RetrogeneDB ID: retro_brap_47

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:10860256..10860693(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra019508
• Aliases: None
• Description: None

Sequence

>retro_brap_47
ATCGGACACAGTAGAGGAGGTAACGTGGTGCTCCTCTACGCCTCCAAGTATTGCAATGATGGTAACGTCCGCAATGTAGT
CAATATATCTGGACGTTATGATCTGAAGAAAGGAATACGTCTTGGTGATGGTTATCTCGAGAGAATCAAGGAACAAGGTT
TCATCGATGCTAAAGAAGGCAAATCTGAGTTCTCGTTACTGAAGAGAGTTTAATGGAGAGGTTAGAGACGGATATGCATG
AAGCTTGTCTCAAGATTGACAAACAAGTCAGAGTCTTGACGGTTCATGGTTCGGGTGATAAGGTGGTACCAGTTCCAGAT
GCCGATGAGTTTGCAAAGATCATACCCAACCACAAGCTCGAGATTGTGAAAAAAGCTGATCATGGTTATACCAAGCATCA
AACTCAACTGGTTTCAACTGTTTTGGAGTTCATAAAG

Alignment

ORF - retro_brap_47 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.15 %
• Parental protein coverage: 55.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGHSKGGDVVLLYASKY---HDIRNVINLSGRYDLKKGITERLGEDFLETIKQQGFIDVKDGKSGYR-VT
          .GHS.GG.VVLLYASKY......RNV.N.SGRYDLKKGI..RLG...LE.IK.QGFID.K.GKS....VT
Retrocopy IGHSRGGNVVLLYASKYCNDGNVRNVVNISGRYDLKKGI--RLGDGYLERIKEQGFIDAKEGKSEFS<VT

Parental  EESLMERLSTDMHEACLKIDKECRGLTVHGSDDEVTPVEDAKEFAKIIPNHKLTIVEGADHCYTKHQTQL
          EESLMERL.TDMHEACLKIDK..R.LTVHGS.D.V.PV.DA.EFAKIIPNHKL.IV..ADH.YTKHQTQL
Retrocopy EESLMERLETDMHEACLKIDKQVRVLTVHGSGDKVVPVPDADEFAKIIPNHKLEIVKKADHGYTKHQTQL

Parental  VATITEFIK
          V.T..EFIK
Retrocopy VSTVLEFIK

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_47 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G47590	1 retrocopy	retro_atha_5,
Oryza sativa indica	BGIOSGA001352	1 retrocopy	retro_oind_81,
Brassica rapa	Bra019508	1 retrocopy	retro_brap_47 ,
Hordeum vulgare	MLOC_20645	1 retrocopy	retro_hvul_20,
Oryza sativa japonica	OS01G0579900	1 retrocopy	retro_osat_70,
Populus trichocarpa	POPTR_0018s06860	1 retrocopy	retro_ptri_17,