RetrogeneDB ID: retro_atri_12

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00157:473106..473466(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00157p00050570
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00012p00262190
• Aliases: None
• Description: None

Sequence

>retro_atri_12
ATGGGATTCATTTCATTTGCAGGAAGAGTTTCCTTCTCTTCGAGTTTTACACTTGCTGCTTGGCAAAGGTTCCATGAATT
CGGTGATGATGGTGGACCTGCTGTAAAGCTATTGGAACCCAAATATGCGCTCTTAAAAAATTATGTCGCATCTTCCCTTG
GGTTTCAAGTGCCAGAAATTGAGATTAAGCATTTAATTGCAGCAAAACTTGCTTTGAAGGGAATTGTTGATTGCTCTATT
GAATGTGCGTACCCAGAGTTGCCGCAATGGGAGGAGGAACAGAAAGTGTGGTGCAGAAGACTCCAAAGAGTCATTCGCTC
TCTTGCAACTAAATCCCCCAAATCTCAACACAAGTATTAG

Alignment

ORF - retro_atri_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84. %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGFISFAGRVLFSSIFILAAWQRFNEFADDGGPAVKLLEPKYSLVKNHVTSSLGFQVPEIEIKHLVAAEI
          MGFISFAGRV.FSS.F.LAAWQRF.EF.DDGGPAVKLLEPKY.L.KN.V.SSLGFQVPEIEIKHL.AA..
Retrocopy MGFISFAGRVSFSSSFTLAAWQRFHEFGDDGGPAVKLLEPKYALLKNYVASSLGFQVPEIEIKHLIAAKL

Parental  ALKGI
          ALKGI
Retrocopy ALKGI

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_12 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00012p00262190	6 retrocopies	retro_atri_10, retro_atri_12 , retro_atri_23, retro_atri_31, retro_atri_35, retro_atri_49,