RetrogeneDB ID: retro_mtru_28

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:48752881..48754015(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_1g107455
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_4g056100
• Aliases: None
• Description: None

Sequence

>retro_mtru_28
ATGTCTTCTTCTTCTTCAACAAGACTTGATCTAGACGGCAACTCAATCAAGCCGATAACAATCTGTATTATTGGCGCCGG
AGGTTTCATTGGTTCTCACCTCTGTGAGAAGCTCATGTTACAAACACCTCACAAAGTTATAGCTCTGGACGTTTACAAGA
ACAAACTAAAACACCTTCTGGAACCCGAAACCCTTCCTTGGAACAATCGCTTTGAGTTTCATCGTTTGAATGTAAAAAAC
GATTCCAGACTCGAAGGTCTCATCAAAACCGCAGATTTGGTCATCAACCTTGCTGCAATCTGCACTCCTGCTGATTACAA
CACTCGTCCTCTTGACACGATTTACAGTAACTTCATTGATGCGATTCCAGTGGTGAAATATTGTTCAGAAAACAACAAGA
GGCTAGTTCACTTCTCTACTTGTGAAGTGTATGGGAAAACTATTGGTAGTTTTCTCCCTAAAGATAGTCCTCTTCGTCAA
GATCCTGCTTACTATATGCTCAAAGAAGATGAATCTCCGTGCATTTTTGGTCCGATCGAAAAGCAAAGATGGTCATATGC
ATGTGCTAAGCAATTGATTGAGAGGTTGATTTATGGAGAAGGTGATGAAAATGGGTTGGAATTTACAATTGTGAGACCTT
TTAATTGGATTGGACCGAGAATGGATTTCATTCCTAGTGTTGATGGTCCAAGTGAGGGAGTTCCTAGGGTTCTTGCTTGC
TTCAGCAACAATCTTCTTCGAGGAGAGCCGTTGAAGCTTGTGGATGGTGGTGAGTCTCAGAGGACTTATCTTTATATCAA
AGATGCTATTGAAGCAGTGTTGTTGATGATTGAAAACCCTGCTAGAGCTAATGGGAAGATATTTAATGTGGGTAACCCGA
ACAATGAGGTTACGGTTCGGGAGCTGGCTGAAATGATGATCAAGGTTTATTCAAAGGTAAGTGGTGATCAACCTCTTGAA
ACACCTACAGTTGATGTGAGCTCGAAAGAATTTTACGGTGAGGGATATGATGATAGTGACAAGAGAATTCCTGACATGAC
CATCATCAACAAGCAGCTTGGATGGAATCCAAAGACTTCACTTGAAGACCTGCTTGAATCCACACTTACCTATCAGCACA
AAGACATATGCTGA

Alignment

ORF - retro_mtru_28 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.04 %
• Parental protein coverage: 95.9 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASPSSTRIDLDGNPIKPLTICMIGAGGFIGSHLCEKLMSETSHKVLALDVYNDKIKHLLEPESLPWNGR
          M.S.SSTR.DLDGN.IKP.TIC.IGAGGFIGSHLCEKLM..T.HKV.ALDVY..K.KHLLEPE.LPWN.R
Retrocopy MSSSSSTRLDLDGNSIKPITICIIGAGGFIGSHLCEKLMLQTPHKVIALDVYKNKLKHLLEPETLPWNNR

Parental  IHFHRLNIKNDSRLEGLIKMADLVINLAAICTPADYNTRPLDTIYSNFIDALPVVKYCSETNKRLIHFST
          ..FHRLN.KNDSRLEGLIK.ADLVINLAAICTPADYNTRPLDTIYSNFIDA.PVVKYCSE.NKRL.HFST
Retrocopy FEFHRLNVKNDSRLEGLIKTADLVINLAAICTPADYNTRPLDTIYSNFIDAIPVVKYCSENNKRLVHFST

Parental  CEVYGKTIGSYLPKDSPLRQDPAYYMLKEDVSPCIFGSIEKQRWSYACAKQLIERLVYAEGAENGLEFTI
          CEVYGKTIGS.LPKDSPLRQDPAYYMLKED.SPCIFG.IEKQRWSYACAKQLIERL.Y.EG.ENGLEFTI
Retrocopy CEVYGKTIGSFLPKDSPLRQDPAYYMLKEDESPCIFGPIEKQRWSYACAKQLIERLIYGEGDENGLEFTI

Parental  VRPFNWIGPRMDFIPGIDGPSEGVPRVLACFSNNLLRGEPLKLVDGGESQRTFVYIKDAIEAVLLMIENP
          VRPFNWIGPRMDFIP..DGPSEGVPRVLACFSNNLLRGEPLKLVDGGESQRT..YIKDAIEAVLLMIENP
Retrocopy VRPFNWIGPRMDFIPSVDGPSEGVPRVLACFSNNLLRGEPLKLVDGGESQRTYLYIKDAIEAVLLMIENP

Parental  ARANGHIFNVGNPNNEVTVRQLAEMMIQVYSKVSGTQPPETPTIDVSSKEFYGEGYDDSDKRIPDMTIIN
          ARANG.IFNVGNPNNEVTVR.LAEMMI.VYSKVSG.QP.ETPT.DVSSKEFYGEGYDDSDKRIPDMTIIN
Retrocopy ARANGKIFNVGNPNNEVTVRELAEMMIKVYSKVSGDQPLETPTVDVSSKEFYGEGYDDSDKRIPDMTIIN

Parental  KQLEWNPKTSLWDLLESTLTYQHR
          KQL.WNPKTSL.DLLESTLTYQH.
Retrocopy KQLGWNPKTSLEDLLESTLTYQHK

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_28 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_4g056100	1 retrocopy	retro_mtru_28 ,