RetrogeneDB ID: retro_mtru_3

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 3:13609402..13610344(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_3g037190
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g091230
• Aliases: None
• Description: None

Sequence

>retro_mtru_3
ATGTCCGACGCATTTTGCAGTGACTGCAAGCGAGCGACGGAGGTGGTGTTTGACCGCTCCGCTGGTGATGCAATCTGTTC
GGAGTGTGGTCTCGTCTTGGAATCACACTCCATTGATGAAACCTCCGAATGGCGAACCTTTGCTAACGAATCCGGCAATA
ATGATGCCGTTCGTGTCGGTGGTCCCAATAACCCTCTCCTCAACGATGGTGGTCTCTCCACCGTCATTGCTAAGCCGAAT
GGAGAGTCCGTTGATTTTCTCTCATCGGCTGTTAATCGTTGGCAGAAACATGGTTCTAATCCCGATCGTGGATTGATCCT
TGCGTTCAAAACTATTGATACTATGGCTGAGAGGTTGGGACTGGTTCCGATCATTAAGGACCGAGCTAATGAGATATATA
AGCGGGTTCAAGATCAGAAGTCTAGTAGGGGAAGAAATCAAGACGCATTATTGGCTGCTTGCCTCTACATTGCTTGTCGA
CAAGAAGACAAGCCACGCACTGTAAAGGAAATTTGCTCGGTTGCCAATGGAGCCACAAAGAAGGAAATTGGCCGTGCAAA
AGAATACATAGTGAAACAACTTGGTTTGGAGAATGGTGGTCAATCTGTAGAAATGGGAACAATTCATGCTGGGGACTTTA
TGAGACGATTTTGTTCTAATCTTGGTATGAATCATCAAGCTGTTAAAGCTGCTCAGGAATCTGTTAAGAAATCAGAGGAA
TTTGATATAAGGAGAAGTCCCATAACAATTGCTGCAGCAGTTATATACATCATTACTCAGCTTTCTGATGATAAAAAACC
TCTGAAAGATATATCAGTTGCTACCGGAGTCGCAGAAGGAACCATTAAGAACTCGTACAAGGATCTCTATCCCCATGTTT
CAAAGATAATACCAACCTGGTATGCGGAGGAAGAGGATCTCAAGAACCTTTGCAACCCTTGA

Alignment

ORF - retro_mtru_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.65 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSDAFCSDCKRATEVVFDHSAGDAVCSECGLVLESHSIDETSEWRTFANESGDNDPVRVGGPSNPLLTDG
          MSDAFCSDCKRATEVVFD.SAGDA.CSECGLVLESHSIDETSEWRTFANESG.ND.VRVGGP.NPLL.DG
Retrocopy MSDAFCSDCKRATEVVFDRSAGDAICSECGLVLESHSIDETSEWRTFANESGNNDAVRVGGPNNPLLNDG

Parental  GLSTVIAKPNGASGDFLSSSLGRWQNRGSNPDRGLILAFKTIGTMAERLGLVPTIKDRANEIYKRVEDQK
          GLSTVIAKPNG.S.DFLSS...RWQ..GSNPDRGLILAFKTI.TMAERLGLVP.IKDRANEIYKRV.DQK
Retrocopy GLSTVIAKPNGESVDFLSSAVNRWQKHGSNPDRGLILAFKTIDTMAERLGLVPIIKDRANEIYKRVQDQK

Parental  SSRGRNQDALLAACLYIACRQEDKPRTVKEICSIANGATKKEIGRAKEYIVKQLGLENGGQSVEMGTIHA
          SSRGRNQDALLAACLYIACRQEDKPRTVKEICS.ANGATKKEIGRAKEYIVKQLGLENGGQSVEMGTIHA
Retrocopy SSRGRNQDALLAACLYIACRQEDKPRTVKEICSVANGATKKEIGRAKEYIVKQLGLENGGQSVEMGTIHA

Parental  GDFMRRFCSNLGMNHQAVKAAQESVQKSEEFDIRRSPISIAAAVIYIITQLSDDKKPLKDISVATGVAEG
          GDFMRRFCSNLGMNHQAVKAAQESV.KSEEFDIRRSPI.IAAAVIYIITQLSDDKKPLKDISVATGVAEG
Retrocopy GDFMRRFCSNLGMNHQAVKAAQESVKKSEEFDIRRSPITIAAAVIYIITQLSDDKKPLKDISVATGVAEG

Parental  TIRNSYKDLYPHVSKIIPNWYAKEEDLKNLCSP
          TI.NSYKDLYPHVSKIIP.WYA.EEDLKNLC.P
Retrocopy TIKNSYKDLYPHVSKIIPTWYAEEEDLKNLCNP

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_3 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Brachypodium distachyon	BRADI4G36290	1 retrocopy	retro_bdis_39,
Aegilops tauschii	F775_29675	1 retrocopy	retro_atau_5,
Hordeum vulgare	MLOC_10647	1 retrocopy	retro_hvul_45,
Medicago truncatula	MTR_7g091230	2 retrocopies	retro_mtru_26, retro_mtru_3 ,
Sorghum bicolor	Sb02g031020	1 retrocopy	retro_sbic_35,