RetrogeneDB ID: retro_mtru_46

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 4:28789381..28789840(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_4g075450
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_1g070450
• Aliases: None
• Description: None

Sequence

>retro_mtru_46
ATGGCGGATGTTGAACCAGAGGTAGCAGCACATGGAGTGGCAAAGAAGAGAACATTCAAGAAGTTCAGTTTCCGTGGAGT
TGATCTCGATGCTCTTTTGGATATGCCCACTGATGAACTTGTGAAGCTTTTCTCTGCACGTGCCCGAAGAAGGTTTCGAC
GTGGTTTAACCCGCAAGCCTATGGCACTGATCAAGAAGCTACGTAAGGCGAAACGTGAGGCACCACCTGGTGAGAAGCCA
GAACCAGTGAGGAATCACCTCCGTAACATGATCATTGTGCCTGAGATGATTGGTAGCATTATTGGTGTCTACAATGGAAA
GACCTTCAATCAAGTTGAAATTAAACCTGAAATGATTGGCCACTATCTTGCTGAATTCTCGATCTCTTACAAGCCGGTTA
AGCACGGTAGGCCTGGTATCGGTGCTACTAACTCCTCCAGGTTTATTCCTCTCAAGTGA

Alignment

ORF - retro_mtru_46 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.39 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MADVEPEVAAQGVPKKRTFKKFSFRGVDLDALLDMSTDELVKLFSSRARRRFQRGLTRKPMALIKKLRKA
          MADVEPEVAA.GV.KKRTFKKFSFRGVDLDALLDM.TDELVKLFS.RARRRF.RGLTRKPMALIKKLRKA
Retrocopy MADVEPEVAAHGVAKKRTFKKFSFRGVDLDALLDMPTDELVKLFSARARRRFRRGLTRKPMALIKKLRKA

Parental  KREAPPGEKPEPVRTHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGI
          KREAPPGEKPEPVR.HLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGI
Retrocopy KREAPPGEKPEPVRNHLRNMIIVPEMIGSIIGVYNGKTFNQVEIKPEMIGHYLAEFSISYKPVKHGRPGI

Parental  GATHSSRFIPLK
          GAT.SSRFIPLK
Retrocopy GATNSSRFIPLK

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_46 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G04270	1 retrocopy	retro_atha_20,
Brassica oleracea	Bo5g004420	1 retrocopy	retro_bole_33,
Brassica rapa	Bra032519	1 retrocopy	retro_brap_20,
Arabidopsis lyrata	fgenesh2_kg.1__358__AT1G04270.1	1 retrocopy	retro_alyr_8,
Medicago truncatula	MTR_1g070450	1 retrocopy	retro_mtru_46 ,
Solanum tuberosum	PGSC0003DMG400007336	1 retrocopy	retro_stub_80,
Solanum lycopersicum	Solyc02g082000.2	1 retrocopy	retro_slyc_75,
Triticum aestivum	Traes_2AL_52D3F9AF41	1 retrocopy	retro_taes_67,