RetrogeneDB ID: retro_bole_15

Retrocopy location

• Organism: Brassica oleracea
• Coordinates: C8:12977490..12978750(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bo8g036800
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bo7g111550
• Aliases: None
• Description: None

Sequence

>retro_bole_15
ATGAGAATCCTCCGCAGGGATTTTGTTCGTGATGGACCAGGAAGCGCTAAACTGATGGCGGAGGACTCGGATGATCTCTG
GTTTACTTATAACTTAATTGGCCCCGGCGATAGTGTAATGGCTGTCACATCGAGAAAGGTTCTGAGAGAGAGAGGAAATT
CTAAACGTGTAGACTCTGAACGTGTTGACTCTAAACGTGAAGACTCTGACTCTGATCAACGTGTTGACTCCAAAAAACGT
GTAGGCTCTAAAAAACGTGGTGACTCTAAAAAACGTTTAGACGCTGAGCTTGACGACTCTAAACCTCTAGTGTCTGAACG
TCTGACACTGAAGCTAGAAGTACAAGTTGAGGAGGTAAACTATGACAAAGACGGTGGTGTTTTGCGCATACTTGGGACGA
ATATCCTTGAGAACGAGCACGTACCGCTTGGTGCATACCATAGTTTGGAGCTCGTGCTGAAACGACGTTTTCTATTGAGG
AAAAAAATATGGGACTCATTGGCTATTGATACACTCAACCAGGCAAAACATCGTATCTCCAGTGATGATTTAGCTGTAGT
TCTAATGCAAGAAGGACATGCACAAATCTTCCTTGTCGGAAAAAGTGTGGGTGCACCAATAGAAACATCAATTCCTAATC
GTAAGCATGCTGGTTACGAGGCTGCTTTGAAGAAATTCTTTGAGAACGTTGTGCGTGCCTTTGTGAAACACGTTGACTTC
AGTGTCGTTCGGTGTGTAGTGATCGCAAGTCCTGGCTTTACAAAGGATCAGTTTCATCGCCACTTGTTGTTGGAAGCAGA
GAGAAGACAGTTGAAACCTATTACTGAGAACAAATCACGTATACTTCTGGTGCATGCAAACTCCGGATATAGACATAGCC
TTGGAGAGGTTCTGTGTGACCCCAAAGTGATGAAGATGATCCAAGATACAAAAGCATCGAAAGAGGTGAGCGCTTTCAGG
GATTTCTTCACCATGTTCGAAAAGGATCCATATCGGGCATGCTACGGACCGAAGCATGTGGAGTTTGCTCATGAACAAAA
GGCAATCCAAACACTTCTCATTACAGATGAGCTGTTTAAAAATTCTGACGTGAAAGAAAGGAAGAAATATGTGGATTTTG
TGGAGTCGGTGAAAAAATTAGGAGGAGAGGCTTTTATATTTTCTTCGATGCATGTTTCAGGTGAACAACTGGCAATGCAT
ACTGGAATTGCAGCTCTTCTCAGGTTCCCTTTACCAGGTCTCGATGACGTTGAGATGTAA

Alignment

ORF - retro_bole_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.02 %
• Parental protein coverage: 84.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SERVRLKLEVQVEEVDYDKDAAVLRIRGKNILENDHVKIGAFHTLEIELKRPFVLRKGIWDSLALDTLKQ
          SER..LKLEVQVEEV.YDKD..VLRI.G.NILEN.HV..GA.H.LE..LKR.F.LRK.IWDSLA.DTL.Q
Retrocopy SERLTLKLEVQVEEVNYDKDGGVLRILGTNILENEHVPLGAYHSLELVLKRRFLLRKKIWDSLAIDTLNQ

Parental  ASDPAASADLAVVLMQEGLGQIFLVGRSVTSSRARIETSIP-RKHGPAIAGYESALKKFFENVLQAFAKH
          A.....S.DLAVVLMQEG..QIFLVG.SV....A.IETSIP.RKH....AGYE.ALKKFFENV..AF.KH
Retrocopy AKHRISSDDLAVVLMQEGHAQIFLVGKSVG---APIETSIPNRKH----AGYEAALKKFFENVVRAFVKH

Parental  VDFSVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTNSGYRHSLGEVLNAPNVMNMI
          VDFSVVRC.VIASPGFTKDQFHRHLLLEAERRQL.PI.ENKSRI.LVH.NSGYRHSLGEVL..P.VM.MI
Retrocopy VDFSVVRCVVIASPGFTKDQFHRHLLLEAERRQLKPITENKSRILLVHANSGYRHSLGEVLCDPKVMKMI

Parental  KDTKAAKEVKALNDFFTMLSNDPARACYGPKHVEVAHERMAVQTLLITDELFRNSDVKTRKKYVDLVESV
          .DTKA.KEV.A..DFFTM...DP.RACYGPKHVE.AHE..A.QTLLITDELF.NSDVK.RKKYVD.VESV
Retrocopy QDTKASKEVSAFRDFFTMFEKDPYRACYGPKHVEFAHEQKAIQTLLITDELFKNSDVKERKKYVDFVESV

Parental  KDSGGEAFIFSSMHVSGEQLAQLTGIAALLRFPLPDLEDIEM
          K..GGEAFIFSSMHVSGEQLA..TGIAALLRFPLP.L.D.EM
Retrocopy KKLGGEAFIFSSMHVSGEQLAMHTGIAALLRFPLPGLDDVEM

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_15 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT4G27650	1 retrocopy	retro_atha_7,
Brassica oleracea	Bo7g111550	1 retrocopy	retro_bole_15 ,
Brassica rapa	Bra019037	1 retrocopy	retro_brap_29,
Aegilops tauschii	F775_08238	1 retrocopy	retro_atau_9,
Hordeum vulgare	MLOC_5075	1 retrocopy	retro_hvul_86,
Hordeum vulgare	MLOC_54416	1 retrocopy	retro_hvul_87,
Theobroma cacao	TCM_025327	1 retrocopy	retro_tcac_21,
Vitis vinifera	VIT_04s0023g00140	1 retrocopy	retro_vvin_2,