RetrogeneDB ID: retro_mtru_45

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 7:38356263..38359452(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_7g095710
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_4g008170
• Aliases: None
• Description: None

Sequence

>retro_mtru_45
ATGTCTAATAATCATAATCTACAATATGATGGTACCTCATTTATCATTGACATCACCAATACCCTCGCCAAAGTCACTTC
CAAATACACCAATGCAAAAAGAAGGTGGCGTTTTGCATACACAGCTATTTATTCTAGAAGGGTTATGCTTTCCCTTGCAA
AAGAGGTTATATCTAGAAAAAACTCTAACCCTTACACAAAACTCTTTCACACAGAATCTTCAAGTTCCACCACTACTCTT
GATATAATTGAACCACTAATTACACAACATAATGGAACCAATCATTACTCTTTGGTTTCTGATGTTGTTGTTGATAAGAC
CAAACTTGCTGATATGGTTAAGGACAAAAACTTGAAGTCCTTAAGTGAGTTTGGTGGAGTTGAAGGTGTTGGACATGTTC
TTGGAACATTTCCAACAAAGGGAATTATTGGAAGTGACGATGATATTTCGAGACGGCTCGAGTTGTTCGGTTCAAATACT
TACAAAAAACCACCACCAAAAGGTCTTTTACATTTTGTGCTTGAAGCTTTCAATGATACAACAATTATCATTCTTCTTGT
TTGTGCTGGTCTTTCCCTTGGTTTTGGTATTAAAGAACATGGACCAGGGGAAGGTTGGTATGAAGGTGGAAGTATATTTC
TAGCAGTTTTTCTTGTTGTGGTTGTAAGTGCACTAAGCAATTTTAGACAAGAAAGACAATTTCACAAATTGTCTAAGATA
AGCAACAATATCAAAGTTGAAGTTGTGAGAAATGGAAGGCCACAACAGATATCAATTTTTGATGTTCTTGTGGGAGATAT
TGTGTCTCTCAAGATTGGTGATCAAATTCCGGCTGATGGAGTATTTTTATCCGGTTATTCGTTGCAAGTGGACGAATCTA
GCATGACAGGTGAGAGCGACCATGTAGAGATTGAGCCTTTAAGAGCTCCTTTTTTGTTGTCCGGCGCAAAAGTTGTGGAT
GGATATGCTCAGATGCTTGTAACATCTGTGGGCAAAAACACATCATGGGGACAAATGATGAGCTCGATATCGCGAGACAC
TAATGAAAGAACGCCGTTACAAGCACGCCTCGACAAGTTAACCTCTTCGATTGGAAAGGTTGGACTTGCAGTAGCGTTTC
TTGTACTTCTAGTGTTGTTAATTCGTTATTTCACAGGTAACTCACATGATGAGAAAGGGAATAAGGAATTTCGAGGAAGC
AAAACCGATATAAATGATGTTATGAATTCTGTTGTGAGTATCGTTGCGGCTGCAGTCACTATTGTGGTCGTTGCCATCCC
TGAGGGTTTGCCATTGGCTGTGACACTAACTCTTGCTTACTCCATGAAAAGAATGATGGCAGATCATGCTATGGTGAGGA
AACTTTCAGCTTGTGAAACTATGGGATCAGCAACAGTTATCTGCACTGATAAAACAGGTACCTTGACATTGAATCAAATG
AGGGTGACCAAGTTTTGTCTTGGTCCTGAAAATATTATAGAAAATTTTTCCAATGCAATGACACCAAAAGTTCTTGAGTT
GTTCCATCAAGGGGTAGGGCTCAATACAACTGGTAGTGTCTACAATCCTCCATCTGGTTCTGAACCTGAAATTTCAGGGA
GTCCAACGGAGAAAGCTATACTCATGTGGGCAGTATTGGATTTGGGTATGGACATGGATGAAATGAAACAGAAGCATAAA
GTCCTTCATGTTGAAACATTTAACTCGGAGAAGAAACGAAGCGGTGTTGCTATAAGGAAAGAGAACGACGACAACAGCGT
TCACGTGCATTGGAAAGGAGCTGCAGAGATGATACTTGCAATGTGTACAAACTATATTGATAGTAACGGCGCGAGGAAGT
CCCTTGATGAAGAAGAACGGAGTAAAATTGAGAGAATCATTCAAGTTATGGCTGCTAGTAGTCTAAGATGTATTGCTTTT
GCTCACACGGAGATTTCAGATTCCGAAGATATTGATTATATGATCAAAAGGGAGAAAAAATCACATCAAATGCTTAGAGA
AGATGGATTGACATTGCTTGGCATCGTTGGCCTCAAGGATCCATGCAGACCAAACACTAAGAAAGCTGTGGAAACTTGCA
AAGCTGCAGGAGTTGAAATTAAGATGATCACCGGCGATAACATATTCACTGCTAAGGCAATAGCAATAGAATGTGGAATA
TTAGATTCTAATAGTGATCATGCAAAAGCTGGAGAAGTGGTGGAAGGTGTTGAATTCAGAAGCTATACAGAGGAAGAGAG
AATGGAAAAAGTCGATAATATCCGAGTAATGGCAAGATCATCCCCTATGGACAAACTTTTGATGGTGCAATGCTTAAGAA
AGAAAGGTCATGTAGTTGCGGTCACAGGCGACGGCACAAACGATGCACCTGCCTTAAAAGAAGCTGATATAGGACTTTCT
ATGGGAATCCAAGGAACCGAAGTCGCCAAAGAAAGTTCCGATATCGTCATCTTAGACGACAACTTCAATTCTGTTGCAAC
TGTTTTAAGGTGGGGAAGATGTGTTTACAACAACATCCAGAAATTTATTCAGTTTCAACTAACAGTGAATGTTGCAGCAC
TTGTGATAAACTTTATTGCAGCAGTTTCTTCTGGTGATGTTCCCTTAACAACAGTTCAACTTCTTTGGGTGAATCTCATT
ATGGATACACTAGGTGCTTTGGCACTAGCAACAGAAAGGCCTACAAAGGAGTTAATGAAGAAAAAGCCGATAGGTCGTAC
CGCGCCTCTAATTACAAACATTATGTGGAGAAACCTTCTAGCTCAAGCTTCATATCAGATTGCAGTTCTTCTGATTATGC
AGTTTTATGGAAAATCAATCTTCAATGTAAGTAAGGAGGTAAAGGATACACTAATTTTTAATACTTTTGTTCTCTGCCAA
GTTTTCAACGAATTCAACTCAAGAAGCATGGAGAAACTTTATGTATTTGAAGGGATTCTTAAAAACCACTTGTTTCTTGG
AATTATTGGTATTACTATTGTTCTTCAAATCCTGATGGTGGAACTGCTAAGGAAATTTGCTGATACAGAAAGATTAACAT
GGGAGCAATGGGGAATTTGTATTGGAATTGCAGTTGTTTCATGGCCACTTGCTTGCTTAGTAAAGCTCATACCTGTTTCA
GATAAACCTTCATTCAGTTATACTAAGTGGGTTAAATTATTAGTCTTCAAGATTAAGAATGCTTTTTAA

Alignment

ORF - retro_mtru_45 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.18 %
• Parental protein coverage: 75.54 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VGDFGVGLEQLASMSKDQNISALQQYGGVKGLSSLLKASPDKGISGDDADLLKRKNAFGTNTYPRKKGRS
          V.D..V....LA.M.KD.N...L...GGV.G....L...P.KGI.G.D.D...R...FG.NTY.......
Retrocopy VSDVVVDKTKLADMVKDKNLKSLSEFGGVEGVGHVLGTFPTKGIIGSDDDISRRLELFGSNTYKKPPPKG

Parental  FWRFLWEAWQDLTLIILIVAAVVSLVLGIKTEGWSDGWYDGGSIAFAVLLVIVVTAVSDYRQSLQFQNLN
          ...F..EA..D.T.IIL.V.A..SL..GIK..G...GWY.GGSI..AV.LV.VV.A.S..RQ..QF..L.
Retrocopy LLHFVLEAFNDTTIIILLVCAGLSLGFGIKEHGPGEGWYEGGSIFLAVFLVVVVSALSNFRQERQFHKLS

Parental  AEKQNIQLEVMRSGRTIKISIFDIVVGDVIPLKIGDQVPADGVLITGHSLEIDESSMTGESKIVHKDQ-K
          ....NI..EV.R.GR...ISIFD..VGD...LKIGDQ.PADGV...G.SL..DESSMTGES..V......
Retrocopy KISNNIKVEVVRNGRPQQISIFDVLVGDIVSLKIGDQIPADGVFLSGYSLQVDESSMTGESDHVEIEPLR

Parental  APFFMSGCKVADGVGVMMVTAVGINTEWGLLMASISEDTGEETPLQVRLNGVATFVGIVGLSVAVLVLAV
          APF..SG.KV.DG...M.VT.VG.NT.WG..M.SIS.DT.E.TPLQ.RL.......G.VGL.VA.LVL.V
Retrocopy APFLLSGAKVVDGYAQMLVTSVGKNTSWGQMMSSISRDTNERTPLQARLDKLTSSIGKVGLAVAFLVLLV

Parental  LLGRYFSGHTYDAKGNPQFVAGKTEISIVVDGVIKIFTIAVTIVVVAVPEGLPLAVTLTLAYSMRKMMAD
          LL.RYF.G...D.KGN..F...KT.I..V...V..I...AVTIVVVA.PEGLPLAVTLTLAYSM..MMAD
Retrocopy LLIRYFTGNSHDEKGNKEFRGSKTDINDVMNSVVSIVAAAVTIVVVAIPEGLPLAVTLTLAYSMKRMMAD

Parental  KALVRRLSACETMGSATTICSDKTGTLTLNQMTVVEAYVGKSKLNPPDDSSKFHPEALSLINESIAQNTT
          .A.VR.LSACETMGSAT.IC.DKTGTLTLNQM.V.....G.........S....P..L.L.......NTT
Retrocopy HAMVRKLSACETMGSATVICTDKTGTLTLNQMRVTKFCLGPENIIE-NFSNAMTPKVLELFHQGVGLNTT

Parental  GNVFVSKDGGELEVSGSPTEKAILSWAV-KLGMNFDVIRSNSTVLHVFPFNSEKKRGGVALKLV--DSGV
          G.V.....G.E.E.SGSPTEKAIL.WAV..LGM..D.......VLHV..FNSEKKR.GVA......D..V
Retrocopy GSVYNPPSGSEPEISGSPTEKAILMWAVLDLGMDMDEMKQKHKVLHVETFNSEKKRSGVAIRKENDDNSV

Parental  HIHWKGAAEIVLGACTQYLDSNSHLQSI-EQEKDFLKEAIDDMAARSLRCVAIAYR----SYELDKIPSN
          H.HWKGAAE..L..CT.Y.DSN....S..E.E.......I..MAA.SLRC.A.A......S...D.....
Retrocopy HVHWKGAAEMILAMCTNYIDSNGARKSLDEEERSKIERIIQVMAASSLRCIAFAHTEISDSEDIDYMIKR

Parental  EEDLAQWSLPEDELVLLAIVGIKDPCRPGVKDAVRICTDAGVKVRMVTGDNLQTAKAIALECGILASNEE
          E....Q..L.ED.L.LL.IVG.KDPCRP..K.AV..C..AGV...M.TGDN..TAKAIA.ECGIL.SN..
Retrocopy EKKSHQM-LREDGLTLLGIVGLKDPCRPNTKKAVETCKAAGVEIKMITGDNIFTAKAIAIECGILDSNSD

Parental  -AVDPCIIEGKVFRELSEKEREQVAKKITVMGRSSPNDKLLLVQALRKGGDVVAVTGDGTNDAPALHEAD
          .A......EG..FR...E.ER......I.VM.RSSP.DKLL.VQ.LRK.G.VVAVTGDGTNDAPAL.EAD
Retrocopy HAKAGEVVEGVEFRSYTEEERMEKVDNIRVMARSSPMDKLLMVQCLRKKGHVVAVTGDGTNDAPALKEAD

Parental  IGLSMGIQGTEVAKESSDIIILDDNFASVVKVVRWGRSVYANIQKFIQFQLTVNVAALVINVVAAISSGD
          IGLSMGIQGTEVAKESSDI.ILDDNF.SV..V.RWGR.VY.NIQKFIQFQLTVNVAALVIN..AA.SSGD
Retrocopy IGLSMGIQGTEVAKESSDIVILDDNFNSVATVLRWGRCVYNNIQKFIQFQLTVNVAALVINFIAAVSSGD

Parental  VPLNAVQLLWVNLIMDTLGALALATEPPTDHLMHRSPVGRREPLITNIMWRNLIVQALYQVSVLLFLNFC
          VPL..VQLLWVNLIMDTLGALALATE.PT..LM...P.GR..PLITNIMWRNL..QA.YQ..VLL...F.
Retrocopy VPLTTVQLLWVNLIMDTLGALALATERPTKELMKKKPIGRTAPLITNIMWRNLLAQASYQIAVLLIMQFY

Parental  GESI
          G.SI
Retrocopy GKSI

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_45 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA014399	1 retrocopy	retro_oind_27,
Medicago truncatula	MTR_4g008170	1 retrocopy	retro_mtru_45 ,