RetrogeneDB ID: retro_mtru_24

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 1:50980387..50981791(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_1g112630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_4g037105
• Aliases: None
• Description: None

Sequence

>retro_mtru_24
ATGGGTATTTCAATTGCTAGTTTTTTATTACCACTAGCTTTAGTTTTGAATTTAGTGTCTGTGTGTAATGGAGGCACAAC
CAGTGCTTTTGTTAGGAATGTTCAGAAAGGCGTTAATATGTCACTTGATAGTGATGTTTTTGCTGTTCCTTCTGGTTATA
ATGCTCCCCAACAGGTTCATATTACACAAGGTGATCTTGTTGGGAAAGAAGTGATCGTATCGTGGGTGACCGAGGATGAA
CCAGGGTCGATCGCAGTGCGCTACTGGAGTACTGACAACAGCAAACAAAAGAAGCTAGCTAAAGGGAAAATTGTTACTTA
TAGATTCTTCAATTACTCATCTGGTTTTATTCATCACACTACTATAAGGAATTTGGAGTACAACACTAAATATTATTATG
AGGTTGGACTTGGGAACACAACAAGACAGTTTTGGTTTATAACTCCTCCTGAAATTGGTCCTGATGTGCCATACACATTT
GGTCTCATAGGAGATCTCGGTCAGAGCTTTGATTCAAACAGAACACTTTCTCACTATGAATTGAATCCTAGAAAGGGGCA
AACAGTGTTGTTTGTTGGAGATCTCTCTTATTCAGATAACTTTCCAAATCATGACAATGTTAGGTGGGATACTTGGGGAA
GGTTTGTAGAAAGGAGCACGGCTTATCAGCCGTGGATATGGACTGTAGGAAACCATGAAATTGATTTTGCCCCAGAAATT
GGCGAAACCAAACCATTCAAACCTTATTCGCACCGATACCACACTCCTTATAAAGCATCACAAAGTACTTCACCCTTTTG
GTATTCTATCAGAAGAGCTTCAGCTCACATCATTGTCTTGGCCTCGTATTCAGGATATGGAAAATATACACCACAGTACC
AATGGCTTGAACAAGAGCTACCTAAAGTTAACAGGACAGAAACTCCTTGGTTGATTGTTCTAATGCATTCACCTTGGTAT
AATAGCAACAATCAACATTATATGGAAGGGGAGACAATGAGAGTAATGTATGAGCCATGGTTTGTTAAGTACAAGGTTGA
TGTTGTGTATGCTGGACATGTGCATGCCTATGAAAGAACCGAACGTGTGTCGAATATTGCATATAATGTTGTGAATGGTA
TTTGCACTCCTATAAAAGATCAATCAGCTCCTGTATACATAACCATTGGAGATGGAGGGAACCTTGGAGGCATGGAAACC
AACATGACAGAACCACAGCCAGAGTACTCAGCATTCAGAGAGGCTAGCTTTGGACATGCCATTTTCGACATAAAGAACAG
AACACATGCTCACTATAGCTGGCACAGAAATCAAGATGGTTATTCGGTTGAGGCTGATTCCCATTGGTTTTTCAACAGAT
TTTGGCATCCAGTTGATGATTCCACCGCTCATGTTTTCCATTGA

Alignment

ORF - retro_mtru_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.46 %
• Parental protein coverage: 98.92 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLLLALCLVLNLVFVCNGGRTSTFVRKVEKTIDMPLDSDVFDVPSGYNAPQQVHITQGDHVGKAVIVSWV
          S.LL.L.LVLNLV.VCNGG.TS.FVR.V.K...M.LDSDVF.VPSGYNAPQQVHITQGD.VGK.VIVSWV
Retrocopy SFLLPLALVLNLVSVCNGGTTSAFVRNVQKGVNMSLDSDVFAVPSGYNAPQQVHITQGDLVGKEVIVSWV

Parental  TEDEPGSNAVRYWSK-NSKQKRLAKGKIVTYRFFNYTSGFIHHTTIRNLEYNTKYYYEVGLGNTTRQFWF
          TEDEPGS.AVRYWS..NSKQK.LAKGKIVTYRFFNY.SGFIHHTTIRNLEYNTKYYYEVGLGNTTRQFWF
Retrocopy TEDEPGSIAVRYWSTDNSKQKKLAKGKIVTYRFFNYSSGFIHHTTIRNLEYNTKYYYEVGLGNTTRQFWF

Parental  TTPPEIGPDVPYTFGLIGDLGQSYDSNKTLSHYELNPTKGQTVLFVGDLSYADNYPNHDNVRWDTWGRFA
          .TPPEIGPDVPYTFGLIGDLGQS.DSN.TLSHYELNP.KGQTVLFVGDLSY.DN.PNHDNVRWDTWGRF.
Retrocopy ITPPEIGPDVPYTFGLIGDLGQSFDSNRTLSHYELNPRKGQTVLFVGDLSYSDNFPNHDNVRWDTWGRFV

Parental  ERSVAYQPWIWTVGNHELDFAPEIGETKPFKPYSHRYRTPYKASQSTSPFWYSIKRASAHIIVLASYSAY
          ERS.AYQPWIWTVGNHE.DFAPEIGETKPFKPYSHRY.TPYKASQSTSPFWYSI.RASAHIIVLASYS.Y
Retrocopy ERSTAYQPWIWTVGNHEIDFAPEIGETKPFKPYSHRYHTPYKASQSTSPFWYSIRRASAHIIVLASYSGY

Parental  GKYTPQYKWLEQELPKVNRTETPWLIVLMHSPWYNSYNYHYMEGESMRVMYEPWFVKYKVDVVYAGHVHA
          GKYTPQY.WLEQELPKVNRTETPWLIVLMHSPWYNS.N.HYMEGE.MRVMYEPWFVKYKVDVVYAGHVHA
Retrocopy GKYTPQYQWLEQELPKVNRTETPWLIVLMHSPWYNSNNQHYMEGETMRVMYEPWFVKYKVDVVYAGHVHA

Parental  YERSERVSNVAYNVVNGICTPIKDQSAPVYITIGDGGNLEGLATNMTEPQPEYSAYREASFGHAIFDIKN
          YER.ERVSN.AYNVVNGICTPIKDQSAPVYITIGDGGNL.G..TNMTEPQPEYSA.REASFGHAIFDIKN
Retrocopy YERTERVSNIAYNVVNGICTPIKDQSAPVYITIGDGGNLGGMETNMTEPQPEYSAFREASFGHAIFDIKN

Parental  RTHAHYSWHRNQDGYSVEADSHWFFNRFWHPVDDSTTHVSH
          RTHAHYSWHRNQDGYSVEADSHWFFNRFWHPVDDST.HV.H
Retrocopy RTHAHYSWHRNQDGYSVEADSHWFFNRFWHPVDDSTAHVFH

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_24 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_4g037105	1 retrocopy	retro_mtru_24 ,