RetrogeneDB ID: retro_mtru_59

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 4:27119019..27119697(+)
• Located in intron of: MTR_4g071660

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_4g103300
• Aliases: None
• Description: None

Sequence

>retro_mtru_59
ATGAACTCTCGAGAAGTTACTCTAGTTGCCACCGCAACTGCGTCCGGAGCATTGGCCTCTGCAATCGCTCTCCATTTCTT
CTACCGCTCTCAAACTCACTCATCCAAAACCAATCCCTCGCAAAACGGCACCATATCTTCTTCTCGCGTTAGAAGTTCTG
GGGACCCTTTTGACCCCACCAAGCGCAAAGGATACTTGTCTTGGGATGATTATTTCATGGCTATTGCGTTTTTGTCTGCT
GAAAGATCCAAAGACCCTAATAGGCAGGTGGGTGCTTGCTTAGTGAGTCAAGATGATATAATTCTCGGCATTGGTTATAA
TGAATTTCCAAGAGGTTGTTCTGATGACAAGTTACCATGGGCCAAGAAATCTAGGACTGGGAATCCTTTGGAGACTAAGT
ACCCTTATGTTTGTCATGCTGAAGTAAATGCTATTCTTAACACAAACCATGCATCTGTGCTGGACAGCGGCTGTATGTGA
CCATGTTTCCTTGCAATGAGTGCGCCAAGATCATAATCCAGTCAGGAGTTTCTGAAGTCATTTATTTTGTGGAGAAGAAA
TTAAGAAAATTCAGATGTTACATATACTGCCTCTCACAAGTTACTTTCATTGGCTGGTGTAAAGGTCAGGAAACTCCAAC
CAGTGATGAGTGAAATTCATCTGAAGTATGAGGATCAC

Alignment

ORF - retro_mtru_59 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MNSREVTLVATATAFGALASAIALHFFYRSQTHSSKTNPSQNGIVSSSSSSSSSRVRSSGDPFDPTKRKG
          MNSREVTLVA..TA....A.A.A...........S.T..S.....S.....SSSRVRSSGDPFDPTKRKG
Retrocopy MNSREVTLVA--TATASGALASAIALHF---FYRSQTHSSKTN-PSQNGTISSSRVRSSGDPFDPTKRKG

Parental  YLSWDDYFMAIAFLSAERSKDPNRQVGACLVSQDDIILGIGYNGFPRGCSDDKLPWAKKSRTGNPLETKY
          YLSWDDYFMAIAFLSAERSKDPNRQVGACLVSQDDIILGIGYN.FPRGCSDDKLPWAKKSRTGNPLETKY
Retrocopy YLSWDDYFMAIAFLSAERSKDPNRQVGACLVSQDDIILGIGYNEFPRGCSDDKLPWAKKSRTGNPLETKY

Parental  PYVCHAEVNAILNTNHAS-AAGQRLYVTMFPCNECAKIIIQSGVSEVIYFVEKKL-ENSDVTYTASHKLL
          PYVCHAEVNAILNTNHAS..AGQRLYVTMFPCNECAKIIIQSGVSEVIYFVEKKL.ENSDVTYTASHKLL
Retrocopy PYVCHAEVNAILNTNHAS<CAGQRLYVTMFPCNECAKIIIQSGVSEVIYFVEKKL>ENSDVTYTASHKLL

Parental  SLAGVKVRKHQPLMSEIHLKYEDH
          SLAGVKVRK.QP.MSEIHLKYEDH
Retrocopy SLAGVKVRKLQPVMSEIHLKYEDH

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_59 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_4g103300	2 retrocopies	retro_mtru_58, retro_mtru_59 ,