RetrogeneDB ID: retro_brap_32

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A07:14812829..14814842(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra003744
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra000445
• Aliases: None
• Description: None

Sequence

>retro_brap_32
ATGGAGAAGAATAAATGGAGTGGAAAAGCTTATAGTCAGAGGTATTACGAGATTCTTGAGAAACGGAAGAGCCTACCTGT
GTATGCGCAGAAACAAGAGTTTCTACAATGCTTGATGAGCAACCAGACGTTGATACTTGTCGGTGAAACCGGTAGTGGTA
AGACTACGCAGATCCCACAGTTTGTTTTGGAAGCCGTGAACGAAAAAAACCCTAGCAAGTGGCTGGTCGGGTGCACACAG
CCTCGTAGAGTCGCAGCCATGTCCGTGGCAAGTCGTGTTGCTGAAGAGATGGATGTAGCTATCGGTGAAGAAGTCGGTTA
CTCCGTTCGCTTTGAGGATTGCACTAGCTCCAAAACAGTGCTTAAGTACTTGACCGATGGTATGCTTATGAGAGAAGCAA
TGACCGATCCGCTTCTACAGAGATATAAAGTGATAGTCCTCGATGAAGCCCATGAAAGAACTTTAGCCACGGATTTACTA
TTTGGTGTTCTGAAACGAGTCTTGAGCAACAGACCGGACCTTAAGCTAGTTGTGATGAGTGCAACTTTGGAAGCTGAAAA
ATGTCTTGAGTATTTTAGCGGTGCACCTCTTATGAAAGTTCCGGGAAGGCTCCATCCCGTAGAGATCTTGTACACGCAAG
AACCTGAGAGAGACTATCTTGACGCTGCTATTCGGACAGTTGTTCAGATTCACATGTCTGAGCCGCCCGGTGATGTTCTT
GTTTTCTTAACCGGCGAGGAGGAGATTGAAGATGCATGCAGAAAAATCGTCTGTGAACTTGGGGATCAAGTAAACGTTGT
GCCTTTGTATTCTTCTCTTCCACCAGCCATGCAGCAGAAGATATTTGATCCTCCTACGGAGAATGTGAGGAAGATTGTTG
TATCCACCAACATAGCAGAGACTTCTTTAACCATCGATGGAGTTGTTTACGTGGTTGATCCTGGCTTCGCTAAGCAGAAA
CTATACAACCCTGAAACTCGTGTTGAGTCGTTGTTGGTGTCTGCAATATCACAAGCAAGTGCTAACCAGAGAGCTGGTCG
TGCAGGTAGAACACGGCCTGGGAAATGTTTCAGGCTTTACACAGAGAAGAGTTTCAACCATGATTTGATTGAGCAGACGT
ATCCTGAGATACTGAGATCAAACCTTGCAAACACTGTTCTGACTTTGAAAAAACTTGGTATAGATAACTTGGTTTGCTTC
GACTATATGGACCCTCCTGCTCCTGTGACGATGGGGCGGGCCTTGAACGATTTGCTTGATCTGGGAGCATTAGATGAAGA
ACTTAACTTGACAAGGACGGGTGAGATGATGAGTGAGTTTCCTTTGGATCCGCAGATGGCAAAGATGCTTATAGTCAGTC
CTAAATTCAACTGCTCCAACGAGATTCTCTCAATTTCAGCTATGTTATCAGTACCAAACTGCTTTGTAAGGCCAAGAGGA
GAGGCGCAAAAAGCAGCAGATGAAGCTAGAGCTAGGTTTGGTCACACTGATGGAGATCACCTAACGTTGCTGAATGTGTA
CCATGATTATAAACAAAACAACGGAGACCCGAATTGGTGCTACCAGAACTTCATCAACCATAGAGCAATGAAGTCTGCTG
ACAATGTTAGAGAGCAGTTGGTGAGGATAATGTCCAGGTTTAATCTCAAGACGTGTAGCTCTGATTTTACCAGCCGTGAC
TACTATATTAACATAAGAAAGGCATTGCTTGCTGGCTATTTCATGCAAGTGGCTCATTTAGACCGCACGGGCCACTACTT
GACCGCCAAAGATGGACAAATGGTTCACCTGCATCCATCGTGTTGCTTGGATCACAAACCGGAGTGGGTAGTCTACAATG
AATATGTTCTGACTAGTCGTAATTTCATAAGGACTGTCACGTATATTCGAGGTGAATGGCTAGTGGATGTTGCACCAGAT
TACTATCATCTTTCCAACTTCCCAAACTGTGAAGCCAAACGAGTCCTCCAGAAGCTTTCTAAGAAGAGAGACAGAGCGGG
GAACCCAAAGTGA

Alignment

ORF - retro_brap_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.64 %
• Parental protein coverage: 52.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKIVVSTNIAETSLTIDGIVYVIDPGFAKQKVYNPRIRVESLLVSPISKASAHQRSGRAGRTRPGKCFRL
          RKIVVSTNIAETSLTIDG.VYV.DPGFAKQK.YNP..RVESLLVS.IS.ASA.QR.GRAGRTRPGKCFRL
Retrocopy RKIVVSTNIAETSLTIDGVVYVVDPGFAKQKLYNPETRVESLLVSAISQASANQRAGRAGRTRPGKCFRL

Parental  YTEKSFNNDLQPQTYPEILRSNLANTVLTLKKLGIDDLVHFDFMDPPAPETLMRALEVLNYLGALDDEGN
          YTEKSFN.DL..QTYPEILRSNLANTVLTLKKLGID.LV.FD.MDPPAP.T..RAL..L..LGALD.E.N
Retrocopy YTEKSFNHDLIEQTYPEILRSNLANTVLTLKKLGIDNLVCFDYMDPPAPVTMGRALNDLLDLGALDEELN

Parental  LTRTGEIMSEFPLDPQMSKMLIVSPEFNCSNEILSVSAMLSVPNCFVRPR-EAQKAADEAKSKFGHIDGD
          LTRTGE.MSEFPLDPQM.KMLIVSP.FNCSNEILS.SAMLSVPNCFVRPR.EAQKAADEA...FGH.DGD
Retrocopy LTRTGEMMSEFPLDPQMAKMLIVSPKFNCSNEILSISAMLSVPNCFVRPRGEAQKAADEARARFGHTDGD

Parental  HLTLLNVYHAYKQNNEDPNWCFENFVNNRAMKSADNVRQQLVRIMSRFNLKMCSTDFNSRDYYVNIRKAM
          HLTLLNVYH.YKQNN.DPNWC..NF.N.RAMKSADNVR.QLVRIMSRFNLK.CS.DF.SRDYY.NIRKA.
Retrocopy HLTLLNVYHDYKQNNGDPNWCYQNFINHRAMKSADNVREQLVRIMSRFNLKTCSSDFTSRDYYINIRKAL

Parental  LSGYFMQVAHLERTGHYLTVKDNQVVHLHPSNCLDHKPEWVIYNEYVLTTRNFIRTVTDIRGDWLVDVAP
          L.GYFMQVAHL.RTGHYLT.KD.Q.VHLHPS.CLDHKPEWV.YNEYVLT.RNFIRTVT.IRG.WLVDVAP
Retrocopy LAGYFMQVAHLDRTGHYLTAKDGQMVHLHPSCCLDHKPEWVVYNEYVLTSRNFIRTVTYIRGEWLVDVAP

Parental  HYYDLSNFPNCEAKRVLEKLYKKRERERN
          .YY.LSNFPNCEAKRVL.KL.KKR.R..N
Retrocopy DYYHLSNFPNCEAKRVLQKLSKKRDRAGN

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_32 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	Bra000445	1 retrocopy	retro_brap_32 ,
Brassica rapa	Bra010168	1 retrocopy	retro_brap_26,