RetrogeneDB ID: retro_atri_52

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold02717:2296..2797(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00152p00020750
• Aliases: None
• Description: None

Sequence

>retro_atri_52
TGGCCGGAATCTTGGATACCCACTGTTTTTTATAACTTTAGTACAAATGTTGTTGTGGATGGGAACACTGTGAACCTTAG
ATTGTGTGATACGGCTAGTCAAGAGGATTACAACAGGTTAAGACCTTTAAGCTATCGAGGAGCAGACGTGTTTCTTCTGG
CCTTTTCTCTTATCAGCAAAGCCAGCTATGAAAATGTTGCAAAGAAATAGATTCTTGAACTTAGGCATTATGCTCCTGGT
GTTCCGATAATTCTAGTTGGGACAAAGCTTGATCTTCGAGATGACAAGCAGTTCTTTATAGATCACCCAAGTGCAGTGCC
CATAGAGTGGTGTTCCAAGACGCAACAAAATGTGATTGGAGCTCCTGCATACATAGAGTGCAGTTCCAAGATGCATTAGA
ATGTGAAGGCAGTTTTTGATGTAGCAATCAAGGTCGTTCTCCAGCCGCCCAAGCAGAAGAAGAAATAGAAGAGAAAGGCA
CAAAAGGGATGTTCCATCTTG

Alignment

ORF - retro_atri_52 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.14 %
• Parental protein coverage: 84.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FPTDYVPTVFDNFSANVVVDGNTVNLGLWDTAGQEDYNRLRPLSYRGADVFLLAFSLISKASYENVAKKW
          .P....PTVF.NFS.NVVVDGNTVNL.L.DTA.QEDYNRLRPLSYRGADVFLLAFSLISKASYENVAKK.
Retrocopy WPESWIPTVFYNFSTNVVVDGNTVNLRLCDTASQEDYNRLRPLSYRGADVFLLAFSLISKASYENVAKK*

Parental  IPELRHYAPGVPIILVGTKLDLREDKQFFIDHPGAVPITTLQGEELKKLIGAPAYIECSSKTQQNVKAVF
          I.ELRHYAPGVPIILVGTKLDLR.DKQFFIDHP.AVPI...........IGAPAYIECSSK...NVKAVF
Retrocopy ILELRHYAPGVPIILVGTKLDLRDDKQFFIDHPSAVPIEWCSKTQ-QNVIGAPAYIECSSKMH*NVKAVF

Parental  DAAIKVVLQPPKQKKKKKRKAQKGCSIL
          D.AIKVVLQPPKQKKK.KRKAQKGCSIL
Retrocopy DVAIKVVLQPPKQKKK*KRKAQKGCSIL

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_52 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 ,