RetrogeneDB ID: retro_mtru_5

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 2:34571416..34571857(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_2g082370
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_4g097170
• Aliases: None
• Description: None

Sequence

>retro_mtru_5
ATGGCGCGTACAAAGCAAACTGCTCGCAAATCCACCGGTGGCAAGGCACCAAGGAAGGAACTCGCCACAAAGGTTGCTCG
TGCTCCAAGAGCAAAAGGAGGCGGAAAATCTATGAGAAAAATGAGGGAAGGCCACGTCAAGAAGCCTCATCGTTTTCGTT
GCGGAACAGTTGCTCTTCGTGAGATACGTAAGTATCAGAAGAGTACCGAACTTTTGATCCGTAAACTTCCATTCCAGCGT
CTTGTTCGTGAAATTGCTCAGGATTTCAAGACGGATTTACGATTCCAGAGCCATGCGGTTCTCGCACTTCAGGAAGCAGC
GGAAGCATATTTGGTTGGTTTGTTTGAGGATACCAATTTGTGTGCAATTCATGCTAAGAGGGTTACCATTATGCCTAAGG
ATATTCAACTTGCTCGCCGTATCCGTGGTGAACGTGCTTAG

Alignment

ORF - retro_mtru_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.39 %
• Parental protein coverage: 80.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTKQNLQMARTKQTARKSTGGKAPRKPLATKAARKSAPTTGG-VKKPHRYRPGTVALREIRKYQKSTELL
          RTKQ...........RK....K..R.P.A............G.VKKPHR.R.GTVALREIRKYQKSTELL
Retrocopy RTKQTARKSTGGKAPRKELATKVARAPRAKGGGKSMRKMREGHVKKPHRFRCGTVALREIRKYQKSTELL

Parental  IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR
          IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR
Retrocopy IRKLPFQRLVREIAQDFKTDLRFQSHAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR

Parental  GERA
          GERA
Retrocopy GERA

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_5 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_1g023630	1 retrocopy	retro_mtru_31,
Medicago truncatula	MTR_4g097170	1 retrocopy	retro_mtru_5 ,
Solanum tuberosum	PGSC0003DMG400003769	1 retrocopy	retro_stub_50,
Solanum lycopersicum	Solyc05g051500.2	1 retrocopy	retro_slyc_13,