RetrogeneDB ID: retro_mtru_43

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 2:24452160..24453195(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_2g059220
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g100960
• Aliases: None
• Description: None

Sequence

>retro_mtru_43
ATGGCTATCCGAGCCACCTTCTCCTTTTCCGGCTATGTCGCCCAAACCCTAGTTTCCTCGGCCAGCGTTCGAGTCGCAAA
TCCTCGCGGTGTCCATGAATGCTGTATCCTCTCTCGTTTCTTTGGATCCAACCAAAAACCCGATCTGGATCGTTCCAGCT
GCGGTATAGGCGAGAATTTCAGGAGGCCAAAAATGTCGACCTATTCTACTCTCGCCGGAGACCTTCTCACTGAAGGTTTG
ATCTGGATGATGAAGTCGTCGGCTGTTGTTCCTGGGTCATCAACTGGTATGATGGGTATTTCACCATTCAAACCTTCTTC
AATTATACCATTGTTACAGGTTTCAAAGTGGCTTCCTTGTAATGAGTCTGTTATTAACCCTACAACGTGTATTAACCCTA
CAACGTGGGAAATTGCTGCTTTTAAACCACCGGAATCTCGTTTGTTGAATTTGAATCAGAAGGAGAAAAATATTAGTTGG
ATTTCCAAATATTCAAAAGATGCTAAAGCTGTATTCACTGCTTTCACTGTTAGTTTACTTTATAAATCGTCTTTGGCTGA
ACCTAAATCTATTCCATCTTCTTCTATGTATCCAACTCTTGAAGTTGGTGACCGTGTTTTAACAGAAAAGTTTTCTTTAT
TCTTTAGAAAGCCTCATGTTTCTGATATTGTTATTTTCAAACCTCCGCAATTTTTGAAGGAATTTGGTTATAGTTCATCT
GATGTTTTTATAAAAAGGATTGTGGCTAAGGCTGGTGATGTTGTCCAAGTTAAGGGTGGAAAACTACTAGTGAATGGTGT
TGCTGAACAAGAGGAATTTGTTTTAGAGCCTCTTGATTACGAGTTGGCTCCAATGGTTGTTCCAGCAGGACATGTGTTTG
TAATGGGAGACAATCGTAACCAGAGTTTTGATTCTCATAACTGGGGTCCACTCCCGATCAAGAACATTGTTGGTAGATCG
ATGTTTCGCTACTGGCCTCCATCCAAAGAAGATCAAACTGTCATGGTTCATAACACCTCACCTTCCACGGCATAG

Alignment

ORF - retro_mtru_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.09 %
• Parental protein coverage: 53.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESRL-DLNQKENTNGWISKLLNVCSEDAKAVFTAVTVSLLFKSFLAEPKSIPSASMYPTLEVGDRVLTEK
          ESRL..LNQKE....WISK.....S.DAKAVFTA.TVSLL.KS.LAEPKSIPS.SMYPTLEVGDRVLTEK
Retrocopy ESRLLNLNQKEKNISWISKY----SKDAKAVFTAFTVSLLYKSSLAEPKSIPSSSMYPTLEVGDRVLTEK

Parental  FSFFFRKPDVSDIVIFKAPSWLKAYGFSSSDVFIKRVVAKAGDVVEVRDGKLLVNGVAEDEEFVLEPLAY
          FS.FFRKP.VSDIVIFK.P..LK..G.SSSDVFIKR.VAKAGDVV.V..GKLLVNGVAE.EEFVLEPL.Y
Retrocopy FSLFFRKPHVSDIVIFKPPQFLKEFGYSSSDVFIKRIVAKAGDVVQVKGGKLLVNGVAEQEEFVLEPLDY

Parental  ELAPMVVPKGHVFVMGDNRNKSFDSHNWGPLPIENIVGRSMFRYWPPSKVSDTVMVHKSSP
          ELAPMVVP.GHVFVMGDNRN.SFDSHNWGPLPI.NIVGRSMFRYWPPSK...TVMVH..SP
Retrocopy ELAPMVVPAGHVFVMGDNRNQSFDSHNWGPLPIKNIVGRSMFRYWPPSKEDQTVMVHNTSP

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_43 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_3g100960	1 retrocopy	retro_mtru_43 ,