RetrogeneDB ID: retro_atri_41

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00087:2762356..2762613(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00060p00095260
• Aliases: None
• Description: None

Sequence

>retro_atri_41
ATGAGCATGGCTCGCTACCTTGTTCTGGCGTTGTTCTTGGCGTTGGCCATTTCATCATCTGTTGAGGGTCTACAAGATGC
CTTTTTCCTTCTGATTGCACGGGTTAGTGTCAGTACCGATGCTCAGCAACTTCACACAAGCAGCCATGCTTGTTCTTCCG
CAACAACTGCTGTGCTGTTTGCTTGTGCATGCCGCCGGGCACCTATCGGAACAAGCAATTCTGCGCTTGCTGGAAGATCC
AGGAAGGGCCCCCTAAA

Alignment

ORF - retro_atri_41 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.22 %
• Parental protein coverage: 97.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAMVRYLLVTLFLVLAISSSVEG-STRRLRPSECSDKCQYRCSATSHKKPCLFFCNKCCAVCLCVPPGTY
          M.M.RYL...LFL.LAISSSVEG.STR.L.PS.C...CQYRCSATSHK.PCLFF.N.CCAVCLC.PPGTY
Retrocopy MSMARYLVLALFLALAISSSVEG<STRCLFPSDCTG*CQYRCSATSHKQPCLFFRNNCCAVCLCMPPGTY

Parental  GNKQSCPCYNNWKTQEGRPK
          .NKQ.C.C...WK.QEG.PK
Retrocopy RNKQFCAC---WKIQEGPPK

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_41 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00060p00095260	1 retrocopy	retro_atri_41 ,
Medicago truncatula	MTR_8g085470	1 retrocopy	retro_mtru_30,