RetrogeneDB ID: retro_bole_38

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C1:17437218..17437957(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo1g071100
• Aliases: None
• Description: None

Sequence

>retro_bole_38
ATACTTGGGCTGAAACCTTCTCGCTCTCGTGCTCCGGATGGATATGTTTGGAACCATACAAAATCTGGAGTTTATTCAGT
AAAAACCGGCTATGACCTACTTCGATCGACCAAGTTGAGTCTTTCACATAAAAGGACTGTAGAACAAAGTTTCACGAGCC
TACAGAGCCATGTGTGGGAGATAAAGGCCCCGAGTAAGATAAAACATTTTTTGTGGCAGGCTATCTCGGGTTGTGTGGCG
ACGACAGATAGGCTCATGTATAGACACCTGGGCACCGATAGAAGTTGTCCTAGATGTGCTGGTCCAGTGGAGTCGATTAA
TCATCTTCTTTTTGAATGCCCACCAGCTCTACAGGTTTGGGTTTTATCGGACTATCCGTCCATTCCGGGTTACTTCCCGA
GTACATCCATATATCAAAACATAAACTTCCTGTTTTGGAAGAGAAAAGCGGTGGCTCCTCTGAGACCACAATTCGATACC
TTCCGATGGATCTGTTGGTACATTTGGAAGGCGAGGAACGATAAACTCTTCAATGGGAAGGACGTATCTCCCATTGACAC
CCTCCAACATGTGTCTCTTGAGGCAGAATGTTAGAGGAAGGCTAACGAAAAGGAGGAAGCAAATGAGGATCATGACGATC
CCCCTACTACAGAGGTTGAGACAGTGCCCCCTTGGATACCCCGAATCCCTACTTGTCAAATTGATGCATCATGGATCCAT
ATTGGCAGTGTCAGTGGCC

Alignment

ORF - retro_bole_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.08 %
• Parental protein coverage: 87.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ILGLKVEASSMSFNFVKLSKSDSAGIVRNVESMGKNEKEEEMIQRSEKSERKGTKSHVWKIKAPSKMKHF
          ILGLK...S......V..........V..........K......R..........SHVW.IKAPSK.KHF
Retrocopy ILGLKPSRSRAPDGYVWNHTKSGVYSVKTGYDLLRSTKLSLSHKRTVEQSFTSLQSHVWEIKAPSKIKHF

Parental  LWQVISGCVATAERLTYRPMSTDMICPRCAGPVESINHLLFECPQALQVWALSDYMSLPGYFPSTSIYQN
          LWQ.ISGCVAT..RL.YR...TD..CPRCAGPVESINHLLFECP.ALQVW.LSDY.S.PGYFPSTSIYQN
Retrocopy LWQAISGCVATTDRLMYRHLGTDRSCPRCAGPVESINHLLFECPPALQVWVLSDYPSIPGYFPSTSIYQN

Parental  MNFLFWFWERKEVAPLGPQFDTFP--CWYIWKARNDKLFNGKDVSPIDTLQHASLEADCWRKANEKEEAN
          .NFL..FW.RK.VAPL.PQFDTF...CWYIWKARNDKLFNGKDVSPIDTLQH.SLEA.C.RKANEKEEAN
Retrocopy INFL--FWKRKAVAPLRPQFDTFRWICWYIWKARNDKLFNGKDVSPIDTLQHVSLEAEC*RKANEKEEAN

Parental  EDHDD-PLLQRLRQCPLGYPE-LPVKLMHHGSIMAASVA
          EDHDD.PLLQRLRQCPLGYPE.L.VKLMHHGSI.A.SVA
Retrocopy EDHDD>PLLQRLRQCPLGYPESLLVKLMHHGSILAVSVA

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_38 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 1 parental gene, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo1g071100	7 retrocopies	retro_bole_38 , retro_bole_45, retro_bole_49, retro_bole_53, retro_bole_66, retro_bole_68, retro_bole_73,