAGGCGGCTGATAAGGAGGGTAAAACGGTAATTGTGGCGGGATTGGATGG
TGATTATCTGAGGAGGAGGTTCGGTTCGGTGCTGGATTTGGTTCCGGTTGCGGATACGGTTACGAAGCTGGCGTCGAGGT
GTGAGGTTTGTGGGAAGAGAGCTTCGTTTACGCTGAGGAAGACGGAGGAGAGGGAGACGGAGCTGATCGGTGGAGCGGAG
GTTTATATGCCTGTGTGTCGGAGTCATTACGTTAGCGGTCAAGGCGTTTTGGAGACCGCTCGTGCCGTTTTGGAAGCTTC
TTCCCAGCGAAACGCGACGCGCGGTTTAGAAGCAACGAGTCTCTCCCCTCCGTTTTAA

Alignment

ORF - retro_brap_33 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.37 %
• Parental protein coverage: 80.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFSGKSTSLLRRIKSEISLGRSVAMVKSSKDTRYAKDSVVTHDGIGFPCWAIPDLMSFHDIFGQDAY-DK
          MFSGK.T.LLRRI.SE...G..VA..KS.KD.RY...S.VTHDG..FPCWA.PDL.SF...FG.DAY...
Retrocopy MFSGKTTTLLRRILSERESGKKVAVIKSDKDDRYCAESIVTHDGEKFPCWALPDLNSFKERFGFDAYRNQ

Parental  LDVIGIDEAQFFGDLYEFCCKAADDDGKTVIVAGLDGDYLRRRFGAVLDIVPIADSVTKLTARCEVCGQK
          LDVIGIDEAQFFGDLYEFC..AAD..GKTVIVAGLDGDYLRRRFG.VLD.VP.AD.VTKL..RCEVCG..
Retrocopy LDVIGIDEAQFFGDLYEFCREAADKEGKTVIVAGLDGDYLRRRFGSVLDLVPVADTVTKLASRCEVCGKR

Parental  AFFTLRKTCDTKTELLGGADVYMPVCRKHYVNNRIVIKASKKVLDSDKER
          A.FTLRKT....TEL.GGA.VYMPVCR.HYV....V......VL.....R
Retrocopy ASFTLRKTEERETELIGGAEVYMPVCRSHYVSGQGVLETARAVLEASSQR

Legend:

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

Expression

RNA-Seq

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

ChIP-Seq

Brassica rapa was not studied using ChIP-Seq data.

EST

Brassica rapa was not studied using EST data.

TSS

Brassica rapa was not studied using FANTOM5 data.

Lab

retro_brap_33 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica rapa 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G07800	1 retrocopy	retro_atha_9,
Brassica oleracea	Bo3g061430	1 retrocopy	retro_bole_16,
Brassica rapa	Bra001266	1 retrocopy	retro_brap_33 ,
Arabidopsis lyrata	fgenesh2_kg.3__818__AT3G07800.1	1 retrocopy	retro_alyr_19,