RetrogeneDB ID: retro_mtru_44

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:51845698..51846145(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_1g115170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g103490
• Aliases: None
• Description: None

Sequence

>retro_mtru_44
ATGAAAGAAACTGTTGCCTTCTATGAAAAAGTTCTTGAATTCATTTCCATCGTAAGGCCTGGATCGTTTGATTTTGGCGG
GGCATGGCTATTTGGCCACGGGATTGGAATTCATTTGCTGCTGGCAGAGGACCCTGAAAAGATTCCAAGGAAGAATGAAA
TTAATACAAAGGATAAGCATATCTCATTCCAGTGTGATGAAAGCATGGATGCAGTAGAGAAATATTTGAAGGATATGAAA
ATTGGTTTAAAACGTGCAATGGTTGAGGAAAATGGAATTCAAGTGGATCAGTTGTTTTTTCATGACCCAGATGGATTCAT
GATTGAGATATGCAATTGTGATAGTCTCCCTGTTATTCCTTTAGCTGGTGGGATGGTTACATTATGCCCTAGACTCAACT
TTGAGTCTATGCCACAACAGATAGACCAAGTTGCAAAGCAAATTTGA

Alignment

ORF - retro_mtru_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.46 %
• Parental protein coverage: 86.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VNESVSFYEKVLGFISIVRPGSFDFEGAWLFGYGIGIHLLQAEDPENIPRKNEINPKDNHISFQCDESMD
          ..E.V.FYEKVL.FISIVRPGSFDF.GAWLFG.GIGIHLL.AEDPE.IPRKNEIN.KD.HISFQCDESMD
Retrocopy MKETVAFYEKVLEFISIVRPGSFDFGGAWLFGHGIGIHLLLAEDPEKIPRKNEINTKDKHISFQCDESMD

Parental  TVEKYLNDKKIGCKRAMVEENGIQVDQLFFHDPDGFMIEICNCDSLPVIPLAGEMVRSCSRLNLEIMPQQ
          .VEKYL.D.KIG.KRAMVEENGIQVDQLFFHDPDGFMIEICNCDSLPVIPLAG.MV..C.RLN.E.MPQQ
Retrocopy AVEKYLKDMKIGLKRAMVEENGIQVDQLFFHDPDGFMIEICNCDSLPVIPLAGGMVTLCPRLNFESMPQQ

Parental  IHQVVKQI
          I.QV.KQI
Retrocopy IDQVAKQI

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_44 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G80160	1 retrocopy	retro_atha_15,
Brassica oleracea	Bo2g096220	1 retrocopy	retro_bole_1,
Brassica rapa	Bra008491	1 retrocopy	retro_brap_10,
Arabidopsis lyrata	fgenesh1_pm.C_scaffold_2001978	1 retrocopy	retro_alyr_14,
Medicago truncatula	MTR_2g103490	1 retrocopy	retro_mtru_44 ,
Setaria italica	Si023259m.g	1 retrocopy	retro_sita_39,