RetrogeneDB ID: retro_brap_13

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:12309791..12311465(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra019550
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra029230
• Aliases: None
• Description: None

Sequence

>retro_brap_13
ATGGCGGCAGGGGGAGTTGAAATCTCGAAAAGCTCTGTCGTCGTTGATCGTGTTCGTGATTTGTATCCTCGTCAGGGTGG
TAGGGACGGTGAGAGGCGTCAAACCAAACGACCCAGTGATTCTGATCGCTGGTTGAAAGATGGGCGACGTGATTTGTATC
AAAGAGGAGAAGCCCGAGAGGGAGATGTTGGTCAGAAGAGGAGGAAGTGTTCTCCAGTTTCAGGGGAGAGAAAAGATCAA
GTCTTTCCACCTCCACTTGGTGAGAAGACCATTGTTGATGTGGGTAAGATTTCATCTGAGGGTGTTGTGAAGTCAACAGA
GTATGTTTCTGCAGTGTCAGTGACGTCTGTTAAACATCCTTTTGATGATCTTGAGGAGGGCCAGTTGGAGGACGAGCAGG
TGGTTCAGGCACCCAATATTGCTACGTCTAAGTGGTGTTTGGAATCTCCAAAGGATGAGGCAGTTCATGTTGTCAGGAAT
AGCAGATGGAATAGGAGCAGTCTTACTCCTGAGAGCGGTGAATTTCAAGTGGATTCGTCTGATGAACGTCGGTCCAATTC
TTCTGAGTCTCGCAGCTTAGAACCCCTCAGCTCTCATGAAAATTCAGAGCATGAGATTAACATGGATGTTGGTGAAGAAG
AATGTTGTGCTTCTGATTTGAACGACTCGGAAGTTGATGAAGCAGAGGGAGGCTTGAGCATGCTATCTGGTAGTAGAGAT
GTTAACGAATACCAGAAGCTAAGCAAGATTAACGAAGGAACTTATGGTGTTGTCTACAAAGCCAAGGACAGAAAGACAGA
GGAGATTGTGGCACTTAAAATGATCAAGATGAACATGGAAGACGAATATGGATTCCCGTTGACATCTTTGAGGGAGATCA
ACATTCTTTTGTCTTGCAATCACCCGTCGATTGTGAACGTCAAGGAAGTCGTGGTGGGAAACGGTGACAGTGTTTTCATG
GTCATGGAACACTTGGAACATGACTTGAGGGGCGTTATGGACAGGATGAAACAGCCTTTTAGCACCAGTGAGGTCAAATG
CTTGATGATTCAGCTGTTGGAGGGTTTGAAGTACCTACATAGCAACTGGATCATCCACAGGGATCTGAAGCCATCTAATC
TTCTACTGAACAACAGTGGGGAGCTGAAAATATGCGATTTTGGAATGGCTAGGCAATATGGGAGTCCTATCAAGCCCTAC
ACGCAGTTGGTTGTCACACAGTGGTACAGGTCCCCGGAGCTTCTTCTAGGAACAAAGGAGTATTCAACCGCAGTTGATAT
GTGGTCCATCGGTTGCATTATGGGTGAGTTGCTGTCTCTAAAACCTCTTTTCCGAGGGAAAAGTCAGAATGACATTGACC
AGCTTCAACAGATATTTGCGGTTCTTGGAACACCGAGTGAGACGACTTGGCCTGGATTCACTTCGCTGCCAGGTTCCAAA
GCCAAGTTTCGTAAGCAGCCATACAATTTACTGCGTAAGAAATTTCCTGCTGCATCTTTTACCGGAGGTCCAGTTCTTTC
AGAATTGGGATTTGATTTGTTGAACAGATTATTGAATGTTGACCCTGAGAAGCGACTAACAGTTGACGAGGCTCTTAACC
ACGCCTGGTTCAATGAAGTACCTCTCCAGAAATCCAAGGAGTTCATGCCTACATTTCCTTCAAAGCGTAACTGA

Alignment

ORF - retro_brap_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.27 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNMLLGSRSVNGFQKLNKINEGTYGIVYRARDEKTKEIVALKKIKMKEDKYEEEYGFPLTSLREINILLS
          ..ML.GSR.VN..QKL.KINEGTYG.VY.A.D.KT.EIVALK.IKM.....E.EYGFPLTSLREINILLS
Retrocopy LSMLSGSRDVNEYQKLSKINEGTYGVVYKAKDRKTEEIVALKMIKMN---MEDEYGFPLTSLREINILLS

Parental  CNHPSIVNVKEVVVGGKNDSDVYMVMEHLEHDLKCLMERKKQPFSTSEVKCLMLQLLEGVHYLHTNWIIH
          CNHPSIVNVKEVVVG..N...V.MVMEHLEHDL...M.R.KQPFSTSEVKCLM.QLLEG..YLH.NWIIH
Retrocopy CNHPSIVNVKEVVVG--NGDSVFMVMEHLEHDLRGVMDRMKQPFSTSEVKCLMIQLLEGLKYLHSNWIIH

Parental  RDLKPSNLLMNNSGELKICDFGMARQYGSPIKPYTQMVITQWYRPPELLLGAKQYSTAVDMWSIGCIMAE
          RDLKPSNLL.NNSGELKICDFGMARQYGSPIKPYTQ.V.TQWYR.PELLLG.K.YSTAVDMWSIGCIM.E
Retrocopy RDLKPSNLLLNNSGELKICDFGMARQYGSPIKPYTQLVVTQWYRSPELLLGTKEYSTAVDMWSIGCIMGE

Parental  LLSQKPLFPGKT--ELDQLQKIFAVLGTPNESIWPGFSSLPNAKAKFPTQSYNLLRKKFPAISFVGGQIL
          LLS.KPLF.GK.....DQLQ.IFAVLGTP.E..WPGF.SLP..KAKF..Q.YNLLRKKFPA.SF.GG..L
Retrocopy LLSLKPLFRGKSQNDIDQLQQIFAVLGTPSETTWPGFTSLPGSKAKFRKQPYNLLRKKFPAASFTGGPVL

Parental  SERGFDLLNGLLTLDPEKRLTVEEALNHSWFHEVPLPKAQDFMPTFPPRR
          SE.GFDLLN.LL..DPEKRLTV.EALNH.WF.EVPL.K...FMPTFP..R
Retrocopy SELGFDLLNRLLNVDPEKRLTVDEALNHAWFNEVPLQKSKEFMPTFPSKR

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_13 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 oleracea	Bo2g165520	1 retrocopy	retro_bole_11,
Brassica rapa	Bra029230	1 retrocopy	retro_brap_13 ,