RetrogeneDB ID: retro_atri_49

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00167:584362..584634(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

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

Sequence

>retro_atri_49
AGAATTTTGTTCTTTTCTAGTTTTATACTCCTGCTTGGCAAAGATTGAATGAATTCGGTGATAATGGTGGACCTTCCGTA
AAGTTATTGGAACCCAAATATGCGCTCTTCAAAAATCATGTGACATCTTCAATTGGGATTCAAGTGCCCAAAATTCAGAT
TAAGTATTAGATTAAGCATTTGGTTGCAACAAGAAGTGCTTTGAAGGGAATTGGGGGCATTCTCTTTATCTTTGAAAGCT
CTTCTGGTGCATATCTTCTCCTGATTTACTTG

Alignment

ORF - retro_atri_49 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.39 %
• Parental protein coverage: 63.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RVLFSSIFILA-AWQRFNEFADDGGPAVKLLEPKYSLVKNHVTSSLGFQVPEIEIKH----LVAAEIALK
          R.LF.S.FIL..AWQR.NEF.D.GGP.VKLLEPKY.L.KNHVTSS.G.QVP.I.IK.....LVA...ALK
Retrocopy RILFFSSFILL<AWQRLNEFGDNGGPSVKLLEPKYALFKNHVTSSIGIQVPKIQIKY*IKHLVATRSALK

Parental  GIGGILFIFGSSFGAHLLDLFI
          GIGGILFIF.SS.GA.LL....
Retrocopy GIGGILFIFESSSGAYLLLIYL

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_49 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 ,