RetrogeneDB ID: retro_mtru_34

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 5:42944061..42944766(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_5g098090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g094860
• Aliases: None
• Description: None

Sequence

>retro_mtru_34
ATGGCGCCGACGAAGGAGAGAGCATCTAGGGTTAGCCGAAACTCTGATTTGATCAGAGGGATTGGAAAGTTCTCAAAGTC
ACAGATGTATCACAAGAAAGGTATCTGGGTTATTAAGGCCAAAAATGGTGGCGTTTTTCCTCATCATGATCCTAAACCTA
AGCCCGAAACTGCTGTTGAAAAACCACCAAAATTTTACCCTGCTGATGATGTGAAGAAACCTCTTCGTAACAAGCATAAG
CCTAAGCAGACTAAGCTCAGGGCAAGCATCACTCCCGGCACAGTGCTGATTCTTCTTGCTGGTAGATTTAAGGGCAAGAG
GGTGGTGTTTTTGAAGCAGCTTCCTTCTGGATTGCTTCTTGTAACTGGTCCCTTCAAGATCAACGGAGTTCCTTTGAGAT
GTGTGAATCAGGCCTATGTGATTGGTACATCAACCAAAGTCGATATCTCCGGTGTTAATGTGGATAACCTTGATGACAAG
TACTTTTCAAAGGAAGCCCCAAAAAAGAAGAGCAAGGGAGAAGGCGAATTCTTTGAGTTAGACAAGGAGGAGAAAAAGGT
GTTACCTCAGCAGAAGAAAGATGACCAGAAAACAGTGGACGCTGCATTGATAAAAGCTATTGATAGCGTTCCAGACTTGA
AAACTTATCTTGGTGCCAGGTTTTCTCTCAAGGCAGGTGTGAAGCCACACGAACTAGTTTTCTAG

Alignment

ORF - retro_mtru_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.04 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAP-KTRTARVSRNPELIRGIGKYSRSAMYHKRGLWAIKAKHGGAFPRHDPVAKPAAPVEKPPKFYPADD
          MAP.K.R..RVSRN..LIRGIGK.S.S.MYHK.G.W.IKAK.GG.FP.HDP..KP...VEKPPKFYPADD
Retrocopy MAPTKERASRVSRNSDLIRGIGKFSKSQMYHKKGIWVIKAKNGGVFPHHDPKPKPETAVEKPPKFYPADD

Parental  VKKPLRNKHKPKPTKLRASITPGTVLILLAGRFKGKRVVFLKQLPSGLLLVTGPFKINGVPLRRVNQAYV
          VKKPLRNKHKPK.TKLRASITPGTVLILLAGRFKGKRVVFLKQLPSGLLLVTGPFKINGVPLR.VNQAYV
Retrocopy VKKPLRNKHKPKQTKLRASITPGTVLILLAGRFKGKRVVFLKQLPSGLLLVTGPFKINGVPLRCVNQAYV

Parental  IGTSTKVDISSVNADKFDDKYFSKESQKKTKKGEGEFFEADKEDKKVLPQEKKDDQKTVDAGLLKAIDSV
          IGTSTKVDIS.VN.D..DDKYFSKE..KK..KGEGEFFE.DKE.KKVLPQ.KKDDQKTVDA.L.KAIDSV
Retrocopy IGTSTKVDISGVNVDNLDDKYFSKEAPKKKSKGEGEFFELDKEEKKVLPQQKKDDQKTVDAALIKAIDSV

Parental  PDLKTYLGARFSLKAGVKPHELVF
          PDLKTYLGARFSLKAGVKPHELVF
Retrocopy PDLKTYLGARFSLKAGVKPHELVF

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_34 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_3g094860	1 retrocopy	retro_mtru_34 ,