RetrogeneDB ID: retro_atri_24

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00022:6246196..6246627(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00069p00126080
• Aliases: None
• Description: None

Sequence

>retro_atri_24
ATGATGATAATCAAGGCAATGACCCCAGGACCTATGACGATGAATGGGAGCTTGAATGGCGATGGCTCTGAAATAGTGGA
TTGGGAGCTCAAGCTAGGATGAATGCTTGTTCAAAAGAGGAGCCTATATTATGATCGGACTTCTTCTACTCCAGCTCCCA
CCCTTAGGATTCGAGTAAAATATGGAGCTTCGATGCATGAGATCCACATCAATTCTCAAGCCACGTTTGGAGAGTTGAAG
AAATTTCTTGTATCCCAGACAAGACTTCACACTCAGGACCAAAAGCTTATCTTTAAAGACAATAAGAGGATTCTAATGCT
TATTTGAACGTGGCAGCAGTGAAGGACAAGTCAAAGATTGTGTTGATCGAATATCCCACTAATCAGAAGAGAAGGTATAT
TGAGATGAGGAAAAATGCAAAGGTGGAGAGA

Alignment

ORF - retro_atri_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.24 %
• Parental protein coverage: 52.94 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MMRIRAKNPGPMTMNGSSNGGGSEIVDWELRPGGMLVQKRSLGIDQASSAPAPTIRVRVKYGALMHEIHI
          MM.I.A..PGPMTMNGS.NG.GSEIVDWEL..G.MLVQKRSL..D..SS.PAPT.R.RVKYGA.MHEIHI
Retrocopy MMIIKAMTPGPMTMNGSLNGDGSEIVDWELKLG*MLVQKRSLYYDRTSSTPAPTLRIRVKYGASMHEIHI

Parental  SSQATFGELKKLLASETGLHTQDQKLLFKDKER-DSNAYLDMAGVKDKSKIVLIEDPTSQERRYIEMRKN
          .SQATFGELKK.L.S.T.LHTQDQKL.FKD..R.DSNAYL..A.VKDKSKIVLIE.PT.Q.RRYIEMRKN
Retrocopy NSQATFGELKKFLVSQTRLHTQDQKLIFKDNKR<DSNAYLNVAAVKDKSKIVLIEYPTNQKRRYIEMRKN

Parental  AKMER
          AK.ER
Retrocopy AKVER

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Amborella trichopoda was not studied using RNA-Seq expression data.

ChIP-Seq

Amborella trichopoda was not studied using ChIP-Seq data.

EST

Amborella trichopoda was not studied using EST data.

TSS

Amborella trichopoda was not studied using FANTOM5 data.

Lab

retro_atri_24 was not experimentally validated.

Homology

Retrocopy orthology:

Amborella trichopoda 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00069p00126080	3 retrocopies	retro_atri_24 , retro_atri_26, retro_atri_3,