RetrogeneDB ID: retro_brap_29

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A08:8680234..8681494(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra038970
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra019037
• Aliases: None
• Description: None

Sequence

>retro_brap_29
ATGAGAATCCTCCGCAGGGATTTTGTTCGTGATGGACCAGGAAGCGCTAAACTGATGGCAGAGGACTCGGATGATCTCTG
GTTTACTTATAACTTGATTGCCCCCGGCGATAGTGTAATGGCTGTCACATCGAGAAAGGTTCTGAGAGAGAGAGGAAATT
CTAAACGTGTAGACTCTGAACGTGTTGACTCTAAACGTGAAGACTCTGACTCTGATCAACGTGTTGACTCCAAAAAACCT
GTAGGCTCTAAAAAACGTGGTGACTCTAAAAATCGTTTAGACGCTGAGCTTGACGACTCTAAACCTCTAGTGTCTGAACG
TCTGACACTGAAGCTAGAAGTACAAGTTGAGGAGGTAAACTATGACAAAGACGGTGGTGTTTTGCGCATACTTGGGACGA
ATATCCTTGAGAACGAGCACGTACCGCTTGGTGCATACCATAGTTTGGAGCTCGTGCTGAAACGACGTTTCCTATTGAGG
AAAAAAATATGGGACTCAATGGCTATTGATACACTCAACCAGGCAAAACATCATAATTCCAGTTCTGATTTAGCTGTAGT
TCTAATGCAAGAAGGACATGCACAAATCTTCCTTGTCGGCAAAAGTGTGGGTGCACCAATAGAAACATCAATTCCTAATC
GTAAGCATGCTGGTTACGAGGCTGCGTTGAAGAAATTCTTTGAGAACGTTGTGCGTGCCTTTGTGAAACACGTTGACTTC
AATGTCGTTCGGTGTGTAGTGATCGCAAGTCCTGGCTTTACAAAGGATCAGTTTCATCGCCACTTGTTGTTGGAAGCAGA
GAGAAGACAGTTGAAACCTATTACTGAGAACAAATCACGTATACTTCTGGTGCATGCAAACTCCGGATATAGGCATAGCC
TTGGAGAGGTTCTGAGTGACCCCAAAGTGATGAAGATGATCCAAGATACAAAAGCATCGAAAGAGGTGAACGCTCTCAGG
GATTTCTTCACCATGTTCGAAAAGGATCCATATCGGGCATGCTACGGACCGAAGCAAGTGGAGTTTGCTCATGAACAAAA
GGCAATCCAAACACTTCTCATTACAGATGAGCTGTTCAAAAATTCTGACGTGAAAGAAAGGAAGAAGTATGTGGATTTTG
TGGAGTCGGTGAAAAAATTAGGAGGAGAGGCTTTTATATTTTCTTCGATGCATGTTTCAGGTGAACAACTGGAAATGCAT
ACTGGAATTGCAGCTCTTCTCAGGTTCCCTTTACCAGGTCTCGATGACGTTGAGATGTAA

Alignment

ORF - retro_brap_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.4 %
• 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.IWDS.A.DTL.Q
Retrocopy SERLTLKLEVQVEEVNYDKDGGVLRILGTNILENEHVPLGAYHSLELVLKRRFLLRKKIWDSMAIDTLNQ

Parental  ASDPAASADLAVVLMQEGLGQIFLVGRSVTSSRARIETSIP-RKHGPAIAGYESALKKFFENVLQAFVKH
          A.....S.DLAVVLMQEG..QIFLVG.SV....A.IETSIP.RKH....AGYE.ALKKFFENV..AFVKH
Retrocopy AKHHNSSSDLAVVLMQEGHAQIFLVGKSVG---APIETSIPNRKH----AGYEAALKKFFENVVRAFVKH

Parental  VDFSVVRCAVIASPGFTKDQFHRHLLLEAERRQLRPIIENKSRIILVHTNSGYRHSLGEVLNAPNVMNMI
          VDF.VVRC.VIASPGFTKDQFHRHLLLEAERRQL.PI.ENKSRI.LVH.NSGYRHSLGEVL..P.VM.MI
Retrocopy VDFNVVRCVVIASPGFTKDQFHRHLLLEAERRQLKPITENKSRILLVHANSGYRHSLGEVLSDPKVMKMI

Parental  KDTKAAKEVKALNDFFTMLSNDPARACYGPKHVEVAHERMAVQTLLITDELFRNSDVKTRKKYVDLVESV
          .DTKA.KEV.AL.DFFTM...DP.RACYGPK.VE.AHE..A.QTLLITDELF.NSDVK.RKKYVD.VESV
Retrocopy QDTKASKEVNALRDFFTMFEKDPYRACYGPKQVEFAHEQKAIQTLLITDELFKNSDVKERKKYVDFVESV

Parental  KDSGGEAFIFSSMHVSGEQLAQLTGIAALLRFPLPDLEDIEM
          K..GGEAFIFSSMHVSGEQL...TGIAALLRFPLP.L.D.EM
Retrocopy KKLGGEAFIFSSMHVSGEQLEMHTGIAALLRFPLPGLDDVEM

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_29 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 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,