RetrogeneDB ID: retro_brap_24

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:7770601..7772065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra025765
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra013613
• Aliases: None
• Description: None

Sequence

>retro_brap_24
ATGAAGAGTGAGAGAGAAGTTAAGAACGGTGGTGTTGAGGAAGAGAGAGCGGTGAAGCGGAAGAGGGTAATAGAGCTATC
TAATGATCACGAGCAGAAGAAGGATATCGGAGTTGCGAGAGTGGAGAAGAAGACGGAGCTCGACGATGATGGTGATGATG
TCTCCAGGAAACATTCACGCCATGTTGAAGTTCGTGGTGATTGCCCTTATCTTGATACTGTTAATCGTCAGGTCTTGGAT
TTTGATTTCGAGAGGTTTTGCTCAGTCTCCTTGTCGAATTTGAATGTGTATGCATGTCTCGTATGCGGGGAGTACTTCCA
AGGAAGAAGCCACAAGTCTCGTGCTTATACACATAGCTTGGAAGCAGGTCACCACGTTTATATCAATCTTCTCACGGAGA
AGGTTTATTGTCTTCCTGATAGTTACGAGATCAATGACCCTTCTTTGGATGACATTCGACGTGTTTTAAACCCAAGGTTC
AGTAGGGCACAAGTAGAAGAGCTTGATAGGAATAAGCAGTGGTCTAGGGCTCTTGATGGCTCTGACTATCTTCCCGGGAT
GGTGGGATTGAACATCATACAAAACACAGAGTTTGTGAACGTTACAATCCAGTCGTTGATGAGAGTTACTCCTCTAAGGA
ACTTTTTCCTTATTCCCGAGAACTATCAGCATTGCAAGTCTCCTCTTGTTCACCGCTTTGGGGAACTCACTCGAAAGATT
TGGCATGCTCGAAACTTCAAAGGACAGGTGAGTCCACATGAGTTCTTGCAGGCTGTCATGAAGCGATTTAAGATAGGCCA
GCAATCAGATCCAGTAGAGTTTATGTCGTGGCTCCTTAACACTTTGCACATGGATCTTCGCACTTCAAAGGACGCCAGCA
GTATCATCCACCAGTGCTTCCAGGGTGAGTTAGAAGTTGTGAGAGAGTATCAAGGCAATGAAAACAAACAAATCTCCAGG
ATGCCTTTTCTGATGCGGGGGCTAGATTTGCCACCGCCTCCTCTTTTCAAAGATGTCATGGAGAAGAACATTATTCCGCA
GGTTGCTCTCCTCCATCTGTTGAAGAAGTTTGATGGAGAAACTGTGACAGCCAGAATGAGATATCGAGTCACCAAATCTC
CTCCTTACTTGATGTTCCATATGGTTCGGTTCAAGAAGAACAACTTCTTCAAGGAGAAGAACCCTACCTTGGTTAACTTC
CCCGTGAAGGACATGGAGCTGAGGGATTACATACCATCATTGCCTACTGCCGCAGAAGGGGAGAAGACGTGTACAAGGTA
TAACTTAATCGCCAACATTGTACATGATGGTAAAGCAGAGGATGGGTGTTTCAGAGTGTTTGTGCAGCGGAAGTCGCAAG
AACTATGGTACGAGATGCAGGATCTGCATGTTGCAGAGACGCTTCCGCAGATGGTACAACTATCAGAAGCATACATGCAG
ATATATGAGCTGCAGGAGGAATAG

Alignment

ORF - retro_brap_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.36 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ENEQKKDNGVAELDDNEDDDADASK-GGKRSRRVEVRRDCPYLDTVNRQVLDFDFERFCSVSLSNLNVYA
          ..EQKKD.GVA........D.D......K.SR.VEVR.DCPYLDTVNRQVLDFDFERFCSVSLSNLNVYA
Retrocopy DHEQKKDIGVARVEKKTELDDDGDDVSRKHSRHVEVRGDCPYLDTVNRQVLDFDFERFCSVSLSNLNVYA

Parental  CLVCGKYFQGRSQKSHAYTHSLEAGHHVYINLLTEKVYCLPDSYEINDPSLDDIRHVLNPRFSRAQVEEL
          CLVCG.YFQGRS.KS.AYTHSLEAGHHVYINLLTEKVYCLPDSYEINDPSLDDIR.VLNPRFSRAQVEEL
Retrocopy CLVCGEYFQGRSHKSRAYTHSLEAGHHVYINLLTEKVYCLPDSYEINDPSLDDIRRVLNPRFSRAQVEEL

Parental  DRNKQWSRALDGSDYLPGMVGLNNIQKTEFVNVTIQSLMRVTPLRNFFLIPENYQHCKSTLVHRFGELTR
          DRNKQWSRALDGSDYLPGMVGLN.IQ.TEFVNVTIQSLMRVTPLRNFFLIPENYQHCKS.LVHRFGELTR
Retrocopy DRNKQWSRALDGSDYLPGMVGLNIIQNTEFVNVTIQSLMRVTPLRNFFLIPENYQHCKSPLVHRFGELTR

Parental  KIWHARNFKGQVSPHEFLQAVMKASKKRFRIGQQSDPVEFMSWLLNTLHMDLRTSKDASSIIHQCFQGEL
          KIWHARNFKGQVSPHEFLQAVMK....RF.IGQQSDPVEFMSWLLNTLHMDLRTSKDASSIIHQCFQGEL
Retrocopy KIWHARNFKGQVSPHEFLQAVMK----RFKIGQQSDPVEFMSWLLNTLHMDLRTSKDASSIIHQCFQGEL

Parental  EVVREYQGNENKEISRMPFLMLGLDLPPPPLFKDVMEKNIIPQVALFDLLKKFDGETVTEVVRPRLAR
          EVVREYQGNENK.ISRMPFLM.GLDLPPPPLFKDVMEKNIIPQVAL..LLKKFDGETVT...R.R...
Retrocopy EVVREYQGNENKQISRMPFLMRGLDLPPPPLFKDVMEKNIIPQVALLHLLKKFDGETVTARMRYRVTK

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_24 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra013613	1 retrocopy	retro_brap_24 ,