RetrogeneDB ID: retro_atri_43

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00102:1069487..1069976(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00007p00238780
• Aliases: None
• Description: None

Sequence

>retro_atri_43
GATTCTACTCAATCCTCTTAACCTTCTCCCTCTTCATGCAGGAATCGTGGTAATAGTACCTTGATACCCATGACGGTGAA
GCAGATAAGCCAAGTATCATCATATGATAATTCTAGCATTGCGTGTTGAAGCTCTGAAATCAAACAATGTTAAGTTGGTT
GGAATGGGGCTCATAAAGTGGAAATGTTCACGAATGTGCAATTCATCCTCGATGATGGTACTAGAAGAATCGATGTACAT
AGATGGGTCAATGATGCTACATACAGTAATGAGATGCCCATAGTAAAGAATGAAATATATGTTTGTGTCATTGGTCACTT
GAAAAGTTTTCAGGGTAAAAAGCATGCTCCAGCTTTCTCAGTTAGACCTATTACGGACTTCAATGAAATTACGTGCCACT
TCTTGGAATGCATATATGTACATCTAACCAACACTAAACAGATGGGTGGGTCTCCACAGCCTCAAAAAAGTTCGGTGACC
ACAGCAATG

Alignment

ORF - retro_atri_43 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 58.63 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DSTQSSEPSPSSSRNRGNSTLIPMTVKQISQVLSDDNSSAG-VEALESNNVRLVGMV-ANKVERVTDVQF
          DSTQSS.PSPSS.RNRGNSTLIPMTVKQISQV.S.DNSS...VEAL.SNNV.LVGM..A.KVE..T.VQF
Retrocopy DSTQSS*PSPSSCRNRGNSTLIPMTVKQISQVSSYDNSSIA>VEALKSNNVKLVGMG<AHKVEMFTNVQF

Parental  ILDDGTGRIDVHRWVNDATDSNEMAIVKNGIYVRVIGHLKSFQGKKHATAFSVRPITDFNEITCHFLECI
          ILDDGT.RIDVHRWVNDAT.SNEM.IVKN.IYV.VIGHLKSFQGKKHA.AFSVRPITDFNEITCHFLECI
Retrocopy ILDDGTRRIDVHRWVNDATYSNEMPIVKNEIYVCVIGHLKSFQGKKHAPAFSVRPITDFNEITCHFLECI

Parental  YVHLSNTKQMGGSPQPQKSSVTTAL
          YVHL.NTKQMGGSPQPQKSSVTTA.
Retrocopy YVHLTNTKQMGGSPQPQKSSVTTAM

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_43 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00007p00238780	1 retrocopy	retro_atri_43 ,