RetrogeneDB ID: retro_mtru_22

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 4:31294715..31295744(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_4g080990
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_3g100710
• Aliases: None
• Description: None

Sequence

>retro_mtru_22
ATGGAACCAAGTTTTGATTGTGTTGCAAGCCTTCTTTGCACCGAAGAAGATAGCAGTGTTTTCGATGATGTTGAATATGG
TGGTTCGATGGAGGATTACGAAGATTTGTGGCATCCTAGGAACGAACAACGCTCTGGTGGTGTCCCTAATGAGTTGCACT
TGCCATTGCAGAGTGAAGAGTGTTTGGTTCTGATGTTGGAAAAAGAATGTCAACAATGGCATGGTGCTGATTACTTGAAT
AGGTTAAAGTTTGGAGATTTGGATTTTGGTGCAAGAAATGAAGCCATTGATTGGATTCAAAAGGTTCAATCACATTTCGG
TTTTGGTCCGCTTTGTGTTTATCTATCCATTAATTACATGGATCGTTTCCTCTCTGCATATCAATTCCCAGAGAGAAGAG
ATTGGTCAATGCAATTGTTGGCTGTTGCTTGCTTATCTTTGGCAGCCAAAGTAGACGAAACCGATGTTCCTCGGATTCTT
GAATTGCAGATTGGTGAATCCAAGTTTGTGTTTGAAGCAAAAACCATTCAGAAAATAGAGCTTCTGGTACTAACCACATT
GAAGTGGAGAATGCAAGCAATTACTCCTTTCTCCTTCATTGAATATTTCCTTTCTAAGATTAATGATGATAAGAGTTCAT
TGAATAATTCTATAATTTTGCAATGTACTCAACTTATATCAAGCACCATTAAAAGTCCTGACTTCTTGGAATTCAAACCA
TCAGAGATTGCAGCAGCAGTGGCAACATATGTTGTAGAAGAATTTCAAGCAATTGATAGTAGCAAATCAATTTCTACTCT
GATTCAATACATAGAAAAGGAGAGATTATTGAAGTGTGTTGAAAAGGTGCAAGAGATGTGTATTTTCACTGCCAAGGATT
CAAATGCCTCTTCTGTCTCTAGTGTGCTTCAAAGCCCAATGGGTATGTTTGATACATTGCGCTTCCGCTACAAATGTGAT
GACAACAATGCTGGTGTTGATGCTAAGAGAAGGAAGCTAAACAAAAGATGTGGATTAGAGCTTCTGTAG

Alignment

ORF - retro_mtru_22 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 82.6 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YGDSWRPRND--HQMTQQRYDGVPDE--LPLQSEECLVLMLEKECQQWPGADYLNKLRFGDLDFEARNEV
          YG.S.....D..H....QR..GVP.E..LPLQSEECLVLMLEKECQQW.GADYLN.L.FGDLDF.ARNE.
Retrocopy YGGSMEDYEDLWHPRNEQRSGGVPNELHLPLQSEECLVLMLEKECQQWHGADYLNRLKFGDLDFGARNEA

Parental  IDWIQKVRAHFGFGPLCAYLSINYMDRFLSVYEFPKGRAWTMQLLAVACLSLAAKVEETAVPQPLDLQIG
          IDWIQKV..HFGFGPLC.YLSINYMDRFLS.Y.FP..R.W.MQLLAVACLSLAAKV.ET.VP..L.LQIG
Retrocopy IDWIQKVQSHFGFGPLCVYLSINYMDRFLSAYQFPERRDWSMQLLAVACLSLAAKVDETDVPRILELQIG

Parental  ESKFVFEAKTIQRMELLVLSTLKWRMQAITPFSFIECFLSKIKDDDKSSLSSSISRSTQLISSTIKGLDF
          ESKFVFEAKTIQ..ELLVL.TLKWRMQAITPFSFIE.FLSKI.DD..S...S.I...TQLISSTIK..DF
Retrocopy ESKFVFEAKTIQKIELLVLTTLKWRMQAITPFSFIEYFLSKINDDKSSLNNSIILQCTQLISSTIKSPDF

Parental  LEFKPSEIAAAVATCVVGETQAIDSSKSISTLIQYVEKGRLLKCVGKVQEMSLNSVFTGKDSSASSVPSV
          LEFKPSEIAAAVAT.VV.E.QAIDSSKSISTLIQY.EK.RLLKCV.KVQEM.....FT.KDS.ASSV.SV
Retrocopy LEFKPSEIAAAVATYVVEEFQAIDSSKSISTLIQYIEKERLLKCVEKVQEM---CIFTAKDSNASSVSSV

Parental  PQSPMGVLDTLCFSYKSDDTNAG
          .QSPMG..DTL.F.YK.DD.NAG
Retrocopy LQSPMGMFDTLRFRYKCDDNNAG

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_22 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_3g100710	1 retrocopy	retro_mtru_22 ,