RetrogeneDB ID: retro_mtru_11

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: scaffold0003:359255..360290(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_0003s0650
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g021040
• Aliases: None
• Description: None

Sequence

>retro_mtru_11
ATGTCGTTCTCCTTCTATACAACGGCGCAGGAAGTGGTAGAGTCTTTGAAAGAGAGTCTCATGGCACTGAATCCCAAAAC
TCATGTTGAAGATAAAGCCCTTAAGAAAGCTTTAGAGAAAGTTGAAAAGAATTTTGGAACAATGAGAACTATGCTTTCTG
AAAATGGAATATATTCAGAATCGCTGAATTTAGATCGAGTTTCACAGTTTGTCGAAGAAATATGCAAGGCGGATGTTCTT
ACTCTTGTAATTCAAAAGCTGCCTATACTTGGATGGCAAGCTAGAAAGGATTTAGTACACTGTTGGTCAATATTTTTTAA
ACAAAAGGTCGTTGACACCAACGATTATTCGTGCGTGGAATACATCGAACAACACATTGAATTACTAGACTTTCTTCTTG
TTTGCTATGATAAGAATGGAACTGCGCCGAGCTCTGGCATAATGTTGCGGGAATGCATCAAATTTCCTAATCTTGCAAAA
GGCTTATTGGAATCTCCAAGATTTGGGCTGTTCTTTAAATATGTAGATTTGCCTAACTTCGATGTAGCATATGATGCATT
TTCTACATTAAAGGAACTTCTCACTAAACATGTTAATGTGGTCTCTGAGTATTTGAAAACTCACTGTGATGTGTTCTTTG
ATCTATACAATGAGAATCTCTTGAAGTCTCCTAATTATGCCACAAGGAGAGGGTCTATAAATCTTCTCTTGGATATTCTT
TTGGAAACTTCAAAAGAAACTTCTGATGCTCGGATAATGAAGCGATACATCTCACAAGTTCGTTATTTGAAAGTTGTGAT
GACATTGTTGACAGATTCAAGTAAAAAAATTCAGTTATCAGCTTTCGACATTTTCAAGTTTTTCGTTGCGAATCCTAATA
AGCCTCGAGAAGTGAAAATTATTCTATGCAAGAATAAGGAAAAACTGTTAGAATTGCTTCATAAATTATCTCTGGTAAAA
GATTCAAAAGAAGATGAGCAATTTAAGGAGGAAAAGGAGTATATCATCAAAGAAATTGAAAGAATATCAATCTAA

Alignment

ORF - retro_mtru_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.4 %
• Parental protein coverage: 96.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TPQEVVKSIKESLMALDTKTVVEVKALEKALEEVEKNFVTMRTMISGDG--ESEPNLDQVSQLVEEICKE
          T.QEVV.S.KESLMAL..KT.VE.KAL.KALE.VEKNF.TMRTM.S..G......NLD.VSQ.VEEICK.
Retrocopy TAQEVVESLKESLMALNPKTHVEDKALKKALEKVEKNFGTMRTMLSENGIYSESLNLDRVSQFVEEICKA

Parental  DVLTLLIHKLPILGWEARKDLVHCWTILLKQKV-DSND-CCVEYIHQHIELLDFLVACYDNKEIALSSGI
          DVLTL.I.KLPILGW.ARKDLVHCW.I..KQKV.D.ND..CVEYI.QHIELLDFL..CYD....A.SSGI
Retrocopy DVLTLVIQKLPILGWQARKDLVHCWSIFFKQKVVDTNDYSCVEYIEQHIELLDFLLVCYDKNGTAPSSGI

Parental  MLRECIKFPNLAKYILESASFVLFFKYVELPNFDVASDAFSTFKDLLSKHATVVAEFLTAHYDEFFDQY-
          MLRECIKFPNLAK..LES..F.LFFKYV.LPNFDVA.DAFST.K.LL.KH..VV.E.L..H.D.FFD.Y.
Retrocopy MLRECIKFPNLAKGLLESPRFGLFFKYVDLPNFDVAYDAFSTLKELLTKHVNVVSEYLKTHCDVFFDLYN

Parental  EKLLTSPNYVTRRQSIKLLSDFLLE----SPNAQIMKRYILEVRFLKVMMTLLTDSSKNIQLSAFHIFKI
          E.LL.SPNY.TRR.SI.LL.D.LLE.......A.IMKRYI..VR.LKV.MTLLTDSSK.IQLSAF.IFK.
Retrocopy ENLLKSPNYATRRGSINLLLDILLETSKETSDARIMKRYISQVRYLKVVMTLLTDSSKKIQLSAFDIFKF

Parental  FVANPNKPRDVKIILGKNKGKLLELLHNLSPGKGS-EDEQFEEEKEFIIKEIERISV
          FVANPNKPR.VKIIL.KNK.KLLELLH.LS..K.S.EDEQF.EEKE.IIKEIERIS.
Retrocopy FVANPNKPREVKIILCKNKEKLLELLHKLSLVKDSKEDEQFKEEKEYIIKEIERISI

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_11 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_2g021040	1 retrocopy	retro_mtru_11 ,