RetrogeneDB ID: retro_mtru_13

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 2:10884880..10886107(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_2g029180
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_2g022700
• Aliases: None
• Description: None

Sequence

>retro_mtru_13
ATGTTATCTTTCAATGTTTTTCCAACATCATCATCTTCCTCTGTCACTTTCACGAAACCAAATCACCATTTTTCCATCAA
TGCATCACCAAATCTTCTCAACAGGTTTCACCATGAAAGCTCCAAACTTTCCTTCAAACCCATATCTCAGATCCATCATT
CAACCACAAAGTTATCATCTTTCAACAGATTTCTCACACACCCTTTTGAGTTTTCACCAAAACCCAGAAACCAAATTTTG
AAAGCTGTATCTGATGAAGGTGAAATTTCACAACCCATTAATCCTAAACCCAAGAATCTCAAAAAACTTGCTCTTGTTTT
TGGGTTTTGGTACTTTCAAAACATTGTTTTCAACATTTACAACAAGAAAGTGTTGAATATTTTCTCTTTTCCATGGCTTC
TTGCTTCTTTTCAGCTCTTTGTTGGTTCCATTTGGATGCTTGTTCTTTGGTCTTTAAAGCTTCAACCATGTCCAAAAATC
TCAAAACCTTTCATTTTTGCACTACTTGGACCTGCTTTGTTTCATACTATAGGTCACATTTCAGCTTGTGTTTCGTTCTC
TAAGGTTGCTGTGTCTTTCACACATGTTATTAAATCAGCAGAACCTGTTTTTTCTGTCATATTTTCTTCTGTTCTTGGTG
ATAGGTATCCAATTCAGGTTTGGCTTTCAATTTTACCAATTGTGCTTGGTTGTTCTTTAGCTGCTGTTACTGAGGTATCT
TTCAATGTTGGAGGATTGTGGTGTGCTCTGATTAGCAATGTTGGTTTTGTGTTGAGGAACATTTATTCGAAAAAAAGTTT
ACAAAATTTCAAAGAAGTTGATGGTTTGAACTTATATGGTTGGATTACTATACTTTCATTTATGTATCTTTTTCCGGTAG
CGATTTTTGTGGAAGGTTCTCAATGGATTCCAGGGTATTATAAGGCGCTTGAAGCTATTGGAACCCCTTCGACTTTTTAT
ATTTGGGTTTTGGTTTCTGGTCTGTTTTATCATCTTTATAATCAATCATCTTATCAAGCATTGGATGAAATTAGTCCATT
AACTTTCTCTGTTGGAAATACAATGAAGAGAGTGGTAGTGATTGTGTCTTCGATTTTGGTGTTCCGGAATCCGGTTAGGC
CTCTTAATGGTCTTGGATCTGCCATTGCTATTCTCGGGACTTTTCTGTATTCACAAGCTACAGCTGCAAAGAAAGCAAAG
AAAATTGAAGGGGAAAAGAGTAGTTAG

Alignment

ORF - retro_mtru_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.42 %
• Parental protein coverage: 73.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIGLYFATWWALNVVFNIYNKKVLNAFPYPWLTSTLSLAAGSLMMLISWATRVAEAPKVNLDFWKALFPV
          K..L.F..W...N.VFNIYNKKVLN.F..PWL.....L..GS..ML..W.......PK....F..AL...
Retrocopy KLALVFGFWYFQNIVFNIYNKKVLNIFSFPWLLASFQLFVGSIWMLVLWSLKLQPCPKISKPFIFALLGP

Parental  AVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRFLLGEAFPMPVYLSLLPIIGGCALAAVTELN
          A..HTIGH..A.VS.SKVAVSFTH.IKS.EP.FSV..S...LG...P..V.LS.LPI..GC.LAAVTE..
Retrocopy ALFHTIGHISACVSFSKVAVSFTHVIKSAEPVFSVIFSS-VLGDRYPIQVWLSILPIVLGCSLAAVTEVS

Parental  FNMIGFMGAMISNLAFVFRNIFSKKGM-NGMSVSGMNYYACLSMLSLLILTPFAIAVEGPKVWVAGWQTA
          FN..G...A.ISN..FV.RNI.SKK...N...V.G.N.Y.....LS...L.P.AI.VEG...W..G...A
Retrocopy FNVGGLWCALISNVGFVLRNIYSKKSLQNFKEVDGLNLYGWITILSFMYLFPVAIFVEGSQ-WIPGYYKA

Parental  VSQIG--PNFVWWVVAQSVFYHLYNQVSYMSLDQISPLTFSIGNTMKRISVIVSSIIIFHTPLQPINALG
          ...IG....F..WV.....FYHLYNQ.SY..LD.ISPLTFS.GNTMKR..VIVSSI..F..P..P.N.LG
Retrocopy LEAIGTPSTFYIWVLVSGLFYHLYNQSSYQALDEISPLTFSVGNTMKRVVVIVSSILVFRNPVRPLNGLG

Parental  AAIAILGTFIYSQA
          .AIAILGTF.YSQA
Retrocopy SAIAILGTFLYSQA

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_13 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_2g022700	1 retrocopy	retro_mtru_13 ,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Prunus persica	PRUPE_ppa006608mg	1 retrocopy	retro_pper_3,