RetrogeneDB ID: retro_mtru_16

Retrocopy location

• Organism: Barrel medic (Medicago truncatula)
• Coordinates: 4:17327559..17328279(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: MTR_4g049340
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: MTR_7g085070
• Aliases: None
• Description: None

Sequence

>retro_mtru_16
ATGGGAGTGATTAAATCAGCCATAGGAGATGCAATTCTAACATCAATATTTGTTTTCTTCATCTCAACATTAAGAATTCT
CTCTACAAAAACATCTCTTTTTCTCAACCTTCAACCACTTTCACTACCAGGCTTATTCATCACAACCATCCTAAACACAA
TAATCATCCTCACAATAAGCCTTATTGGAAGAATCTTAGGTGGTGCTAGTTTTAACCCTTCATCCACAATTTCCTTCTAC
ACATTAGGACTAAGACCAGATTCATCTCTTCTATCTTTTGCCATAAGGTTTCCTGCTCAAGCAATAGGTGGAGCTATTGG
CATCAAATCCATCCTTCAAGTTATACCAACAGAATACAAAGACATGGTGAAAGGTCCATCTTTGAAGGTTGATTTGCATA
CAGGTGCTATTGCTGAAGGGGTTTTGACTTTTACTCATAACTTTGTTATTCTTCTTGTTATGCTTAAGGGTCCTAAAAAT
CCTTGGTTGAAGGTTTATTTGCTTTCTGTGGCTACTTTGGTTTTGGTTATTATAGGTTCTGGCTACACTGGACCTTCTAT
GAACCCTGCTAATGCATTTGGTTGGGCTTATATGAACAATAAGCACAATACTTGGGAGCAATTTTATGTTTTTTGGATAT
GTCCTTTAATTGGTGCTAGTTCTGCTGCTATGGTTTATCGGTTTCTATTTATGTCACCAGTTAAGGAGAAGAAAGCTTGA

Alignment

ORF - retro_mtru_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.06 %
• Parental protein coverage: 80.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PSLIVTTTLVFLLVFLFTMIGNAMGGASFNPTGTAAFYSVGLGSDT-LFSMALRFPAQALGAAGGAMAIA
          P.L..TT.L..........IG...GGASFNP..T..FY..GL..D..L.S.A.RFPAQA.G.A.G...I.
Retrocopy PGLFITTILNTIIILTISLIGRILGGASFNPSSTISFYTLGLRPDSSLLSFAIRFPAQAIGGAIGIKSIL

Parental  ELIHPKYKHMIRGPSLKVDLHTGAAAELVLTFVITFAVLCIFLKGPRNDLMKIWLLAMSTVTLVMVGSAY
          ..I...YK.M..GPSLKVDLHTGA.AE.VLTF...F..L...LKGP.N...K..LL...T..LV..GS.Y
Retrocopy QVIPTEYKDMVKGPSLKVDLHTGAIAEGVLTFTHNFVILLVMLKGPKNPWLKVYLLSVATLVLVIIGSGY

Parental  TGPSMNPANAFGWAYLNNWHNTWDQFYVYWICPFTGAILAAWLFKAIFPPPEVKQKKA
          TGPSMNPANAFGWAY.NN.HNTW.QFYV.WICP..GA..AA......F..P.VK.KKA
Retrocopy TGPSMNPANAFGWAYMNNKHNTWEQFYVFWICPLIGASSAAMVYRFLFMSP-VKEKKA

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_16 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g085070	1 retrocopy	retro_mtru_16 ,
Populus trichocarpa	POPTR_0013s05030	1 retrocopy	retro_ptri_8,
Prunus persica	PRUPE_ppa010591mg	1 retrocopy	retro_pper_47,
Theobroma cacao	TCM_026035	1 retrocopy	retro_tcac_30,