RetrogeneDB ID: retro_mtru_4

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 7:30174702..30175746(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_7g079490
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g461970
• Aliases: None
• Description: None

Sequence

>retro_mtru_4
ATGTCTCAAGTAATTATCAACGACAACGAAGTTGACATTGTGATCGGCGCGCTGCACTCTAACCTCACTCCTTTTATGAA
TGAGTGGAAGTCAATTTTCTCCCGTTTCCACCTGATAATAGTCAAAGATCCTGCCCTCAAGGAAGAACTCCAAATTCCCG
AAGGATTTAGCGCAGATGTCTATACAAACTCTGAAATTGAGCGAGTGGTGGGTTCCTCCACTTCTATTCGCTTCTCTGGT
TACGCTTGTAGATATTTTGGCTTTCTAGTTTCAAAGAAGAAGTATGTTGTCTGTATTGATGATGATTGTGTTCCAGCAAA
AGATGACGCGGGGAATGTAGTAGATGCTGTGGCTCAGCATATTGTGAACCTCAAGACCCCTGCCACACCTTTCTTCTTTA
ATACACTATATGATCCATTCCGTAAGGGTGCAGATTTTGTTCGCGGCTACCCATTTAGCCTCCGAAGTGGGGTTGATTGT
GCTCTGTCGTGTGGACTGTGGCTCAATCTGGCAGACCTAGATGCGCCAACACAGGCTCTCAAGCCAACACAGAGGAATTC
AAGATACGTGGATGCAGTTCTGACCGTTCCTACGAGAGCCATGTTGCCAGTGAGTGGAATCAACATCGCCTTTAACCGAG
AATTAGTTGGCCCGGCTTTGGTCCCAGCTTTGGTGTTGGCAGGAGAAGGAAAACTCAGGTGGGAAACTGTGGAAGATATA
TGGTGTGGATTGTGTGTGAAAATTGTATGTGACCACCTAAGCCTCGGTGTGAAAAGTGGGTTGCCGTATGTTTGGAGAAA
TGAAAGAGGCAATGCCATAGACAGCTTGAAGAAAGAATGGGAAGGGGTGAAATTGATGGAGGACGTTGTTCCTTTCTTTC
AGTCTGTAAAGTTGCCACAATCAGCTACGACGGCCGAGGACTGCGTGATCGAGATGGCAAAATCAGTGAAGGAACAACTT
GGGAAGGTTGATCCTATGTTTTTGAAAGCCGCTGATGCCATGGCAGAGTGGGTTAAGCTCTGGAAGTCAGTTGGATCTGC
TTGA

Alignment

ORF - retro_mtru_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.4 %
• Parental protein coverage: 91.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DELDIVIPTIRN--LDFLEQWRQFFQPYHLIIVQDGDPSKVIKVPEGFDYELYNRNDINRILGPKASCIS
          .E.DIVI.........F...W...F...HLIIV.D.........PEGF....Y....I.R..G...S.I.
Retrocopy NEVDIVIGALHSNLTPFMNEWKSIFSRFHLIIVKDPALKEELQIPEGFSADVYTNSEIERVVGSSTS-IR

Parental  FKDSACRCFGFIVSKKKYIFTIDDDCFVAKDPSGKEIDALQQHIKNLLTPSTPFFFNTLYDPYREGADFV
          F...ACR.FGF.VSKKKY...IDDDC..AKD..G...DA..QHI.NL.TP.TPFFFNTLYDP.R.GADFV
Retrocopy FSGYACRYFGFLVSKKKYVVCIDDDCVPAKDDAGNVVDAVAQHIVNLKTPATPFFFNTLYDPFRKGADFV

Parental  RGYPFSLREGVPTAISHGLWLNIPDYDAPTQLVKPLERNTRYVDAVMTIPKGTLFPMCGMNLAFNRELIG
          RGYPFSLR.GV..A.S.GLWLN..D.DAPTQ..KP..RN.RYVDAV.T.P.....P..G.N.AFNREL.G
Retrocopy RGYPFSLRSGVDCALSCGLWLNLADLDAPTQALKPTQRNSRYVDAVLTVPTRAMLPVSGINIAFNRELVG

Parental  PALYFGLMGEGQPIGRY---DDMWAGWCMKVISDHLGLGVKTGLPYIWHSKASNPFVNLKKEYKGIYWQE
          PAL...L...G....R.....D.W.G.C.K...DHL.LGVK.GLPY.W.....N....LKKE..G....E
Retrocopy PALVPALVLAGEGKLRWETVEDIWCGLCVKIVCDHLSLGVKSGLPYVWRNERGNAIDSLKKEWEGVKLME

Parental  ELIPFFQSVSLPKECTTPQKCYIELSKQVKAKLGLVDDYFNKLADAMVTWIEVW
          ...PFFQSV.LP...TT...C.IE..K.VK..LG.VD..F.K.ADAM..W...W
Retrocopy DVVPFFQSVKLPQSATTAEDCVIEMAKSVKEQLGKVDPMFLKAADAMAEWVKLW

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_4 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_2g461970	1 retrocopy	retro_mtru_4 ,
Prunus persica	PRUPE_ppa007588mg	1 retrocopy	retro_pper_48,
Setaria italica	Si030277m.g	1 retrocopy	retro_sita_19,