RetrogeneDB ID: retro_bole_10

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C8:19049531..19050887(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo8g058840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo8g083640
• Aliases: None
• Description: None

Sequence

>retro_bole_10
ATGGCCTCCTCGACCCTCCATTTCTTCTTCGTGGCCCTTCTCTTGCCGTTCACGCTAACCACCGCTACACGTGACACATG
TGCGACCGCCGCTCCCGATGGTTCCGACGATCTCTCAATCATCCCCGTTAACGCCAGATGCTCACCTTTCGCAGCAAATC
CTACCTCCACCTCCGTCATGGACACCGTCCTCCACATGGCCTCCGCAGACTCTCACCGCCTCATCTACCTCTCGAGCCTC
GTCGCCGACAAACCCAACCGAACCTCCGTCCCTATAGCCTCCGCTAACCAGCTCCTCCACACCGGCAACTACGTCGTCCG
ATCCAGGCTCGGCACTCCTCCTCAGCTCATGTTCATGGTCCTAGACACCAGCAACGACGCCGTTTGGCTCCCTTGCTCCG
GCTGCTCGGGCTGTTCCACCGCCGCAACCGCCGCTTGCTTCAATCCCAACTCCTCCTCCACATACTCCACCGTCTCTTGC
TCCGCCGCAGAATGCACGCAAGCACGTGGCCTCACGTGCCCATCCTCCTCGCCGTCACCACCGTCCACCTGCTCCTTCAA
CCAATCATACGGCGGAGGTTCGTCATTCTCCGCCTCGCTCGTCCAAGACACGCTGACGTTAGCCTCTGACGTCATCTCAA
ACTTCTCATTCGGATGCATCAACTCTGCTTCCGGGAACTCTCTACCACCGCAAGGACTAATGGGCCTGGGACGTGGGCCC
ACGTCGTTAATCTCCCAAACGACGTCGCTTTACTCAGGCGTGTTCTCGTACTGCCTCCCTAGCTTCAGGTCGTTCTACTT
CTCCGGGTCGTTGAAACTGGGCCCGATGGGCCAACCGAGATCCATCAGATACACTCCTCTCCTCCGCAGCGCTCACCGTC
CTTCACTTTACTACGTCAATCTCACCGGAGTGAGTGTGGGACCCACACAGGTCCCCGTTGACCCTACGTACTTGACGTTT
GACTCAAATTCAGGCGCCGGTACGATAATCGATTCCGGTACTGTGATCACCCGGTTTGTCCAACCGGTTTACGAGGCAAT
CAGAGACGAGTTTAGGAGCCAGGTGAAAGGCCCGTTCTCGACGCTGGGAGCGTTCGACACGTGTTTCGCGGCGGATAGCG
ATAGCTTGGCGCCAAAGGTAACGCTGCACATGACGTCACTCGATTTGAAGCTGCCGGTGGAGAACACGCTTATACACAGC
AGCGCGGGAACGCTGGCGTGTCTGTCGATGGCGGGGATACCGCTGAACGCGAACGCTGTTCTGAACGTGATCGCGAATCT
CCAGCAGCAGAATCTGAGGATCTTGTTTGATGTTCCTAATTCTCGCCTAGGTATTGCTACTGAGGCATGCAACTAA

Alignment

ORF - retro_bole_10 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.92 %
• Parental protein coverage: 71.63 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SACVGCASSVLFDPSKSSSSRTVQCEASQC-KQAPNPTCTVSKSCGFNMTYGG-STITASLTQDTLTLAN
          .AC....SS........S.....Q.....C....P.P..T....C.FN..YGG.S...ASL.QDTLTLA.
Retrocopy AACFNPNSSSTYSTVSCSAAECTQARGLTCPSSSPSPPST----CSFNQSYGGGSSFSASLVQDTLTLAS

Parental  DAIPGYTFGCINKATGTSLPAQGLMGLGRGPLSLISQTQNLYKSTFSYCLPNSKSSSFSGTLRLGPKFQP
          D.I....FGCIN.A.G.SLP.QGLMGLGRGP.SLISQT..LY...FSYCLP...S..FSG.L.LGP..QP
Retrocopy DVISNFSFGCINSASGNSLPPQGLMGLGRGPTSLISQTTSLYSGVFSYCLPSFRSFYFSGSLKLGPMGQP

Parental  VRIKTTPLLKNPRRSSLYYVNMVGIRVGNKIVDIPPSALAFNPATGAGTIFDSGTVYTRLVEPAYVAVRN
          ..I..TPLL....R.SLYYVN..G..VG...V...P..L.F....GAGTI.DSGTV.TR.V.P.Y.A.R.
Retrocopy RSIRYTPLLRSAHRPSLYYVNLTGVSVGPTQVPVDPTYLTFDSNSGAGTIIDSGTVITRFVQPVYEAIRD

Parental  EFRRRVKNANATSLGGFDTCYS--GSVVFPSVTFMFAGMNVTLPPDNLLIHSSSGSTSCLAMAAAPNNVN
          EFR..VK....T.LG.FDTC.........P.VT.........LP..N.LIHSS.G...CL.MA..P.N.N
Retrocopy EFRSQVKGPFST-LGAFDTCFAADSDSLAPKVTLHMTSLDLKLPVENTLIHSSAGTLACLSMAGIPLNAN

Parental  SVLNVIASMQQQNHRVLIDLPNSRLGISRETC
          .VLNVIA..QQQN.R.L.D.PNSRLGI..E.C
Retrocopy AVLNVIANLQQQNLRILFDVPNSRLGIATEAC

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Brassica oleracea was not studied using RNA-Seq expression data.

ChIP-Seq

Brassica oleracea was not studied using ChIP-Seq data.

EST

Brassica oleracea was not studied using EST data.

TSS

Brassica oleracea was not studied using FANTOM5 data.

Lab

retro_bole_10 was not experimentally validated.

Homology

Retrocopy orthology:

Brassica oleracea 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10 ,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,