RetrogeneDB ID: retro_mtru_54

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 3:1530548..1530788(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g098290
• Aliases: None
• Description: None

Sequence

>retro_mtru_54
TTGATGGCTACTGTGAAGAAGGGGAAACCTGATCTCAGGAAGAAGGTTTTGCCAGTTGTCATCGTTCGTCAGCGTAAGCC
TTGGCGCCAAAAGGATCGTGTCTTCATGTACTTCAAAGATAATGACGGCATTATTGTGAATCCTAAGGGAGAAATGAAAG
ATTATGCTATCACTGGACCAATTGGTAACGAGTGTGCTGAGCTTTGGCCTATGATTGCAAGTGCTGCCAATGCCATTGTA

Alignment

ORF - retro_mtru_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.75 %
• Parental protein coverage: 64. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMATVKKGKPDLRKKVLPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIAKECADLWP
          .MATVKKGKPDLRKKVLP.VIVRQRKPWR.KD.VFMYF.DN.G.IVNPKGEMK..AITGPI..ECA.LWP
Retrocopy LMATVKKGKPDLRKKVLPVVIVRQRKPWRQKDRVFMYFKDNDGIIVNPKGEMKDYAITGPIGNECAELWP

Parental  RIASAANAIV
          .IASAANAIV
Retrocopy MIASAANAIV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Medicago truncatula was not studied using RNA-Seq expression data.

ChIP-Seq

Medicago truncatula was not studied using ChIP-Seq data.

EST

Medicago truncatula was not studied using EST data.

TSS

Medicago truncatula was not studied using FANTOM5 data.

Lab

retro_mtru_54 was not experimentally validated.

Homology

Retrocopy orthology:

Medicago truncatula 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g098290	1 retrocopy	retro_mtru_54 ,
Solanum tuberosum	PGSC0003DMG400017151	2 retrocopies	retro_stub_123, retro_stub_87,
Solanum lycopersicum	Solyc09g090610.2	1 retrocopy	retro_slyc_83,