RetrogeneDB ID: retro_mtru_18

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 7:37183443..37184811(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_7g093510
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g434840
• Aliases: None
• Description: None

Sequence

>retro_mtru_18
ATGGCCTATCCGGAGTATACCATTGAGTTTGCCGCGCTTGTTGCGGTCGTAAATTCCAAGTTTCCTGAAGTCGGTAATCT
TTTACTCAGAAGAATTGTTTTGCAATTCAAATGGGCTTATCATAGGAATGACAAGCCTCATCAGTTACATGCTACTGTTA
AGTTTATAGCACATTTGGTGAAACAGCTAGTTGCACATGAGATTATTGCTTTGGAAATACTCACGGTTTTGCTTGATAAC
CCTATTGATGATAGTCTTGAAGTAGCTGTTAGTTTTCTTATAGAATGCGGTTCAACTTTGCAGAATCTTTCACCTAAAGC
CCTTCATGCTGTATTTGAGCGTTTTCGTTGGATTTTATATGGTGAAGTTGATAAGCGTGTTCAGTTTCTAATTCAAGACT
TATTTGCTGTAAGAAAAACTAGGTTTCAGAGTTATCCAGCTGTTCCACCTGAATTAGACCTCGTGGACGAGGAGGATCAG
TTGACGCATGAAGTGTCGTTGAATGAGAGTATAGATCCAGAGTTTTCGCTTGATGTATTTAGACTGGATCCAGATTATGT
AGAGAACGAAAAACATTATGAGCAGTTGAAGAAAACTATCTTGGGAGACGAAGAAGAAATCGAGGGTGATCAGGAAGGCG
ACTCAGTCGTTGAATCAGATGAAGAAGATGGCGAGAAGCATATGCAGATAAGGGATGAAGCCGATACCAATCTTGTGAAT
CTTCGAAGGGCTATATATCTGACCATTATGTCGTGTTTAGATTTTGAGGAAGCTGGTCATAAGCTTCTCAGAATTATTCA
TCGCCAGAAAGGTCAAGAGATCCAATTATGCAATATGATTCTACAATGCTGCAGGTATGAAAAAGTTTATCGTCCATACT
ATGGTCTTCTGGGGGAGCGTTTTTGTATGATCAACAAAGTTTATCAACAAAACTTTGAAAAGTGTTTTGCTCAACAGTTG
TCAACAATTCACAGGCTTCAAACAAATCAACTCCGAAATGTGGCACAGTTTTTTGCTCATTTGCTTGCCACATCGACTCT
CCCTTGGAACGTGTTATCATATATCCGGTTGACTGAAGAGGACACAACTTCTTCTTCGCGGATATTTATTAAGATTCTGT
TCCAAGAGTTATCTGAGCATCTTGGCATCCAGGTGCTGAATGATCGGTTGAATGATCCAGTAATGCAGGATTGTTTTGAA
TCATTATTTCCCAAAGATAGCACAAAAAACACACGGTTTTCCATTAACTTCTTCACGTCGATTGGACTTGGCGAGCTTAC
TAAGAATCTAGGCGTCTATTTGAAAAATCTGACCTTGCGGAGCTCCCATTCATTGGATGAAAGTGGCAGAAAACGTAGAA
GAAAATAA

Alignment

ORF - retro_mtru_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.62 %
• Parental protein coverage: 57.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPGFTDVFAAMVAVVNTKFPQVGDLLLRRIVLQLKRAYKRNDKP-QLLAAVKFVAHLVNQQVAHEIIA
          MA.P..T..FAA.VAVVN.KFP.VG.LLLRRIVLQ.K.AY.RNDKP.QL.A.VKF.AHLV.Q.VAHEIIA
Retrocopy MAYPEYTIEFAALVAVVNSKFPEVGNLLLRRIVLQFKWAYHRNDKPHQLHATVKFIAHLVKQLVAHEIIA

Parental  LELLTVLLEKPSDDSVEVAVGFVTEVGSMLQDLSPRGLHGIFERFRGILHEGEIDKRVQFLIEGLFAIRK
          LE.LTVLL..P.DDS.EVAV.F..E.GS.LQ.LSP..LH..FERFR.IL..GE.DKRVQFLI..LFA.RK
Retrocopy LEILTVLLDNPIDDSLEVAVSFLIECGSTLQNLSPKALHAVFERFRWILY-GEVDKRVQFLIQDLFAVRK

Parental  AKFQGYPAVRPELDLVEQEDQLTHEVSLDEEIDPETSLDIFKPDPNYLENEKRYEELKKTLLGEEEESEG
          ..FQ.YPAV.PELDLV..EDQLTHEVSL.E.IDPE.SLD.F..DP.Y.ENEK.YE.LKKT.LG.EEE.EG
Retrocopy TRFQSYPAVPPELDLVDEEDQLTHEVSLNESIDPEFSLDVFRLDPDYVENEKHYEQLKKTILGDEEEIEG

Parental  EEGSDAESDEDDESDEED-EEAMQIKDETETNLVNLRRTIYLTIMSSVDFEEAGHKLLKI-HLEPGQEME
          ....D.E.D...ESDEED.E..MQI.DE..TNLVNLRR.IYLTIMS..DFEEAGHKLL.I.H...GQE..
Retrocopy ----DQEGDSVVESDEEDGEKHMQIRDEADTNLVNLRRAIYLTIMSCLDFEEAGHKLLRIIHRQKGQEIQ

Parental  LCTMLLECCSQERTYLRYYGLLGQRFCMINKVHQENFEKCFVQQYSLIHRLETNKLRNVAKFFAHLLGTF
          LC.M.L.CC..E..Y..YYGLLG.RFCMINKV.Q.NFEKCF.QQ.S.IHRL.TN.LRNVA.FFAHLL.T.
Retrocopy LCNMILQCCRYEKVYRPYYGLLGERFCMINKVYQQNFEKCFAQQLSTIHRLQTNQLRNVAQFFAHLLATS

Parental  ALPWHVLSYIRLTEDDTTSSSRIFIKILFQELSEHLGIRLLNERLNDPTMQDSFESIFPKDNPKNTRFCI
          .LPW.VLSYIRLTE.DTTSSSRIFIKILFQELSEHLGI..LN.RLNDP.MQD.FES.FPKD..KNTRF.I
Retrocopy TLPWNVLSYIRLTEEDTTSSSRIFIKILFQELSEHLGIQVLNDRLNDPVMQDCFESLFPKDSTKNTRFSI

Parental  NFFTSIGLGGLTENLREYLKNM
          NFFTSIGLG.LT.NL..YLKN.
Retrocopy NFFTSIGLGELTKNLGVYLKNL

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_18 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G39400	1 retrocopy	retro_bdis_57,
Medicago truncatula	MTR_3g434840	1 retrocopy	retro_mtru_18 ,
Sorghum bicolor	Sb03g029810	1 retrocopy	retro_sbic_32,
Arabidopsis lyrata	scaffold_202963.1	1 retrocopy	retro_alyr_10,
Solanum lycopersicum	Solyc04g079920.2	1 retrocopy	retro_slyc_47,