RetrogeneDB ID: retro_mtru_20

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 3:46229163..46230480(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_3g100500
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_8g039540
• Aliases: None
• Description: None

Sequence

>retro_mtru_20
ATGAAAATTAAATTGGCTACGGCCTTAATACTTTGCTCTGCAATTTTCATGAGCATGAGCAATGCCACTGATCCATGTGC
ATCTCAACCAGATGACTCCGATCTCAACGTAATTCCCATGTATGGAAAATGCTCACCATTCAACCCACAAAAAACAGACT
CATGGGACAATAGAGTCCTAAACATGGCCTCCAAAGATCCAGCCAGAATGAGCTATCTATCCTCTTTAGTAGCCCAAAAG
ACCGTCTCTTCGGCCCCAATTGCTTCGGGCCAGGCCTTCAACATTGGCAACTACATAGTCCGTGTTAAAATCGGAACACC
CGGTCAACTCCTCTTCATGGTCCTTGACACAAGCACCGACGAGGCTTTTATCCCTAGCTCTGGCTGCATTGGTTGCTCCG
CAACAACTTTCTCACCCAATGCCTCCACCAGTTATGTGCCATTGGAGTGTTCCGTTCCACAATGCAGTCAGGTCCGTGGG
CTCTCATGTCCAGCCACGGGCTCTGGCGCATGTTCCTTCAACAAATCTTACGCAGGTTCGACTTACTCTGCCACACTTGT
TCAAGATTCACTTAGATTAGCTACGGATGTTATCCCTAGCTACTCTTTTGGATCCATCAATGCTATCTCTGGTTCTTCAA
TTCCAGCCCAAGGACTTTTGGGCTTGGGCCGTGGCCCGTTATCTTTATTATCACAAACCGGGTCACTTTACTCGGGTGTA
TTCTCCTACTGCCTTCCAAGTTTCAAATCTTACTATTTTTCCGGGTCACTTAAACTTGGACCCGTGGGTCAACCCAAAAG
CATTCGAACCACACCACTTCTTCGCAATCCTCGCCGTCCATCTCTTTATTTTGTCAATTTAACCGGAATTACCGTGGGAA
AAGTAAATGTACCTTTCCCCAAAGAACTTTTAGCGTTCGACGTGAATACCGGATCCGGAACCATAATTGATTCGGGTACA
GTTATTACCCGTTTTGTGGAACCCGTTTACAACGCGGTTAGGGATGAGTTTAGAAAACAAGTAACCGGACCTTTTTCGAG
CTTAGGAGCATTTGACACATGTTTTGTGAAGAACTATGAAACTTTGGCACCAGCTATTACATTGCATTTCACAGATTTGG
ATCTAAAATTACCATTGGAGAATAGTTTGATCCATAGCAGTTCAGGATCATTGGCTTGTCTTGCAATGGCGTCTACACCA
AAGAATGTGAACTACACTGTGTTGAATGTGATTGCTAATTATCAACAACAGAATTTGAGGGTTTTGTTTGATACCGTGAA
TAATAAGGTTGGTATTGCCCGTGAGCTTTGTAACTAG

Alignment

ORF - retro_mtru_20 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.3 %
• Parental protein coverage: 99.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKIPIFLTPFLLC--LFISLVQAQTPKCDIQDDGSTLKVFHIFSQCSPFKPSKPMSWEESVLNLQAKDQA
          MKI....T...LC...F.S...A..P.C..Q.D.S.L.V......CSPF.P.K..SW...VLN...KD.A
Retrocopy MKIKL-ATALILCSAIFMSMSNATDP-CASQPDDSDLNVIPMYGKCSPFNPQKTDSWDNRVLNMASKDPA

Parental  RMQYFSSLVARKSV--VPIASARQIIQSPTYIVKAKFGTPPQTLLLALDTSSDAAWIPCSGCVGCSTSKP
          RM.Y.SSLVA.K.V...PIAS..Q......YIV..K.GTP.Q.L...LDTS.D.A.IP.SGC.GCS....
Retrocopy RMSYLSSLVAQKTVSSAPIASG-QAFNIGNYIVRVKIGTPGQLLFMVLDTSTDEAFIPSSGCIGCSATT-

Parental  FAPIKSTSFRNVSCGSPHCKQVPNPTC---GGSACAFNFTYGSSSIAASVVQDTLTLATDPIPGYTFGCV
          F.P..STS.....C..P.C.QV....C...G..AC.FN..Y..S...A..VQD.L.LATD.IP.Y.FG..
Retrocopy FSPNASTSYVPLECSVPQCSQVRGLSCPATGSGACSFNKSYAGSTYSATLVQDSLRLATDVIPSYSFGSI

Parental  NKTTGSSAPQQGLLGLGRGPLSLLSQSQNLYKSTFSYCLPSFKSINFSGSLRLGPVYQPKRIKYTPLLRN
          N...GSS.P.QGLLGLGRGPLSLLSQ...LY...FSYCLPSFKS..FSGSL.LGPV.QPK.I..TPLLRN
Retrocopy NAISGSSIPAQGLLGLGRGPLSLLSQTGSLYSGVFSYCLPSFKSYYFSGSLKLGPVGQPKSIRTTPLLRN

Parental  PRRSSLYYVNLVAIKVGRKIVDIPPAALAFNPTTGAGTIFDSGTVFTRLAEPVYTAVRNEFRRRVGPKLP
          PRR.SLY.VNL..I.VG...V..P...LAF...TG.GTI.DSGTV.TR..EPVY.AVR.EFR..V....P
Retrocopy PRRPSLYFVNLTGITVGKVNVPFPKELLAFDVNTGSGTIIDSGTVITRFVEPVYNAVRDEFRKQVTG--P

Parental  VTTLGGFDTCY--NVPIVVPTITFLFSGMNVTLPPDNIVIHSTAGSTTCLAMAGAPDNVN-SVLNVIANM
          ...LG.FDTC...N.....P.IT..F......LP..N..IHS..GS..CLAMA..P.NVN..VLNVIAN.
Retrocopy FSSLGAFDTCFVKNYETLAPAITLHFTDLDLKLPLENSLIHSSSGSLACLAMASTPKNVNYTVLNVIANY

Parental  QQQNHRVLFDVPNSRIGIARELC
          QQQN.RVLFD..N...GIARELC
Retrocopy QQQNLRVLFDTVNNKVGIARELC

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_20 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10,
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20 ,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,