RetrogeneDB ID: retro_atri_27

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00032:5193968..5194298(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00088p00117460
• Aliases: None
• Description: None

Sequence

>retro_atri_27
CTTATCAGCAAAGCTAGCTACTAAAATGTTGCAAAGAAGTGGATTCCTGAACTTAAGCATTATGCTCTTGATGTTCCGAT
AATTCTGGTTGGGACAAAGCTTGATCTTCGAGATGACAAGCAGTTCTTTATAGATCACCCAAGTACAGTGCCCAAAGAGT
GGTGTTCCAAGACGCAACATAATATGATTGGAGCTCCTGCACACATAGAGTGCAGTTCCAAGACGCAACATAATGTGAAG
GTAGTTTTCGATGCATCCATCAAGGTGGTTCTCCAGCCGCCAAAGCAGAAGAAGAAAAAGAAGAGCAAGGCACAAAAGGG
TTGTTCCATC

Alignment

ORF - retro_atri_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.16 %
• Parental protein coverage: 54.73 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVSRASYENVMKKWIPELQHYAPGVPVVLVGTKLDLREDKYYLSDHPGMVPVTTAQGEELRKQIGVAYYI
          L.S.ASY.NV.KKWIPEL.HYA..VP..LVGTKLDLR.DK....DHP..VP............IG....I
Retrocopy LISKASY*NVAKKWIPELKHYALDVPIILVGTKLDLRDDKQFFIDHPSTVPKEWCSKTQ-HNMIGAPAHI

Parental  ECSSKTQQNVKSVFDAAIKVVIQPPKQKEKKK-KPRRGCSL
          ECSSKTQ.NVK.VFDA.IKVV.QPPKQK.KKK.K...GCS.
Retrocopy ECSSKTQHNVKVVFDASIKVVLQPPKQKKKKKSKAQKGCSI

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_27 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00088p00117460	1 retrocopy	retro_atri_27 ,
Amborella trichopoda	AMTR_s00152p00020750	2 retrocopies	retro_atri_21, retro_atri_52,