RetrogeneDB ID: retro_mtru_9

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:18219458..18222635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_1g048130
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g107440
• Aliases: None
• Description: None

Sequence

>retro_mtru_9
ATGGAAGATCAACCTCCACCTTCAACTCGTCGTTCCAAGAGGGGTAGACCTCTAAAGCAACCGCCAAAGGAAATCGATAC
CGATGTAGATATGGCGGAACATGAAAGTTTGCCGGAAGATTTCGAAGAAGCACGTCCGGTTCCTAAATCGAAGCAAAATC
GTGCTAACAAAGGAACTGCTGGGGCGACGCTTAAACCTACTGATCAGACTTTGTTTGAAACAATCAAAGGTAACGGAAAA
CTTATTCCTCATGTAGTAAAACTTTGGGTTGAAAGCTATGAAAAAGATCCAAAATCTGCTATGGTTGAACTCTTGACAAT
GCTGTTTGAGGTATGTGGAGCCAAATTTCACGACAAAAGGGTTCTCATGCATGAGATTAACGTTAATGATGTTGTTGTTG
CTCTTGTCAACTATGCAAAAAAAAGTGGTGAAGTTGAATGTTATCAAAATTCCATAAAGAAGGAGTTTAAAAACTTGAAA
GAGAATCTAGAATCATTCTGGGATAATTTGGTACGTGAATGTCAGCATGGACCTTTGTTTGACAAAGTTTTATTTGAAAA
GTGCATGAAGTACATCATTGCACTTTCATGCACCCCTCCACGAGTTTATCGTCAAGTTGCTTCATTGATGGGTCTTTCAT
TGATCACATCATATATAACTATTGCTAATATGCTTGCTGTACAACGAGACATTACTCGTAGACAATTGGATGGTCAAAAG
AAGAAAAAATCCGAGGGGCCTCGGATGAAGTCACTAAATATAAAGTTGTCGGATATGCACGATAAAATAACATTGTTGGA
GGAGATGATGGGCAAGATATTTACTGGGTTATTTGTGCATCATTACCGGGACCTTGATCCAAATATTAGAATGTCATGCA
TTGAATCGCTCGGTGTATGGATCCTGTCATACCCATCAATTTTTTTGAAGGATGTATACTTGAAATATCTTGGGTGGACA
CTGAATGACAAATATGCTGGTGTAAGAAAATCTTCAATAAGAGCACTGCAAAATCTCTATGAGATGGATGATAAAGTACC
GTCCCTTGGTTTGTTTACTGAGAGATATTCTGGCCGGATGATTGAGCTTGCTGATGACATTGATGTTGATGTGGCTGTTC
AGGCCATAGGCCTTGTTAAACAACTGATTAGACATCAATTTATTACCGGAGATGAATTAGGTAATTTGTATAATTTGCTG
ACTGATGATCCTCCAGAAATCAGGCATGCCATTGGAGCATTAGTATATGATCACTTGATTGCTAAAAAATTTAATAGCTC
CGAATCAGAATCAAGAGGTGAAAATGACAATTCTTCTAAGGTCCATCTTGAAAGAATGTTGCGGATTCTGGATGAGTTCC
CACCTAATCCAATTTTGACTAGTTGTATGATTGATGATGTGTGGGATTACATGGAAGCTATGAAGGATTGGAAGTGCATC
ATATCCATGCTCCTTGATGAAAATTCATTAATCACCAACGAAAGTAAAACAAACTTGGTTCGTCTCCTATGTGCATCGGT
GAAAAAGGCTGTTGGAGAGAAGATTGTTCCTGCTATTGATAACAGAAAGCAGTACTACAACAAAACCCAAAAAGAAGTAT
TTGAAAATAATAAACACGATATTACTATTGCCATGATGGAGAGTTTCCCATTACTCTTGCAGAAGTTTATTTCGGATGAA
GCTAAAGTGTCATTGCTGGTCGAGATTGTTTTGTATATGAATCTTGAATTTTATTCTTTGAAGAGGCAGGAACAGAATTT
CAAAAATCTCCTCCAGCTTATGAAAAATGCATTTTTTAAGCATGGTGACAAGGAACCTCTGAGAGGTTGTGTGAAGGCAA
TTAATTTCTGTTGTGTAGAAAGTCGAGGGGAATTGCAAGATGTTGCTCGAAACAATTTAAAGGAAGTCGAGGATTTAGTT
ATTGACAAATTGGAATCTGCAATTAGAGAAGTAAAGGCCGGGGGTGATGAATATTCTCTTCTTGTAAATTTGAGAAGGTT
GTATGAACTTCAATTGTCTAAATACGTGCCTATTGATAAACTATATGAAGACATTGTAATGGTGCTACGTGATGTTAGGA
ATATGGAAGATGAGGTTGTTGGTTTGCTGCTTCAGAACTTGTATTTTGATCTGGCTTGGAGTTTGAAGTTTGTACTAGAC
GGAGAAAGTGTTTCGGATGCATCATTAAAGACTCTCCTATCGAAGCGTGATACTTTGTTACAAGAACTTGAATACTTCGT
AAATTTGGTAACTGATGAAAGCAATGAAGGAGATAAAAGTGGAAGTGAACTTGGCGGCAGAGTATGCACAATGCTTGCAG
AAACATGGTGCTTATTTAGGATGACAAATTTTAGTAAGACAGGGCTGGAAAGATTGGGATATCGGCCTAATTCATATGTG
CTTCAAAAGTTCCAGAAACTTTGTCAACAACAGCTAAATGTTTCAGACGAGGTAGAAGATGACGATGTAAACAAAGAGGA
GACAAATAGATGTGCTGTTTTAGTTGGTGCTTGCAAGCTGATTTATACTGATGTTGTCCCAAAGGATTATCTTGCTCCGG
AGATTATTTCGCATTTTGTAATGCATGGAACCGGTGTGGCTGAGATTGTAAAAAACTTGATCACATTTTTGAAAAAAAGA
AAGGATGATTTGGCTGACATTTTTCTTGAAGCACTTAAAAAGGCATACCACCGGCATACTGTCGATAACTCTGGAAATGA
TGATATGTCATCAGAAAACCTTTTCTCAGAATGTAAAAATCTGGCTGTTCAGCTTTCTAGAACCTACATCGGTGGTGCCC
GGAACAAGTACAAGTCAGAAATTTTAAAACTTGTCAAGGATGGTATTGAATATGCTTTTGAAGATGCTCCAAAACATTTG
TCTTTTCTGGAAGCGGCAGTGGTCCATTTTGCGGCAAAACTCCCTGCATCAGATGTGTTGGAAATTAAGAAGGACGTTGA
AAAGAGAACAGAAAATGTAAATAAAGATGAAAATCCCAATGGCTGGCGTCCCTATTGCACATTTGTTGAGGTCTTGCAGG
AAAAAGGCGCGAAGAATGAAGTCTTTCAAATTATAAAAGAAGGGGTTTCTGTTAAGCGTCAGGGTCGTCCACAGGGAAAG
AAGCTTTCTTATGACCATAGCTCAAGTGAAGATGAGGATTCCATTAGTACATCCTAA

Alignment

ORF - retro_mtru_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.77 %
• Parental protein coverage: 92.65 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDQPPPSEVSTRRSKRGRPPKQPPKEIDVDVDMAERESSPEDSDEPRPVQKSKRNRVKEGTTSTTLKPT
          MEDQPPP...STRRSKRGRP.KQPPKEID.DVDMAE.ES.PED..E.RPV.KSK.NR...GT...TLKPT
Retrocopy MEDQPPP---STRRSKRGRPLKQPPKEIDTDVDMAEHESLPEDFEEARPVPKSKQNRANKGTAGATLKPT

Parental  DETLIEAIKGNGKLIPHVVKLWVESYEKDPRSAMVELLTMLFEACGAKFHDKRDLMHEIDVDDVVVALVN
          D.TL.E.IKGNGKLIPHVVKLWVESYEKDP.SAMVELLTMLFE.CGAKFHDKR.LMHEI.V.DVVVALVN
Retrocopy DQTLFETIKGNGKLIPHVVKLWVESYEKDPKSAMVELLTMLFEVCGAKFHDKRVLMHEINVNDVVVALVN

Parental  CAKR-GEVEDYQNSKKKEFKNFKENLESFWDNLVRECQHGPLFDQVLFDKCMDYIIALSCTPPRVYRQVA
          .AK..GEVE.YQNS.KKEFKN.KENLESFWDNLVRECQHGPLFD.VLF.KCM.YIIALSCTPPRVYRQVA
Retrocopy YAKKSGEVECYQNSIKKEFKNLKENLESFWDNLVRECQHGPLFDKVLFEKCMKYIIALSCTPPRVYRQVA

Parental  SLMGLSLVTSYITVANMLGVQRETTRRQLDAEKKKKTEGPRMESLNKRFSDMHEKITLLEEMMRKIFTGL
          SLMGLSL.TSYIT.ANML.VQR..TRRQLD..KKKK.EGPRM.SLN...SDMH.KITLLEEMM.KIFTGL
Retrocopy SLMGLSLITSYITIANMLAVQRDITRRQLDGQKKKKSEGPRMKSLNIKLSDMHDKITLLEEMMGKIFTGL

Parental  FVHRYRDIDPNIRMSCIESLGAWILSYPSLFLQDLYLKYLGWTLNDKNAGVRKTSIRALQNLYEMDDNIQ
          FVH.YRD.DPNIRMSCIESLG.WILSYPS.FL.D.YLKYLGWTLNDK.AGVRK.SIRALQNLYEMDD...
Retrocopy FVHHYRDLDPNIRMSCIESLGVWILSYPSIFLKDVYLKYLGWTLNDKYAGVRKSSIRALQNLYEMDDKVP

Parental  TLGLFTERFSGRMIELADDIDVAVAVQAIGLVKQLFRHQLIPEDDLGNLYDLLIDDPPEIRHAIGALVYD
          .LGLFTER.SGRMIELADDIDV.VAVQAIGLVKQL.RHQ.I..D.LGNLY.LL.DDPPEIRHAIGALVYD
Retrocopy SLGLFTERYSGRMIELADDIDVDVAVQAIGLVKQLIRHQFITGDELGNLYNLLTDDPPEIRHAIGALVYD

Parental  HLIAQKFISSQSESRGENVSPSEVHLTRMLRILDEFPPNPILTIYVIDDVWDYMKAIKDWKCIISMLLDE
          HLIA.KF.SS.SESRGEN...S.VHL.RMLRILDEFPPNPILT...IDDVWDYM.A.KDWKCIISMLLDE
Retrocopy HLIAKKFNSSESESRGENDNSSKVHLERMLRILDEFPPNPILTSCMIDDVWDYMEAMKDWKCIISMLLDE

Parental  NSSITDKSKTNLVRLLCASVKKAVGEKIVPAIDNRKQYHSKAQKEVFENNKQDITVAMMEKYPELLRKFI
          NS.IT..SKTNLVRLLCASVKKAVGEKIVPAIDNRKQY..K.QKEVFENNK.DIT.AMME..P.LL.KFI
Retrocopy NSLITNESKTNLVRLLCASVKKAVGEKIVPAIDNRKQYYNKTQKEVFENNKHDITIAMMESFPLLLQKFI

Parental  SDKAKVSLLVEIVMYMNLEFYSLKRQEQNFKNLLQLMEDAFLKIGDKDPLRACVKAINFCCVESRGELQD
          SD.AKVSLLVEIV.YMNLEFYSLKRQEQNFKNLLQLM..AF.K.GDK.PLR.CVKAINFCCVESRGELQD
Retrocopy SDEAKVSLLVEIVLYMNLEFYSLKRQEQNFKNLLQLMKNAFFKHGDKEPLRGCVKAINFCCVESRGELQD

Parental  FARIKLKKLEVKIIKNLKSAISEVKAGGDEYSLLVNLKRLYELQLSRYVPIDNLYEDIVMVLRDVRNMED
          .AR..LK..E...I..L.SAI.EVKAGGDEYSLLVNL.RLYELQLS.YVPID.LYEDIVMVLRDVRNMED
Retrocopy VARNNLKEVEDLVIDKLESAIREVKAGGDEYSLLVNLRRLYELQLSKYVPIDKLYEDIVMVLRDVRNMED

Parental  EVVGLLLQNMHIHLAWSLQSVIDGESVSDASLTSLRSKRDTLLQELEYYVNLATD-SNEVDKIGSELAGR
          EVVGLLLQN....LAWSL..V.DGESVSDASL..L.SKRDTLLQELEY.VNL.TD.SNE.DK.GSEL.GR
Retrocopy EVVGLLLQNLYFDLAWSLKFVLDGESVSDASLKTLLSKRDTLLQELEYFVNLVTDESNEGDKSGSELGGR

Parental  VCAVLAEAWCLFRMANFSKTGLEGLGYQPNAHVLQKFWELCQQQLTVPDEVEDDDVNKDVTTEYSEETDR
          VC..LAE.WCLFRM.NFSKTGLE.LGY.PN..VLQKF..LCQQQL.....V.D.....DV.....EET.R
Retrocopy VCTMLAETWCLFRMTNFSKTGLERLGYRPNSYVLQKFQKLCQQQLN----VSDEVEDDDVN---KEETNR

Parental  CAVLIAACKLISSDVVPKDYLAPEIISHFVMHGARVAEIVKHLITFLKKGEDDLAAIFLEALKKAYHRHI
          CAVL..ACKLI..DVVPKDYLAPEIISHFVMHG..VAEIVK.LITFLKK..DDLA.IFLEALKKAYHRH.
Retrocopy CAVLVGACKLIYTDVVPKDYLAPEIISHFVMHGTGVAEIVKNLITFLKKRKDDLADIFLEALKKAYHRHT

Parental  VDNSGNDNISSENSFSECKNLAVQLSGTFIGAARNKYKSDILKLVKDGIEYAFVDAPKQLSFLEAAVVHF
          VDNSGND..SSEN.FSECKNLAVQLS.T.IG.ARNKYKS.ILKLVKDGIEYAF.DAPK.LSFLEAAVVHF
Retrocopy VDNSGNDDMSSENLFSECKNLAVQLSRTYIGGARNKYKSEILKLVKDGIEYAFEDAPKHLSFLEAAVVHF

Parental  VSKLPASDVLEIKKDVEKRTENVNKDENPSGWRPYCTFVEVLREKCVKNEVFQDEKEGVSVKRRGRPR
          ..KLPASDVLEIKKDVEKRTENVNKDENP.GWRPYCTFVEVL.EK..KNEVFQ..KEGVSVKR.GRP.
Retrocopy AAKLPASDVLEIKKDVEKRTENVNKDENPNGWRPYCTFVEVLQEKGAKNEVFQIIKEGVSVKRQGRPQ

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_9 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_7g107440	1 retrocopy	retro_mtru_9 ,