RetrogeneDB ID: retro_ptri_21

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 1:16054713..16055170(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0001s40270
• Aliases: None
• Description: None

Sequence

>retro_ptri_21
GATCATAAGAACTTCATCTGTATTCTCAAGCTCGCTAAGTAAGCTAAACGCTATTATGAAATGATTGATGCAATGAAGAA
AATGATAAAAACTTGATATTGAATTAACAATGAAGAAGAAACACTTACTCTTTATTGGCTATTCTAATATGAATGGTGTG
ATGAAGGGATCATAGAGAATATTGTGCAAGAGGAGTATTCAAAACGGAATGAAAACCAATGTGAAAAGGATAAAAGAGTA
TAAGAAGGTAGAAGTAGATTTAACTCATATTTGTAATGTTATTATAACTATGATTGATGGGCATCTCATTTCATTATTTG
AAGCTTGAAATTCCTTTGTGTTTTACTATAAAATGAAAGATGGTTATTACCAATATCTAGCAAAATTTCATGGTAGTAAT
AGGAGGAAGGAGGTAGTTAATCAACCACTTAAGGCATATAATATTGCCACAACAACT

Alignment

ORF - retro_ptri_21 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.5 %
• Parental protein coverage: 60.23 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DRENFVYVAKLAEQAERYDEMVDAMKKVA-KLDVELTVEERNLLSVGYKNVIGARRASWRILSSIEQKEE
          D..NF....KLA..A.RY.EM.DAMKK...KLD.ELT.....LL..GY.N..G....S.RIL........
Retrocopy DHKNFICILKLAK*AKRYYEMIDAMKKMI>KLDIELTMKKKHLLFIGYSNMNGVMKGS*RILC---KRSI

Parental  SKGNETNVKRIKEYRQKVEAELTGICHDIMTVIDEHLIPSCTAGESTVFYYKMKGDYYRYLAEFKSGNER
          ..G..TNVKRIKEY..KVE..LT.IC..I.T.ID.HLI....A..S.VFYYKMK..YY.YLA.F...N.R
Retrocopy QNGMKTNVKRIKEYK-KVEVDLTHICNVIITMIDGHLISLFEA*NSFVFYYKMKDGYYQYLAKFHGSNRR

Parental  KEAADQSLKAYETATTT
          KE...Q.LKAY..ATTT
Retrocopy KEVVNQPLKAYNIATTT

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Populus trichocarpa was not studied using RNA-Seq expression data.

ChIP-Seq

Populus trichocarpa was not studied using ChIP-Seq data.

EST

Populus trichocarpa was not studied using EST data.

TSS

Populus trichocarpa was not studied using FANTOM5 data.

Lab

retro_ptri_21 was not experimentally validated.

Homology

Retrocopy orthology:

Populus trichocarpa 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0001s40270	3 retrocopies	retro_ptri_21 , retro_ptri_37, retro_ptri_38,
Populus trichocarpa	POPTR_0011s11210	1 retrocopy	retro_ptri_11,