RetrogeneDB ID: retro_brap_16

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A02:23858113..23858617(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra020665
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra000458
• Aliases: None
• Description: None

Sequence

>retro_brap_16
ATGGCTAGTGGAAGTGAGCGTGTGGTGGTCGTAGGAGTCGATGATTCAACTCATAGCTACCACGCACTAGAGACAGCTCT
CGATCTCTTCTTCACACCTTTCAAATCAAACCCACAATTCAAACTCGTCGTCCTTCACGCCAGACTCCCCGCTACCTCCG
TCCTCGGCTTTGCCGGACCCGGAACGGTCGATATAATACCACTGGTGGAACAAGATTTAGACAAGACTGCAGACTTGGTT
AAGAAGAAGTGTACCGATGTGTGCTCGGCTAAATCCGTTGAGATCACTTCGTTGGAGGTTGTAGAAGGAGATCCCAGGAA
CATAATGCTGGAAGCAGCGGAGAGACACCATGCATCTGTTCTTGTTCTTGGGAGCCATGGCTATGGAGCTGTCAAGAGGG
TGTTTTTGGGGAGCGTGAGTGACTATTTAGCTCATCATGCTCATTGCTCCGTTATGATCGTCAAGAAGCCTAAGGCTAAA
CATGCTTCTAACGATAAACACTAA

Alignment

ORF - retro_brap_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.76 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATGEEKPVMVVGVDESEQSTYALEWTLDRFFAPYAPNFPFKLIIVHAKPNAVSAVGLAGPGTAEVVPYV
          MA.G.E..V.VVGVD.S..S..ALE..LD.FF.P...N..FKL...HA...A.S..G.AGPGT....P.V
Retrocopy MASGSER-VVVVGVDDSTHSYHALETALDLFFTPFKSNPQFKLVVLHARLPATSVLGFAGPGTVDIIPLV

Parental  DADLKHTAVKVIEKAKALCLSKSVHGAMIEVFEGDARNILCEVVDKHHASLLVVGSHGYGAIKRAVLGSV
          ..DL..TA..V..K....C..KSV.....EV.EGD.RNI..E....HHAS.LV.GSHGYGA.KR..LGSV
Retrocopy EQDLDKTADLVKKKCTDVCSAKSVEITSLEVVEGDPRNIMLEAAERHHASVLVLGSHGYGAVKRVFLGSV

Parental  SDYCAHHAHCSVMIVKKPKIK
          SDY.AHHAHCSVMIVKKPK.K
Retrocopy SDYLAHHAHCSVMIVKKPKAK

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_16 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo3g039740	1 retrocopy	retro_bole_20,
Brassica rapa	Bra000458	1 retrocopy	retro_brap_16 ,
Arabidopsis lyrata	scaffold_403747.1	1 retrocopy	retro_alyr_1,