RetrogeneDB ID: retro_mtru_41

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 6:26536123..26537866(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_6g071555
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_1g090110
• Aliases: None
• Description: None

Sequence

>retro_mtru_41
ATGTCTTCGTCGGTGCAACAAGTTGTCAAGCGTGCCAAATATAAATCCACCGTGAAAGATCCTGGTACTCCTGGTGTTAT
CAAATTGACTCGACCGAAACTTGTTTTCAAGCCTAATGATCCAACATCAAACAACAAGCTTGACGTTGATTTCAGATTAA
TCAAAAGTCAAAAAAACACCAAAGAGGGGTCAAACAAACAAACGTGGCTTAAGCTTTTACATTCTCAAGGCAGTTACATC
TTTGAGTTTGAAAGCTTTTCGGATCTTCATGTTTGCCGGGAATTCGCTGCTGGTATTATTAGCAAGCCTGTAGAAGCTCC
AAAAGTTGTTTCAGATGAACAACTTAGCACTGCTGAAATGACACTGAGGATAAAGCTATTGGGAGAAGATAGTAAATTGA
AGAAGATTCATAAGGAACTTGTGATGAGTGATAAGCTTACAGAATCAGAATTTTGGGCTACAAAGAAGAAATTGCTCGAC
CAAGATGAAAGCCGAAAGTTAACACAAAGGATTGGATTTAAAAATTGTTTGATCTTCGACACAAAGCCTACTACTAGTGA
CGGTCGGATAAATATAGTTAAATTTCAATTGACTCGAGAAATAAAATATCAGATTTTTGCTCTCAAACCAGCAATTCACC
AGGCATTCCTCAATTTTGTACCGAGTAACATGAGCGAGGTAGATTTCTGGAACAAATACTTCAAAGCTGAATATCTCCAT
AGTACCAAAAATGCTATTGCAGCAGCTGCTGAGGCTGCTGAAGATGAGGATCTTGCTGTTTTTTTGAAAGATGACGAGAT
ATTAAAAAATGAAGCTCGAAAGAAGGTTCGACGGATTGATCCAACTTTAGACATGGAAGCAGACCAAGGAGATGATTACA
CTCATCTTCCTGACCACGGGATCTTCCGTGATGGTTGCAAGGAAACATCTGAAGCTCAAAATACTCTTTATCGAAGAACG
TTGTTGCAAGATCTCAACAGACAAAGTGAGGTGGTTCTTGAAGGAAAAACTTTAGATATAGATATGGAACATCCAAGAAC
AGAAGTAGAAGTGCTTGCTCGGAGAAAACATGAATCTGATGGGGTTGTGGAGGAGAGGCGAAACAGAATTTCTAAGACAG
CCCAGATTGAAGATCTTCAGGCACAAGATAATCATCCATTTGTACCACTTTGTATCAAGGATCCTCGTGACTATTTTGAT
TCTCAACAAGCTAACGTAGTAAAAACCTTTGATGAGTCCCTAGCCGATAAGGAGAAAATAAGACGCAATTTGGGTTCTGA
GGAAGCCTATGACTCTTTGAGGGAGTCCATATCTAACATCAAAACTATGGGATTAAGGGATCCTCTATTGAGTCATAAGG
TTGCTTTTAAGGTCCTTACTGTATTGAATAAAAGCATCTCAAGCACAACTAAGGAGTGTGTCCTTGATATTTTACCCAAC
TCAACTAAGGAGAAACTACTAGATCATTGGGTTTGTAGTCAGGAATTACTGAGGCACTTTTGGTCTTCTTATCCAGTATC
AACACAAAGTCTTGTTAGTAAGGCTACAAGACTGAAAGACGCCATATCACAAATATATTCTAAACTTGAGGAAATAAAGG
TATCTGCACAGTCGAACCTACGGGACCAGGTTTCCCTTGTTGTCGATCCAATGCAGCAGGCTCTGGATGCTGCTTTGTTA
CATTACGATGCTGACATTCGGAGAAGAAATGATAAAGGGTCGAAGCCTAATGGTTATGTTTAG

Alignment

ORF - retro_mtru_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.32 %
• Parental protein coverage: 79.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSSVQQVVKRAKYKSTVKDPGTPGVIKLTRQKVVFKPNDPTSNNKLDVDFRLIKSQKNTKEGSTKPPWL
          MSSSVQQVVKRAKYKSTVKDPGTPGVIKLTR.K.VFKPNDPTSNNKLDVDFRLIKSQKNTKEGS.K..WL
Retrocopy MSSSVQQVVKRAKYKSTVKDPGTPGVIKLTRPKLVFKPNDPTSNNKLDVDFRLIKSQKNTKEGSNKQTWL

Parental  NLVHSQGSYIFEFESFSDLHVCREFAAGIISKPVEAPKVVSDEQLSTAEMTLRMKLLGEDSKLKKIHMEL
          .L.HSQGSYIFEFESFSDLHVCREFAAGIISKPVEAPKVVSDEQLSTAEMTLR.KLLGEDSKLKKIH.EL
Retrocopy KLLHSQGSYIFEFESFSDLHVCREFAAGIISKPVEAPKVVSDEQLSTAEMTLRIKLLGEDSKLKKIHKEL

Parental  VMSDKLTESEFWATKKKLLDQDESRKLKQRIGFKNSLIFDTKPT-SDGRINQVKFQLTPEIKYQIFALKP
          VMSDKLTESEFWATKKKLLDQDESRKL.QRIGFKN.LIFDTKPT.SDGRIN.VKFQLT.EIKYQIFALKP
Retrocopy VMSDKLTESEFWATKKKLLDQDESRKLTQRIGFKNCLIFDTKPTTSDGRINIVKFQLTREIKYQIFALKP

Parental  AVHQAFLNFVPSKMSEVDFWNKYFKAEYLHSTKNAIAAAAEAAEDEDLAVFLKDDEILENEARKKVRRVD
          A.HQAFLNFVPS.MSEVDFWNKYFKAEYLHSTKNAIAAAAEAAEDEDLAVFLKDDEIL.NEARKKVRR.D
Retrocopy AIHQAFLNFVPSNMSEVDFWNKYFKAEYLHSTKNAIAAAAEAAEDEDLAVFLKDDEILKNEARKKVRRID

Parental  PTLDMEADQGDDYTHLPDHGIFRDGSKETSEAQNTLYRRTLLQDLNRQSEVVLEGKTLDIDMEHPRTAVE
          PTLDMEADQGDDYTHLPDHGIFRDG.KETSEAQNTLYRRTLLQDLNRQSEVVLEGKTLDIDMEHPRT.VE
Retrocopy PTLDMEADQGDDYTHLPDHGIFRDGCKETSEAQNTLYRRTLLQDLNRQSEVVLEGKTLDIDMEHPRTEVE

Parental  ALARRKHESDGVVEERRNRISKMAQIEDLQAQDDHPFAPLCIKDPRDYFDSQQANAVKTLDDSLSGKEKI
          .LARRKHESDGVVEERRNRISK.AQIEDLQAQD.HPF.PLCIKDPRDYFDSQQAN.VKT.D.SL..KEKI
Retrocopy VLARRKHESDGVVEERRNRISKTAQIEDLQAQDNHPFVPLCIKDPRDYFDSQQANVVKTFDESLADKEKI

Parental  RCNLGSEEAYGSLRESISNIKTMGLRDPLLSHEVAFKVLSELTKNISST
          R.NLGSEEAY.SLRESISNIKTMGLRDPLLSH.VAFKVL..L.K.ISST
Retrocopy RRNLGSEEAYDSLRESISNIKTMGLRDPLLSHKVAFKVLTVLNKSISST

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_41 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_1g090110	1 retrocopy	retro_mtru_41 ,