RetrogeneDB ID: retro_atri_3

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00174:554426..554912(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00174p00056430
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_atri_3
ATGATGAGAATCAGGGCAAAGACCCCTGGACCCATGACCATGAATGAGAGCTCGACTGGCAATGGCTCTGAAAAAATGGA
TTGGGAGCTTAGACCAGAAGGAATGCTTGTTCAGAAGAGGTGCCTAGGTTCTAATCAGGTTTCTTCTGCTCCAACTCCCA
CCATTAGGGTTAGAGCAAAATATGGAGCTTTGATACATGAGATCCACATTAGTTCTCAAGCCGCGTTTGGGGAGTTGAAG
AAATTTCTTGCACTCGAGACAAAACTCCACACTCAAGACCAAAAGCTTCTCTTTAAAGACAAGGAGAGGGATTCTAATGC
TTATTTGGACATGGCCGGAGTGAAGGGCAAGTCAAATATTGTGTTGATCAAAGATCCCACAAGTCAAGAGAGAAGGTATA
TAGAGATGAGGAAGAATGAAAAGATGGAGAGAGCTTCAAAATCCATTGCAAAGATCAATTTAGAGGTGGACAAGCTTGCG
GCCTAG

Alignment

ORF - retro_atri_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.09 %
• Parental protein coverage: 59.19 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MMRIRAKNPGPMTMNGSSNGGGSEIVDWELRPGGMLVQKRSLGIDQASSAPAPTIRVRVKYGALMHEIHI
          MMRIRAK.PGPMTMN.SS.G.GSE..DWELRP.GMLVQKR.LG..Q.SSAP.PTIRVR.KYGAL.HEIHI
Retrocopy MMRIRAKTPGPMTMNESSTGNGSEKMDWELRPEGMLVQKRCLGSNQVSSAPTPTIRVRAKYGALIHEIHI

Parental  SSQATFGELKKLLASETGLHTQDQKLLFKDKERDSNAYLDMAGVKDKSKIVLIEDPTSQERRYIEMRKNA
          SSQA.FGELKK.LA.ET.LHTQDQKLLFKDKERDSNAYLDMAGVK.KS.IVLI.DPTSQERRYIEMRKN.
Retrocopy SSQAAFGELKKFLALETKLHTQDQKLLFKDKERDSNAYLDMAGVKGKSNIVLIKDPTSQERRYIEMRKNE

Parental  KMERASKSIAEISLEVDKLAA
          KMERASKSIA.I.LEVDKLAA
Retrocopy KMERASKSIAKINLEVDKLAA

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_3 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 ,