RetrogeneDB ID: retro_brap_30

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A03:2518983..2520168(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra006207
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra007180
• Aliases: None
• Description: None

Sequence

>retro_brap_30
ATGGCCACCCGTCTTCAGTTTGAGAACAGCTGCGAAGTTGGCCTCTTTTCAAAACTCACTAATGCCTATTGCTTAGTTGC
TGTTGGAGCCTCTGAGAACTTCTATAGTGCCTTTGAGTCAGAGTTAGCTGATGATATCCCTATCGTTAAAACCTCTATTG
GAGAAACACGGATCATTGGGCGCCTATGCGTTGGAAACAGGAACGGGCTTCTTGTGCCTCATACAACTACTTACCAAGAG
CTTCAACACTTGAGGAACAGTCTACCTGATCAAGTTGTGGTCCAGAGAATCGAGGCGCCTCTGCCTGCTCTTGGAGACTG
CATCGTCTGCAACGACCATGTTGCTCTTGCTCACATCGATCTCGACGAGGAGACTGAGGAAATAATATCGGACGTTCTCG
GTGTCGAAGTTTTCCGTCAGACGATTGCAGGCAACATTCTTGTAGGCTGTTACTGTGCCTTGTCCAACAGAGGTGGCATC
GTCCATGCTTACATCTCGGAGGAAGAGTTGGACGAGCTCTCGGCGCTGCTTCGAGTCCCGCTCGTTGCGGGGACTGTGAA
CCGTGGTAGTGAAGTTATAGCTGCGGGAATGACCGTCAATGACTGGACTGCTTTCTGTGGCTCAGACACAACTGAAACGG
AGCTCTCTGTAATAGACAGTGTCTTCGAGCTAAGTGAATCTTGTGATATAAACAAGATCTCTACATCGGAATGGGATTTG
CTTGTGACCAAGTCAGAAGTCCCGGTGTTGGTTATGTTCATACAAGATTGGCGCCCCTCATGTCGATACGTGAGGCATGT
AATGGACGAATTCAACTCGAAATACACTGGTCGGTTCAAATTCTACACACTCAACGTTCGTCAAGAGAGAGGCATCGTAA
TACGCTACGACATATTCAATGTCCCGGCTAGTATTGTCTTCAAAGGCGGAGACGAGATGGCTAGAGTAAATGGATTCCAT
CTTTATGAATTAGAAAGACTAGTGAAGCAGTACGATGACTTGGTCTATGCATCCAAGCTTAAGGATAACTTAGCAAAAGA
AAATAATTTGCTAATCAAGACAACAAATCACCATAAAATCAAAGGAGAACTGATAAATTTATTTGCATATGTAGGCATGT
GTGTTTTGGTATTCAGCTCTGTTCTTTACTTTTCTTTTCTTTTTGTTCTTGGATACTTTGAGTAA

Alignment

ORF - retro_brap_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.46 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATRLQFENNCEVGVFSKLTNAYCLVAIGGSENFYSAFESELADVIPIVKTSLGGTRIIGRLCAGNKNGL
          MATRLQFEN.CEVG.FSKLTNAYCLVA.G.SENFYSAFESELAD.IPIVKTS.G.TRIIGRLC.GN.NGL
Retrocopy MATRLQFENSCEVGLFSKLTNAYCLVAVGASENFYSAFESELADDIPIVKTSIGETRIIGRLCVGNRNGL

Parental  LVPHTTTDQELQHLRNSLPDAVVVQRIEERLSALGNCIACNDHVALAHTDLDKETEEIIADVLGVEVFRQ
          LVPHTTT.QELQHLRNSLPD.VVVQRIE..L.ALG.CI.CNDHVALAH.DLD.ETEEII.DVLGVEVFRQ
Retrocopy LVPHTTTYQELQHLRNSLPDQVVVQRIEAPLPALGDCIVCNDHVALAHIDLDEETEEIISDVLGVEVFRQ

Parental  TIAGNILVGSYCALSNRGGIVHPHTSVEDLDELSTLLQVPLVAGTVNRGSEVIGAGMTVNDWTAFCGSDT
          TIAGNILVG.YCALSNRGGIVH...S.E.LDELS.LL.VPLVAGTVNRGSEVI.AGMTVNDWTAFCGSDT
Retrocopy TIAGNILVGCYCALSNRGGIVHAYISEEELDELSALLRVPLVAGTVNRGSEVIAAGMTVNDWTAFCGSDT

Parental  TATELSVIDSIFKLREA
          T.TELSVIDS.F.L.E.
Retrocopy TETELSVIDSVFELSES

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_30 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra007180	1 retrocopy	retro_brap_30 ,
Solanum lycopersicum	Solyc12g010210.1	1 retrocopy	retro_slyc_11,