RetrogeneDB ID: retro_brap_14

Retrocopy location

• Organism: Chinese cabbage (Brassica rapa)
• Coordinates: A06:19535168..19536032(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: Bra010119
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: Bra029247
• Aliases: None
• Description: None

Sequence

>retro_brap_14
ATGGGGAATTTATTTTGCTGTGTACAAGTGGACCAATCAACGGTGGCGATAAAAGAAACGTTTGGGAAGTTCGAAGAGGT
TCTTGAGCCTGGTTGCCATTTTCTCCCTTGGTGTCTTGGTCAGCAAGTCGCTGGTTACCTCTCTCTCAGGCTTCAGCAGT
TGGATGTTCGCTGCGAGACCAAGACTAAGGACAATGTGTTTGTTAACGTTGTTGCATCGATTCAATACCGTGCATTGGCT
AATAATGCTAACGATGCCTTCTACAAGCTCAGTAACACAAGGAGCCAGATCCAAGCTTACGTCTTTGATGTTATCAGAGC
AAGTGTCCCCAAGCTGATTCTGGATGATGTCTTTGAGCAGAAGAATGAAATTGCCAAAGCTGTTGAAGAGGAGCTCGAGA
AGGCAATGTCTGCTTACGGTTTTGAGATTGTCCAAACTCTCATTGTTGACATCGAGCCTGACGAACATGTCAAACGAGCC
ATGAACGAAATCAACGCTGCTGCAAGGATGAGGTTGGCTGCAAACGAAAAGGCTGAGGCTGAGAAAATCCTGCAGATCAA
GCGCGCTGAAGGTGAAGCCGAGGCCAAGTACCTTTCTGGTCTTGGTATCGCTCGTCAGAGGCAAGCCATCGTTGACGGGC
TACGCGACAGTGTCTTGGGCTTCTCTGTGAATGTTCCCGGGACAACTGCTAAAGATGTCATGGACATGGTGCTCGTTACG
CAGTACTTTGACACCATGAAGGAGATTGGTGCTAGTTCCAAATCCTCTGCTGTGTTCATTCCCCACGGACCAGGAGCGGT
TCGTGATGTGGCTACTCAGATCAGAGATGGCCTCCTTCAAGGCTCGTTCGCAGACCAGTCTTGA

Alignment

ORF - retro_brap_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.9 %
• Parental protein coverage: 99.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNLFCCIQVDQSTVAIKETFGKFEDVLEPGCHFLPWCLGQQVAGHLSLRLQQLDVRCETKTKDNVFVNV
          MGNLFCC.QVDQSTVAIKETFGKFE.VLEPGCHFLPWCLGQQVAG.LSLRLQQLDVRCETKTKDNVFVNV
Retrocopy MGNLFCCVQVDQSTVAIKETFGKFEEVLEPGCHFLPWCLGQQVAGYLSLRLQQLDVRCETKTKDNVFVNV

Parental  VASIQYRALANKANDAFYKLSNTRSQIQAYVFDVIRASVPKLLLDDVFEQKNEIAKAVEEELEKAMSAYG
          VASIQYRALAN.ANDAFYKLSNTRSQIQAYVFDVIRASVPKL.LDDVFEQKNEIAKAVEEELEKAMSAYG
Retrocopy VASIQYRALANNANDAFYKLSNTRSQIQAYVFDVIRASVPKLILDDVFEQKNEIAKAVEEELEKAMSAYG

Parental  FEIVQTLIVDIEPDEHVKRAMNEINAAARMRLAANEKAEAEKILQIKRAEGEAEAKYLSGLGIARQRQAI
          FEIVQTLIVDIEPDEHVKRAMNEINAAARMRLAANEKAEAEKILQIKRAEGEAEAKYLSGLGIARQRQAI
Retrocopy FEIVQTLIVDIEPDEHVKRAMNEINAAARMRLAANEKAEAEKILQIKRAEGEAEAKYLSGLGIARQRQAI

Parental  VDGLRDSVLGFSVNVPGTTAKDVMDMVLVTQYFDTMKEIGASSKSSAVFIPHGPGAVRDVATQIRDGLLQ
          VDGLRDSVLGFSVNVPGTTAKDVMDMVLVTQYFDTMKEIGASSKSSAVFIPHGPGAVRDVATQIRDGLLQ
Retrocopy VDGLRDSVLGFSVNVPGTTAKDVMDMVLVTQYFDTMKEIGASSKSSAVFIPHGPGAVRDVATQIRDGLLQ

Parental  GSFAEQ
          GSFA.Q
Retrocopy GSFADQ

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_14 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Brassica rapa	Bra029247	1 retrocopy	retro_brap_14 ,