RetrogeneDB ID: retro_mtru_87

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: scaffold1739:271..1378(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g099040
• Aliases: None
• Description: None

Sequence

>retro_mtru_87
GAAATTATGAAATCACGTGCAGCTGTTGCCTTTGGGCCGGGTAAGCCACTTGAAATCGTCGAGATCGACGTAGAACCGCC
CCGTAAGGGTGAGGTGCTTGTGAAGATCACGCACACCGGTGTGTGCCATACCGACGCGTTCACTCTTTCCGGCGACGATC
CGGAAGGCGTCTTCCCGGCTGTCCTCGGCCATGAAGGAGCGGGTGTGGTTGTTGAGGTGGGTGAGGGCGTCACCAGCGTG
AAGCCGGGCGATCATGTGATCCCTCTCTATACGGCTGAGTGTGGCGAATGCCTGTTCTGCAAGTCGGGAAAAACCAACCT
CTGTACTGCAGTTCGTGCCACTCAGGGTAAGGGGTTGATGCCCGACGGTACGACCCGCTTCTCGTATAACGGGCAGCCGC
TTTTCCACTATATGGGTTGCTCTACCTTCAGTGAGTACACCGTGGTGGCGGAAGTTTCGCTCGCGAAGATCAATCCGCAA
GCCAATCACGAGCATGTATGTTTGCTCGGTTGTGGCGTCACCACCGGCATCGGTGCCGTTCATAACACTGCCAAGGTTCA
GCCTGGCGATTCGGTGGCCGTCTTTGGTCTCGGGGGCATCGGCCTTGCCGCAATCCAGGGAGCGCGTCAGGCGAAAGCTG
GCCGCATTATCGCAATCGATACCAATCCGGAAAAGTTCGAGCTTGCTCGGGCGTTCGGTGCGACCGATTGCGTGAATCCG
AAAGACTTCCAGAAGCCGATCCAGGAGGTCCTCATCGAGATGACGGGCTGGGGTGTGGACCACACCTTTGAATGCATCGG
AAACGTGAATGTCATGCGGGCGGCGCTTGAGGCGGCGCATCGCGGTTGGGGGCAGTCAATCGTGATCGGTGTTGCGGGTG
CTGGTAAGGAGATTTCCACCCGACCGTTCCAGCTGGTTACGGGCCGTGTCTGGAAGGGGTCTGCGTTCGGTGGCGTCAAG
GGGCGTACTCAGCTTCCCGGTATGGTCGAAGACGCGATGAAGGGCGAAATTGATCTCGCACCTTTCGTCACCCATACCAT
GGGGCTTGACGATATCAACGAAGCCTTCGACCTGATGCACGAAGGTAAGTCAATCCGCACGGTCATT

Alignment

ORF - retro_mtru_87 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.35 %
• Parental protein coverage: 97.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QVITCKAAVAWEPNKPLTIEDVEVAPPQANEVRIQILFTALCHTDAYTWSGKDPEGLFPCILGHEAAGIV
          ......AAVA..P.KPL.I....V.PP...EV...I..T..CHTDA.T.SG.DPEG.FP..LGHE.AG.V
Retrocopy EIMKSRAAVAFGPGKPLEIVEIDVEPPRKGEVLVKITHTGVCHTDAFTLSGDDPEGVFPAVLGHEGAGVV

Parental  ESVGEGVTDVKPGDHVIPCYQAECGECKFCKSGKTNLCGKVRAATGVGVMMNDRKPRFSIKGKPIYHFMG
          ..VGEGVT.VKPGDHVIP.Y.AECGEC.FCKSGKTNLC..VRA..G.G..M.D...RFS..G.P..H.MG
Retrocopy VEVGEGVTSVKPGDHVIPLYTAECGECLFCKSGKTNLCTAVRATQGKG-LMPDGTTRFSYNGQPLFHYMG

Parental  TSTFSQYTVVHDVSVAKIHPDAALDKVCLLGCGVPTGLGAVWNTAKVEPGSIVAIFGLGTVGLAVAEGAK
          .STFS.YTVV..VS.AKI.P.A....VCLLGCGV.TG.GAV.NTAKV.PG..VA.FGLG..GLA...GA.
Retrocopy CSTFSEYTVVAEVSLAKINPQANHEHVCLLGCGVTTGIGAVHNTAKVQPGDSVAVFGLGGIGLAAIQGAR

Parental  SAGASRIIGIDIDSNKFDTAKNFGVTEFINPKDHEKPIQQVISDLTDGGVDYSFECIGNVSVMRSALECT
          .A.A.RII.ID....KF..A..FG.T...NPKD..KPIQ.V....T..GVD..FECIGNV.VMR.ALE..
Retrocopy QAKAGRIIAIDTNPEKFELARAFGATDCVNPKDFQKPIQEVLIEMTGWGVDHTFECIGNVNVMRAALEAA

Parental  HKGWGTSVVVGVAASGQEISTRPFQLVTGRVWKGTAFGGFKSRSQVPWLVEKYLKKEIKVDEYVTHNLTL
          H.GWG.S.V.GVA..G.EISTRPFQLVTGRVWKG.AFGG.K.R.Q.P..VE...K.EI.....VTH...L
Retrocopy HRGWGQSIVIGVAGAGKEISTRPFQLVTGRVWKGSAFGGVKGRTQLPGMVEDAMKGEIDLAPFVTHTMGL

Parental  AEINEAFDLMHEGKCLRCVL
          ..INEAFDLMHEGK..R.V.
Retrocopy DDINEAFDLMHEGKSIRTVI

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_87 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 2 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g099040	2 retrocopies	retro_mtru_86, retro_mtru_87 ,
Triticum aestivum	Traes_6DL_FD8A6A45F	4 retrocopies	retro_taes_174, retro_taes_182, retro_taes_183, retro_taes_198,