RetrogeneDB ID: retro_mtru_23

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 3:7122558..7124094(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_3g023480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_0009s0370
• Aliases: None
• Description: None

Sequence

>retro_mtru_23
ATGGCTAAGGAAGGAATCATGGATGTTGCAACCCAATATCCTGGAAAACTCACCTTTAGGGTTATTATCACTTGTGTCAT
GGCAGCAAGTGGTGGATTAATTTATGGATATGATCACGGTGTTTCTGGTGGTGTAACATCTATGGATTCCTTCTTAAAAC
AATTCTTTCCTTCTGTTTATGAACAGCAAATAAATACAAAAGCTTCTTCAAATCAATATTGCAAATTCAACAGTCAAACA
TTGACATTCTTTACATCTTCCATTTATATAAGTGCTCTTATATCTAGTCTTGGGGCATCAAGCTTAACAAGAATGATGGG
TAGGCGAGCAACAATGATTTTAGGTGGATTATTCTTTGTGTCGGGTGCCTTACTCAATTCATTCGCCCAGAACATTGCGA
TGCTTATCATTGGAAGGTTGTTACTTGGTTTTGGTATTGGATGTGCCAATCAGTCGGTTCCAATCTATATCTCAGAAATG
GCACCTTCTCAATATAGAGGAGCCTTAAACATGTGTTTTCAATTTTCGATTACTATTGGTATGTTTGCAGCCAATCTGGC
AAACTATTACTGTGCCAAGTTATGGAATGGTGAGGGATGGCGATTAAGCTTGGGGCTAGGTGCGGTACCTGCGGTGATTT
TCGTTGTAGGCACACTTTTTCTTCCTGATTCACCAAGCTCACTTGTTTCACGCGGTCGCCATGAAGCCGCAAGAAAGGAG
CTTGCAAAAATTCGCGGTACTGATGATGTTGATGCCGAGTTTAATGATATTGTTGCTGCTAGTGAAGCCTCGGATCAAGT
GAAAAACCCGTGGAAAACCTTGAACAAGAGAAAAAATAGGCCCCCGATGGTTTTCGCTATAATGATTCCTTTCTTCCAAC
AATTCACTGGATTGAATGTGATCACATTCTACGCTCCTATTCTATTCAGAACGATTGGTTTTGGAAGTCAAGCTTCACTC
ATGTCTGCCGCGATCATTGGAGGCTTTAAACCTCTTGCCACTCTGGTTTCAATCGTACTTGTGGATAAATTTGGACGACG
CACCCTTTTCCTTGAGGGTGGTGCTCAAATGTTGGTTTGTCAAATTTTGATGGCAATTGCTATTGGTGTAACATTTGGAA
CAAGTGGGAACCCAGGGCAATTACCTCAATGGTTTGCAATTACCATCGTAGGCGTAATCTGCATATATGTTTCAGGTTTC
GCTTGGTCTTGGGGACCTCTAGCATGGTTAGTACCTAGCGAAATTTTTCCACTCGAAATTCGATCTGCTTGTCAGAGTAT
TACAGTTGCTGTCAACATGACCAGCATTTTCATCATAGCTCAATTCTTCACCGAAATGCTTTGTCACTTCAAGTTTGGTT
TGTTCCTCTTCTTTTCCGGCTTTGTAATCATCATGACTTTATTCATCTACAAGTTGTTTCCAGAAACTAAGGGTGTCCCA
CTTGAGGATATGCAGATGGTTTGGAAGAAACACCCCTTTTGGGGAAAGTATTTGGAGAAAGAGAGTAAGAAAAAAACTGT
CAAGCAAGACACCTAA

Alignment

ORF - retro_mtru_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGVEANVDGPSKYPGKLTFRVIITCIMAATGGLIFGYDHGVSGGVTSMDSFLKRFFPSVYEQESNLKPSA
          M..E...D....YPGKLTFRVIITC.MAA.GGLI.GYDHGVSGGVTSMDSFLK.FFPSVYEQ..N.K.S.
Retrocopy MAKEGIMDVATQYPGKLTFRVIITCVMAASGGLIYGYDHGVSGGVTSMDSFLKQFFPSVYEQQINTKASS

Parental  NQYCKFNSQILTLFTSSLYISALVAGLGASSITRALGRRTTMILGGIFFVSGALLNGLAMNIAMLIAGRL
          NQYCKFNSQ.LT.FTSS.YISAL...LGASS.TR..GRR.TMILGG.FFVSGALLN..A.NIAMLI.GRL
Retrocopy NQYCKFNSQTLTFFTSSIYISALISSLGASSLTRMMGRRATMILGGLFFVSGALLNSFAQNIAMLIIGRL

Parental  LLGFGIGCANQAVPIYLSEMAPYKYRGALNMCFQLSITIGIFTANMFNYYFSKILNGEGWRLSLGLGAVP
          LLGFGIGCANQ.VPIY.SEMAP..YRGALNMCFQ.SITIG.F.AN..NYY..K..NGEGWRLSLGLGAVP
Retrocopy LLGFGIGCANQSVPIYISEMAPSQYRGALNMCFQFSITIGMFAANLANYYCAKLWNGEGWRLSLGLGAVP

Parental  AVVFIIGSICLPDSPNSLVTRGRHEEARKELVKIRGTDDVDAEFRDIVAASEASAKVKHPWKTLQERKYR
          AV.F..G...LPDSP.SLV.RGRHE.ARKEL.KIRGTDDVDAEF.DIVAASEAS..VK.PWKTL..RK.R
Retrocopy AVIFVVGTLFLPDSPSSLVSRGRHEAARKELAKIRGTDDVDAEFNDIVAASEASDQVKNPWKTLNKRKNR

Parental  PQLVFAILIPFFQQFTGLNVITFYAPILFRTIGFGSQASLMSAAIIGSFKPVSTLVSIFVVDKFGRRALF
          P..VFAI.IPFFQQFTGLNVITFYAPILFRTIGFGSQASLMSAAIIG.FKP..TLVSI..VDKFGRR.LF
Retrocopy PPMVFAIMIPFFQQFTGLNVITFYAPILFRTIGFGSQASLMSAAIIGGFKPLATLVSIVLVDKFGRRTLF

Parental  LEGGVQMLICQIIMTVAIAVTFGTSGNPGKLPHWYAITIVGIICVYVSGYAWSWGPLGWLVPSEIVPLEI
          LEGG.QML.CQI.M..AI.VTFGTSGNPG.LP.W.AITIVG.IC.YVSG.AWSWGPL.WLVPSEI.PLEI
Retrocopy LEGGAQMLVCQILMAIAIGVTFGTSGNPGQLPQWFAITIVGVICIYVSGFAWSWGPLAWLVPSEIFPLEI

Parental  RSACQSITVAVNMTSTFFIAQLFTEMLCHFKFGLFIFFGCFVILMTFFIYKFFPETKGVPLEEMHMVWRK
          RSACQSITVAVNMTS.F.IAQ.FTEMLCHFKFGLF.FF..FVI.MT.FIYK.FPETKGVPLE.M.MVW.K
Retrocopy RSACQSITVAVNMTSIFIIAQFFTEMLCHFKFGLFLFFSGFVIIMTLFIYKLFPETKGVPLEDMQMVWKK

Parental  HPFWGKFLEAEDQKIQSSKLDT
          HPFWGK.LE.E..K....K.DT
Retrocopy HPFWGKYLEKESKK-KTVKQDT

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_23 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 16 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA024972	1 retrocopy	retro_oind_19,
Brachypodium distachyon	BRADI1G24820	1 retrocopy	retro_bdis_38,
Hordeum vulgare	MLOC_55525	1 retrocopy	retro_hvul_80,
Medicago truncatula	MTR_0009s0370	1 retrocopy	retro_mtru_23 ,
Oryza barthii	OBART07G00410	1 retrocopy	retro_obar_21,
Oryza glumaepatula	OGLUM07G00430	1 retrocopy	retro_oglu_47,
Oryza glumaepatula	OGLUM07G18360	1 retrocopy	retro_oglu_7,
Oryza meridionalis	OMERI07G15470	2 retrocopies	retro_omer_15, retro_omer_8,
Oryza nivara	ONIVA07G16940	1 retrocopy	retro_oniv_2,
Oryza punctata	OPUNC07G17520	1 retrocopy	retro_opun_36,
Oryza glaberrima	ORGLA07G0149800	1 retrocopy	retro_ogla_30,
Oryza rufipogon	ORUFI07G00430	1 retrocopy	retro_oruf_37,
Oryza rufipogon	ORUFI07G19310	1 retrocopy	retro_oruf_45,
Oryza sativa japonica	OS07G0106200	1 retrocopy	retro_osat_43,
Oryza sativa japonica	OS07G0559700	1 retrocopy	retro_osat_29,
Triticum aestivum	Traes_2BS_7DF366FE1	1 retrocopy	retro_taes_36,