RetrogeneDB ID: retro_mtru_38

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:32716835..32717732(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_1g073720
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g070740
• Aliases: None
• Description: None

Sequence

>retro_mtru_38
ATGGGTGAGAGGAAGGTTTTGAACAAGTATTACCCACCGGATTTCGATCCTGCCAAGCTTCCTCGAGGAAAAAAGACCAA
ACAAATCCCTGTTCGTCATATGCTTTCGATGACCATTCGATGCAACACTTGCGGTAATTTTATGTACAAAGGTACCAAGT
TAAACTCCAGAAAAGAAGTTGTCGAAGGCGAGACATATCTTGGAATTCAAATTTTCAGATTCTATGGCAAATGCACCTGC
TGCTCAGCTGAATATACCATGAAGACTGATCCGCGGAATTCAGATTACGTCGTTGAGTTTGGTGCAACGAGAAATTTTGA
ACCTTGGCGCGCAGAGGATAAGGAAAGCGACGAAAGGAAAAAGAAGAGGGAAGCCGAAGAAATTGGAGATGCAATGAAAT
CGTTAGAGAATAAAACCCTAGATTCTAAAAGAGAGATGGATATCCTTGCTGCACTGGATGAGATGAAGTCAATGAAGTCT
AGGCATGCAACTGTTAGTGTTGATAAAATGCTTGCTGCCTTGCAACGTAAGGCAGCAGACAAGGAGAAAAGGCTGGTAGA
AGAAGATGAAGCACTGATAAAATCAATTTTCTCGAATAATTCTGAAGTTTCTATCAGCAGAATTCGTGACAGACATGGTG
AAACATCCAATAATAATCTGAAGAGGCGAAAAATTTCCAAAGATCTTTCAGAAAAAGCCGCTGGTACTCTGACAAAAGCC
GGTTTGGATGATTCTGACAAACAAGGAAAATTGATCGGCGGTCGTCAAAAGCCTAATCCTTTGGCGATGATTTCTGTTGT
CAAGAAACCAGAGACCTCTAATGTCAAACGTTCTACAAATACTAATGGTGCACTGTTATCTTTGTGCCTAAGCTATGGAA
GTAGTGATGAGGATTAG

Alignment

ORF - retro_mtru_38 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.96 %
• Parental protein coverage: 64.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGERKVLNKYYPPDFDPAKLPRVRRPKNLQIKVRMMLPMSIRCNTCGNYIYKGTKFNSRKEDVIGETYLG
          MGERKVLNKYYPPDFDPAKLPR....K..QI.VR.ML.M.IRCNTCGN..YKGTK.NSRKE.V.GETYLG
Retrocopy MGERKVLNKYYPPDFDPAKLPRGKKTK--QIPVRHMLSMTIRCNTCGNFMYKGTKLNSRKEVVEGETYLG

Parental  IQIFRFYFKCTRCSAELTMKTDPQNSDYVVESGATRNFEPWRAEDEETDEMKKKRETEEMGDAMKSLENR
          IQIFRFY.KCT.CSAE.TMKTDP.NSDYVVE.GATRNFEPWRAED.E.DE.KKKRE.EE.GDAMKSLEN.
Retrocopy IQIFRFYGKCTCCSAEYTMKTDPRNSDYVVEFGATRNFEPWRAEDKESDERKKKREAEEIGDAMKSLENK

Parental  TLDSKREMDILAALDEMKSMKSRHATVSVDEMLAALQRTAADKEKRIEEEDEALIKSIFSNKPEVPIRRI
          TLDSKREMDILAALDEMKSMKSRHATVSVD.MLAALQR.AADKEKR..EEDEALIKSIFSN..EV.I.RI
Retrocopy TLDSKREMDILAALDEMKSMKSRHATVSVDKMLAALQRKAADKEKRLVEEDEALIKSIFSNNSEVSISRI

Parental  RD
          RD
Retrocopy RD

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_38 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Aegilops tauschii	F775_28326	1 retrocopy	retro_atau_32,
Hordeum vulgare	MLOC_44559	1 retrocopy	retro_hvul_103,
Medicago truncatula	MTR_2g070740	1 retrocopy	retro_mtru_38 ,