RetrogeneDB ID: retro_mtru_19

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 7:10320772..10322053(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_7g029240
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g112430
• Aliases: None
• Description: None

Sequence

>retro_mtru_19
ATGAGTCGGAAAGAATTGTCAAAGATTTCACCGTCGCCGGTTTCATTGGCCACTCTCCTTGACCGTGAGCTTCGAGAAGA
GAAAGGTGAAAAAAGGTTTGTTAAGTATGGAGAAGAAAGCATGACCAAGAAAGGAGAAGATTATGGTCTGATCAAAACAT
GTTGCCACCGGGTTCCCGGGGATCCATCAACTGCGTTTTCGGTCTTTGCAATTTTTGATGGGCATAGCGGTATATCAGCC
GCAGTTTATGCAAAAGAAAACTTGCTAAATAATGTTTTGAAGGAAATACCGAAAGATATTATCAGCAGCAGCAGGGATGC
TTGGCTACATGCCCTTCCTCGTGCTCTAGTGGCTGGTTTTGTGAAGACTGACATGGATTTTCAGAGTATCAAAGGAGAAA
TGTCTGGAACTACAGCTACGTTTGTTGTTGTTGATGAGAGTATTGTCACTGTTGCATCTGTTGGTGATTCGCGTTGCATA
TTAGTAGATAATAAAGGAGGAGGTGTAGTTTCTATTCTTACTGTTGATCACAGGCTGGAAGATAACGTGGAGGAGAGGGA
GCGTGTTATTGCAAGTGGTGGTGAAGTTAAAAGACAAGATTATCGTGGTGGCCCTCTTCGCGTCTGGCCTGGTGGATTAT
GTCTATCTAGATCAATAGGAGACGCAGATCTAGGGAAATATATTGTTCCAATACCACATGTTAAGCAAGTCAAACTACTT
TCCAATGGTGGCAATGGAAGGCTTATCATAGCCTCTGATGGTGTTTGGGATGCTTTATCGAATGAAATGGCAGCAGCAGC
ATGTCGGGGTGTAGCTGCAGAATTTGCTGCAAAGCTAGTGGTTGAGGAAGCTATAATATCTAAAGGCTTGAGAGATGATA
CATCATGCATTGTTGTAGATATTCCTTCTGATCACCTCCCTGTATTACAACGAAATTCAACTACACAAAAGAAATTACAT
AATCTTCTAAAACCGCTTCTTTTTCCTTTTCGAAAGAAATCTAAGAAGAACTCTACAAACAAAGCTACCAGCAAGGTTGG
TGTTGTTGTGGAAGATTTATTTGAAGAGGGTTCTGTGTTTATAGAAAGGTTTGGCAATGATTTTTCACTTAATAACAACT
CTGATCAGATTTTCAGCTGTGCGATTTGCCAAGTGGATCAACGCCCTGGAAATGGTATATCAAGACCGTTGAATTCTCCA
TTGGAAGTCCCATTTTTCTGCACAAACTGTCGGAAGAAAAAAGTTATAATGGAAGGAAAGAGGCCAATGGTCTATCAGTA
G

Alignment

ORF - retro_mtru_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.42 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKRELSRMKPSPVPLATLIGREIRNEKVEKPFVKFGQAGLAKKGEDYFLIKTDCHRVPGDPSTAFSVFA
          MS..ELS...PSPV.LATL..RE.R.EK.EK.FVK.G.....KKGEDY.LIKT.CHRVPGDPSTAFSVFA
Retrocopy MSRKELSKISPSPVSLATLLDRELREEKGEKRFVKYGEESMTKKGEDYGLIKTCCHRVPGDPSTAFSVFA

Parental  IFDGHNGISAAIYTKENLLNNVLSAIPQDI---SRDAWLQALPRALVVGFVKTDTEFQK-KGETSGTTAT
          IFDGH.GISAA.Y.KENLLNNVL..IP.DI...SRDAWL.ALPRALV.GFVKTD..FQ..KGE.SGTTAT
Retrocopy IFDGHSGISAAVYAKENLLNNVLKEIPKDIISSSRDAWLHALPRALVAGFVKTDMDFQSIKGEMSGTTAT

Parental  FVIVDGWTVTVASVGDSRCIL--DTQGGVVSLLTVDHRLEENVEERERVTASGGEVGRLNIFGGNEVGPL
          FV.VD...VTVASVGDSRCIL.....GGVVS.LTVDHRLE.NVEERERV.ASGGEV.R....GG....PL
Retrocopy FVVVDESIVTVASVGDSRCILVDNKGGGVVSILTVDHRLEDNVEERERVIASGGEVKRQDYRGG----PL

Parental  RCWPGGLCLSRSIGDTDVGEYIVPIPHVKQVKLSSAG--GRLIIASDGIWDTLSNDIAAMSCRGLPAELA
          R.WPGGLCLSRSIGD.D.G.YIVPIPHVKQVKL.S.G..GRLIIASDG.WD.LSN..AA..CRG..AE.A
Retrocopy RVWPGGLCLSRSIGDADLGKYIVPIPHVKQVKLLSNGGNGRLIIASDGVWDALSNEMAAAACRGVAAEFA

Parental  AKLVVKEALRSRGLKDDTTCLVVDIIPSDH-PVL---LPTPKKKHNMLTTLFF---GKKSENSTNKATSK
          AKLVV.EA..S.GL.DDT.C.VVD.IPSDH.PVL.....T.KK.HN.L..L.F....K...NSTNKATSK
Retrocopy AKLVVEEAIISKGLRDDTSCIVVD-IPSDHLPVLQRNSTTQKKLHNLLKPLLFPFRKKSKKNSTNKATSK

Parental  LSAVGVVEELFEEGSAMLIERLGKDFPFDKNS-EIFRCAICQVDQPPGNGLSVNSGPFFSPASKPWEGPF
          .....VVE.LFEEGS...IER.G.DF....NS..IF.CAICQVDQ.PGNG.S....P..SP...P....F
Retrocopy VGV--VVEDLFEEGS-VFIERFGNDFSLNNNSDQIFSCAICQVDQRPGNGIS---RPLNSPLEVP----F

Parental  LCTNCRNKKDAMEGKRP
          .CTNCR.KK..MEGKRP
Retrocopy FCTNCRKKKVIMEGKRP

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_19 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_7g112430	1 retrocopy	retro_mtru_19 ,