RetrogeneDB ID: retro_mtru_49

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:29589305..29590082(+)
• Located in intron of: MTR_1g069020

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g091700
• Aliases: None
• Description: None

Sequence

>retro_mtru_49
TCCCAACCTGAAATCACTCAAGGCTCCAACTGGTATCACAATGTTCAACCTCAACAAAACGACAAATACAAAATCATGGG
TATTGCGCCATTTGATGATTTCTTTGAGTTTGATTGGGCAACTCAATTTTCATACCGAAGTAATCATATTTACAAGAATG
ACTTCGATGATCTTGAAAATTTCAACTTTAATTTCAACCTCCCACACCTTGATCAGAATAATTTTGAGGTTGATCAAAAA
CCCCTCAATGTTGTCTTGCCTGAGTTGGGGCATTACAATCATAAAGGTGAGACTGTTGCTGAGAGTGGTTATGTTGAAGA
TTCTGTGAAAACTGGAAGTGGATTTGTGAGTTTTGTGAAGAAAGAGAATGAATGGGAGAATCAGGAATTGTCATTAGTTC
CATTGGCATTGCCAAGCAGCAGCACTGGCATCATTAGGAAGAGGTCATCTTCATTGCAGTATGATGACATAAAGAAACAT
TTTGATGTTCCTATAACAATGGCTGCTGAGAAAATGAATGTTGGTGTGACCCTTTTGAAAAAAAGATGCAGGGAGCTCAA
CATCACTAGGTGGTCTCACAGAAAATTGAGGAGTTTGATGTTACTCATCGAGAACCTTAAGGAAAAGGGTTTGACTGAGG
AAATTGCCATGTTGGAGAAGCCAAAAAAGATGTTGGAGAAACTTCCGGGAATGGATTTGAATGACGAAATCAAGAAGCTG
AGGCAAGCATGCTTTAAAGCTAATTACAAGAACAGAAAATTAATTGCCCTCTGTCCT

Alignment

ORF - retro_mtru_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 98.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TQPEITQSFNWFCNVQPQQNDTDKIMGIAPFDDFFEFDWATQFSYQSNHFYMNDFDDLENFNFDFNLPHL
          .QPEITQ..NW..NVQPQQND..KIMGIAPFDDFFEFDWATQFSY.SNH.Y.NDFDDLENFNF.FNLPHL
Retrocopy SQPEITQGSNWYHNVQPQQNDKYKIMGIAPFDDFFEFDWATQFSYRSNHIYKNDFDDLENFNFNFNLPHL

Parental  DQNNFEVDKKPLNVVLPELGHYNHKGETV---GYVEASVKTESGFVSFVKKENEWENQELSSLVPLALQS
          DQNNFEVD.KPLNVVLPELGHYNHKGETV...GYVE.SVKT.SGFVSFVKKENEWENQELS.LVPLAL.S
Retrocopy DQNNFEVDQKPLNVVLPELGHYNHKGETVAESGYVEDSVKTGSGFVSFVKKENEWENQELS-LVPLALPS

Parental  SSTSIIRKRSSSLQFDDIKKHFDVPITMAAKKLNVGVTFLKKRCRELNITRWPHRKLRSLMLLIDNLKDK
          SST.IIRKRSSSLQ.DDIKKHFDVPITMAA.K.NVGVT.L...CRELNITRW.HRKLRSLMLLI.NLK.K
Retrocopy SSTGIIRKRSSSLQYDDIKKHFDVPITMAAEKMNVGVTLLXXXCRELNITRWSHRKLRSLMLLIENLKEK

Parental  GLTKEVAMLEKQKKMLEKLPGMHLNDEIKKLRQACFKANYKNRKLIALCP
          GLT.E.AMLEK.KKMLEKLPGM.LNDEIKKLRQACFKANYKNRKLIALCP
Retrocopy GLTEEIAMLEKPKKMLEKLPGMDLNDEIKKLRQACFKANYKNRKLIALCP

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_49 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_3g091700	1 retrocopy	retro_mtru_49 ,