RetrogeneDB ID: retro_brap_11

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A03:2073047..2074652(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra006112
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra015463
• Aliases: None
• Description: None

Sequence

>retro_brap_11
ATGGATTCCGATGACTACTATATGGAATCTGGAGAGGAAGATCTTTACAGCGACGGTGCAGGTGATTACAACGACGGGGC
CGATCATGATGATGATACAGATGACACGGGTTTCCTTGGGGATGACGATGACGATTCCTCAATGATCTCCTCGCCTCGCT
CCCATATGAATTATGTCGTTCTTAAGGAAGAAGATATACGTAGACAACAAGAGAGTGATATTGCACAAGTTTCCATGATA
CTCTCCCTAAGCAAGGTCGAAGCTAGTGTTCTGCTTCTTCACTATCACTGGAATGTTGGTAAAGTTAATGATGAATGGTT
TGCGGATGAGAGGAGAGTTCGGACAAGTGCTGGCTTGGAAGGAGGATCTGTTATTGTTCCATATTCCGAAGGAGGAAAAG
TTGCTTGTGGAATATGCTTTGACTACTTCTGTCGTATAGATATTGTACCGATTATGTGTGGTCATGCTTTCTGTTCTACA
TGCTGGACAAGTTACATCAGCATAGCCATCAACGATGGCCCGGGATGTTTGATGCAAAAATGTCCTGAGCCATCTTGTCC
AGTTGCTGTTGGTCGAGACATGGTCGAGAAACTGGCTTCCTTTGAAGCCAAGGACAAGTATGATAGGTATTTTCTTAGAT
CTTATGTGGAAGAAAACAAAAAGACCAAGTGGTGTCCTGCCCCAGGATGTGAGCATGCCATTGAGTTTTCTGCCACCGGG
ACCGGAAGTAGTTACGATGTTTCATGCTTGTGTTCGCATAGCTTCTGCTGGAATTGCACCCAAGACGCTCACCGTCCTGT
GGATTGTGACAGGGTTTCGCAATGGATACGCAAGAACAGCGTTGAAGCTGAAAATACCAAGTGGATACTCGACAATTCCA
AGCCTTGTCCCAAGTGTAAGCGTCCAATTGAAAAGAACCGTGGATGCATGCACATGTCATGCACACCACCTTGCAGATAT
CAGTTTTGTTGGCTTTGCCTTGGCGCATGGTCGGAACACGGGGAAGGCACTGGCGGGCCTTATACATGCAACCGGTATTC
GAAGGCTAAGGGACAAGGACTGCATGATGAGGCTGAAATGAAGCGAGAGATGGCAAAGGACTCGCTAGAGAAATACACTC
ATTATTATGAGCGCTGGGCAGGCAATCAAACGTCGAGGCAAAAAGCTATAGGGGATCTAGAGAAGTTCCTATCAGTGGAT
GTTATGAAGCTTAGTGACAAACAATGCATACCAGAAACTGAGCTCGGGTTCATCACAGATGCGTGGCTTCAGATCATTGA
ATGCAGAAGGGTGCTGAAATGGACATATGCATACGGGTACTATCTACTTGAATCTGAACAGGAAAAGAGACAGTTTTTCG
AGTATATGCAAGGAGAGGCTGAGTCTGGTCTGGAGAGGCTCCACAAATGCGTAGAGTTGGAATCAGAGGTGTTTCAATAT
CCTGAAGACACTCCAAAACAAGACTTCAAGGGTTTTCGGACAAAACTAACTACTTTGACCAGTGTAACCAAAACCCACTT
TGAAACTCTGGTGAAAGCTCTGGAGAATGATCTTTCTGATGTTGGATTCGCAAGCGACGTAGAGGTAACTACTTTAGCTC
TTTGA

Alignment

ORF - retro_brap_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.93 %
• Parental protein coverage: 90.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESGEDDFYSGGGSD-DDYIESDGDEPDYGFVEEDVDDSLMIASHRSQINYVVLKEEDIRKLQMDDIGRV
          MESGE.D.YS.G..D..D....D.D..D.GF...D.DDS.MI.S.RS..NYVVLKEEDIR..Q..DI..V
Retrocopy MESGEEDLYSDGAGDYNDGADHDDDTDDTGFLGDDDDDSSMISSPRSHMNYVVLKEEDIRRQQESDIAQV

Parental  SMVLSISEAEASILLLHYHWSVSKVHDEWFADEEGVRKAVGILERPVVSAPH--GGELTCGICFEPFQRE
          SM.LS.S..EAS.LLLHYHW.V.KV.DEWFADE..VR...G.LE...V..P...GG...CGICF..F.R.
Retrocopy SMILSLSKVEASVLLLHYHWNVGKVNDEWFADERRVRTSAG-LEGGSVIVPYSEGGKVACGICFDYFCRI

Parental  EVVSLACGHPFCSTCWTGYISTTINDGPGCLMLKCPEPSCPAAVGQDMFEKFASKEDKEKYYKYFLRSYI
          ..V...CGH.FCSTCWT.YIS..INDGPGCLM.KCPEPSCP.AVG.DM.EK.AS.E.K.KY..YFLRSY.
Retrocopy DIVPIMCGHAFCSTCWTSYISIAINDGPGCLMQKCPEPSCPVAVGRDMVEKLASFEAKDKYDRYFLRSYV

Parental  EDNRKMKWCPAPGCENAIEFAA-GT-SNYDVSCLCSRSFCWNCTEEAHRPVDCHTVAQWIRKNSAESENM
          E.N.K.KWCPAPGCE.AIEF.A.GT.S.YDVSCLCS.SFCWNCT..AHRPVDC..V.QWIRKNS.E.EN.
Retrocopy EENKKTKWCPAPGCEHAIEFSATGTGSSYDVSCLCSHSFCWNCTQDAHRPVDCDRVSQWIRKNSVEAENT

Parental  NWILANSKPCPKCKRPIEKNHGCMHMTCTPPCKYEFCWLCLNAWTAHGERTGGFYACNRYESAKQEGLYD
          .WIL.NSKPCPKCKRPIEKN.GCMHM.CTPPC.Y.FCWLCL.AW..HGE.TGG.Y.CNRY..AK..GL.D
Retrocopy KWILDNSKPCPKCKRPIEKNRGCMHMSCTPPCRYQFCWLCLGAWSEHGEGTGGPYTCNRYSKAKGQGLHD

Parental  EAEKRREMAKNSLERYTHYYERWASNQTSRQKAVEDLQKAQLEKLEKLSDIQCTPESQLKFISEAWLQII
          EAE..REMAK.SLE.YTHYYERWA.NQTSRQKA..DL.K.......KLSD.QC.PE..L.FI..AWLQII
Retrocopy EAEMKREMAKDSLEKYTHYYERWAGNQTSRQKAIGDLEKFLSVDVMKLSDKQCIPETELGFITDAWLQII

Parental  ECRRVLKWTYAYGYYL--PDHDKKQFFEYLQGEAESGLERLHKCVEKELEVFLVAEG-PSDDFNHFRTKL
          ECRRVLKWTYAYGYYL......K.QFFEY.QGEAESGLERLHKCVE.E.EVF...E..P..DF..FRTKL
Retrocopy ECRRVLKWTYAYGYYLLESEQEKRQFFEYMQGEAESGLERLHKCVELESEVFQYPEDTPKQDFKGFRTKL

Parental  TGLTSITKTYFENLVKALENGLADV
          T.LTS.TKT.FE.LVKALEN.L.DV
Retrocopy TTLTSVTKTHFETLVKALENDLSDV

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_11 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	AT1G05890	1 retrocopy	retro_atha_22,
Brassica oleracea	Bo5g007100	1 retrocopy	retro_bole_13,
Brassica rapa	Bra015463	1 retrocopy	retro_brap_11 ,
Oryza sativa japonica	OS04G0492100	1 retrocopy	retro_osat_31,