RetrogeneDB ID: retro_atri_45

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00133:130326..130716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00012p00219470
• Aliases: None
• Description: None

Sequence

>retro_atri_45
AAAAAGTTATTTGTTGGTAGCAATTGGAAGTATAATGGGACAAAAGAGAGTATCAGTAAGCTTGTTTCCGATATAAACAA
TGCCAAACTTGAGAAAGATGTTGATGTTGTTGTTTCACCTCCTTATGTATATATCCATTAGGTAAAAAGCTCATTGACTG
ATCGCATTGAGATATATGCTCAGAACTCTTGGGTTGGTCAGGGTGGAGCTTTCACGAGTGAACTTTTTGTGGAGCAACTA
AAAGATATTGGTTGCAAGTGGGTTATTTTTGGCCATTCTGAATGGAGACATGCTATTGGTGAAGATGACCAGTTTATTGG
GAAGAAAGGTGCTTATGCCTTAAGCGAGAACTTGAAGGTAATCGCATGCATCAGAGAGAAACTCGAAAAA

Alignment

ORF - retro_atri_45 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.52 %
• Parental protein coverage: 51.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RKFFVGGNWKCNGTVEEVKKIVSMLNEAEVPSEDIVEVVVSPPFVFLPLVKSLLRPDFLVAAQNCWVRKG
          .K.FVG.NWK.NGT.E...K.VS..N.A.......V.VVVSPP.V....VKS.L.......AQN.WV..G
Retrocopy KKLFVGSNWKYNGTKESISKLVSDINNAKLEKD--VDVVVSPPYVYIH*VKSSLTDRIEIYAQNSWVGQG

Parental  GAFTGEISAEMLVNLGIPWVIIGHSERRSLLNETNEFVGDKVAYALSRGLKVIACVGETLEQ
          GAFT.E...E.L...G..WVI.GHSE.R....E...F.G.K.AYALS..LKVIAC..E.LE.
Retrocopy GAFTSELFVEQLKDIGCKWVIFGHSEWRHAIGEDDQFIGKKGAYALSENLKVIACIREKLEK

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_45 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00012p00219470	1 retrocopy	retro_atri_45 ,