RetrogeneDB ID: retro_mtru_25

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 2:4982021..4983359(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_2g016340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g049790
• Aliases: None
• Description: None

Sequence

>retro_mtru_25
ATGGAGAACAAAGGAACAATTCTAATGCAAAAGTATGAGGTAGGACGCATGCTTGGCCAAGGAAGTTTTGCCAAAGTTTA
CCATGCAAGGAACTTAAAGACAGGACAAAATGTTGCTATCAAGGTGTTCGACAAAGCGATGATCATGAAAGTCGGTTTGA
AGGAGCAAATCAAGCGTGAAATCTCGGTTATGCGTCTTGTTCGACACCCTAACATTGTCGAATTCTACGAGGTCATGGCA
AGCAAAACAAAGATATATTTTGCAATGGAACAAGTGAAAGGTGGCGAGCTTTTCCATAAAGTGTCTCGAGGGAAGCTGAG
GGAAGATATGGCTAGGAAATATTTCCAGCAACTTATTGCAGCTGTTGATCATTGTCATAGAAGAGGGATTTATCATCGCG
ACCTTAAACCAGAAAATCTTCTCCTCGACGAAAATGGTAACCTTAAAGTTGCTGATTTTGGTCTTAGTGCATTGTTGGAA
TCAAAAAAAAAAGACGATCTTCTTCATACAACATGCGGTACTCCAGCTTATGTAGCACCTGAGATTATCAGGAAGAAAGG
TTATGATGGAGCCAAGGCAGATATTTGGTCTTGTGGTGTTATTCTCTTTGTTCTATTGGCAGGTTTTCTTCCTTTCAATG
ATAGAAATTTAATGGAGATGTATAAGAAGATTGCAACTGCTGATTTCAAGTTTCCACAATGGTTTCATTCTGATGTGAAA
AGGCTTCTTTATAGAATCCTTGATCCTGATCCAAAAACAAGAATTACTATTAACAAGATTATGCAAAATAGTTGGTTTAG
AAAAGGGTATAAACAGATTGAAGGACCACATTTATCGCCTACACACGGCGATATCTCAGATGTTCATAATGCATTTGATG
ATTTGTCAACACTATCAAGTCCAATGTCTGTTAAAGATGAACAATGTCCTATGAAACTATATTGTTTCAATGCATTTGAT
ATCATATCACTCTCTTCGGGACTTGATCTTTCGGGTTTGTTTGAAAAAGATACGAGTGAAGGACAACATGCAAGATTTGC
TACAAATAGACCACCTTCAACAATTGTGTCAAAACTTGAAGAGACAGCACAATTAGTTGGTAGATTTAAGGTGATGAAGC
AAAATGGGATTGTTAGAGTGGAGGGATTTGAGACAGGAGTAAGTGAACAACTCACCATTGATACAGAAATTTTTGAAGTT
GCATCTTCATTTTATATTGTTGAGGTGAACAAAATTTCCGGAGATACAGTGGAATATACGAAATTCTGGAACCAGTACTT
AAAGCCTTCTCTTAGTGAAATTGTTTGGGATTCTCAAGGATATGAACAATACATATAA

Alignment

ORF - retro_mtru_25 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.06 %
• Parental protein coverage: 93.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NGGRAKAGKYELGRTLGEGNFAKVKFARHIETGDHVAIKILDKEKILKHKMIRQIKQEISTMKLIRHPNV
          N.G.....KYE.GR.LG.G.FAKV..AR...TG..VAIK..DK..I.K.....QIK.EIS.M.L.RHPN.
Retrocopy NKGTILMQKYEVGRMLGQGSFAKVYHARNLKTGQNVAIKVFDKAMIMKVGLKEQIKREISVMRLVRHPNI

Parental  IRMHEVIANRSKIFIVMELVTGGELFDKIARSGRLKEDEARKYFQQLICAVDYCHSRGVCHRDLKPENLL
          ....EV.A...KI...ME.V.GGELF.K..R.G.L.ED.ARKYFQQLI.AVD.CH.RG..HRDLKPENLL
Retrocopy VEFYEVMASKTKIYFAMEQVKGGELFHKVSR-GKLREDMARKYFQQLIAAVDHCHRRGIYHRDLKPENLL

Parental  LDTNGTLKVSDFGLSALPQQVREDGLLHTTCGTPNYVAPEVIQNKGYDGAIADLWSCGVILFVLMAGYLP
          LD.NG.LKV.DFGLSAL......D.LLHTTCGTP.YVAPE.I..KGYDGA.AD.WSCGVILFVL.AG.LP
Retrocopy LDENGNLKVADFGLSALLESKKKDDLLHTTCGTPAYVAPEIIRKKGYDGAKADIWSCGVILFVLLAGFLP

Parental  FEEDNLVALYKKIFKADFTCPPWFSSSAKKLIKRILDPSPITRIKIAEVIENEWFKKGYKP---PVFEQA
          F...NL...YKKI..ADF..P.WF.S..K.L..RILDP.P.TRI.I.....N.WF.KGYK....P.....
Retrocopy FNDRNLMEMYKKIATADFKFPQWFHSDVKRLLYRILDPDPKTRITINKIMQNSWFRKGYKQIEGPHLSPT

Parental  DVSLDDVNSIFNGYMDSDNIVVERQEEGPVAPVTMNAFELISKSQGLNLSSLFEKQMGLVKRETRFTSKC
          .....DV...F..............E..P......NAF..IS.S.GL.LS.LFEK.........RF....
Retrocopy HGDISDVHNAFDDLSTLSSPMSVKDEQCPMKLYCFNAFDIISLSSGLDLSGLFEKDTS-EGQHARFATNR

Parental  SANEIISKIEKTAGPLG-FDVKKNNCKLRIYGEKTGRKGHLSVATEILEVAPSIYMVEMRKSEGDTLEFH
          ....I.SK.E.TA...G.F.V.K.N...R..G..TG....L...TEI.EVA.S.Y.VE..K..GDT.E..
Retrocopy PPSTIVSKLEETAQLVGRFKVMKQNGIVRVEGFETGVSEQLTIDTEIFEVASSFYIVEVNKISGDTVEYT

Parental  KFYKS-ITTGLKDIVW
          KF........L..IVW
Retrocopy KFWNQYLKPSLSEIVW

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_25 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_2g049790	1 retrocopy	retro_mtru_25 ,