RetrogeneDB ID: retro_atri_46

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00136:890292..890658(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00136p00057270
• Aliases: None
• Description: None

Sequence

>retro_atri_46
GCATTGCAAAGAGGTCATCTCAGGCTGCTTCAACATGCCTTGCAAGAGTATGAGGATCAATTCTTGAGATCAGGTCTGTA
TCTTGTCCTCGAAAAGCTTGAGCTTCAAGTTTACAAGAGATTGGTAAAGGAAATATACATAATCTAAAATAAAAAGGATC
CAAATGAAGCACACCAAGTTAAATTAGAAGCCATTGTGAAAGCCTTTAGACGGCTTGAAATAGATATGGATGTCGATGAG
GTTGAGTGTATAATAGACATCCTCATCCACAAGAATCGGATGAAATGTGACTTTGCCCATAAAAGTAAGGTGGTTATACT
TAGCAAGCAGGATCATTTTCCCATGATAAATGGAAGACTAATGAAT

Alignment

ORF - retro_atri_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.51 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ALRRGDLRLLRHALQEHEDRFLRSGVYLVLEKLELQVYQRLVKKIYIIQKQKDPNKAHQVKLEVIVKAFR
          AL.RG.LRLL.HALQE.ED.FLRSG.YLVLEKLELQVY.RLVK.IYII...KDPN.AHQVKLE.IVKAFR
Retrocopy ALQRGHLRLLQHALQEYEDQFLRSGLYLVLEKLELQVYKRLVKEIYII*NKKDPNEAHQVKLEAIVKAFR

Parental  WLEIDMDVDEVECIMAILIHKNLMKGYFAHKSKVVVLSKQDPFPRLNGRPVN
          .LEIDMDVDEVECI..ILIHKN.MK..FAHKSKVV.LSKQD.FP..NGR..N
Retrocopy RLEIDMDVDEVECIIDILIHKNRMKCDFAHKSKVVILSKQDHFPMINGRLMN

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_46 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00136p00057270	2 retrocopies	retro_atri_36, retro_atri_46 ,