RetrogeneDB ID: retro_atri_4

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00041:88425..88836(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00041p00020660
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00225p00023630
• Aliases: None
• Description: None

Sequence

>retro_atri_4
ATGGCTCGTACGAAGCAAACAGCTCGTAAATCAACAGGAGGAAAGGCTCCAAGGAAGCAGCTCGCAACCAAGGCTGCAAG
GAAGTCCGCTCCAACAACAGGTGGTGTCAAGAAGCCTCATCGTTTTCGCCCTGGGACTGTCGCTCTTAGGGAAATTCGAA
AGTATCAGAAGAGCACTGAGCTCCTTATTCGCAAACTCCCTTTCCAGAGGCTTGTTCGTGAGATAGCCCAGGACTTCAAG
ACTGATCTTCGTTTCCAGAGTCATGCGGTTCTCGCTCTCCAAGAAGCTGCTGAGGCTTATTTGGTTGGCCTCTTTGAGGA
TACCAACCTTTGCGCCATTCATGCCAAGAGGGTAACCATCATGCCCAAGGATATGCAGCTTGCTAGGCGTATTCGTGGGG
AGCGGGCTTAA

Alignment

ORF - retro_atri_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.53 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRYRPGTVALREIRKYQKSTELLIRKLPFQR
          MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHR.RPGTVALREIRKYQKSTELLIRKLPFQR
Retrocopy MARTKQTARKSTGGKAPRKQLATKAARKSAPTTGGVKKPHRFRPGTVALREIRKYQKSTELLIRKLPFQR

Parental  LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIRGERA
          LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKD.QLARRIRGERA
Retrocopy LVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDMQLARRIRGERA

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_4 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00225p00023630	1 retrocopy	retro_atri_4 ,
Triticum aestivum	Traes_2BL_BB2C0F695	1 retrocopy	retro_taes_79,