RetrogeneDB ID: retro_ptri_7

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 4:2557520..2558075(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0004s03690
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0011s04490
• Aliases: None
• Description: None

Sequence

>retro_ptri_7
ATGGCAGCGGGTCCTTACTATAGTAGTCTACTCTTCAATAAAGTAAACCCCTTTGCAGATGAAATAGATGGCCATTTGCA
AAAGTTGCAGAATGTTGCATTCCTAACATGTCTAGGATTGACACAGTGTCTTATGTGGAATTGCGCATCTGTTGCATTTG
TGTGGATGGTAGGTGGGGTAGAAACAAAAATCTTGTTCCTTGCATTGGCCTACCTAGTCTGTGGACTTCCAGCTGCAAAC
TGGTTATGGTTTCGTCCACTTTGTCAAGCTTTGAGGACAGAAAATACTTCCATGTTTCGTTATTTTTTCCTGTTCTACCA
GCTCCACATTGCCTTCTGCATGTTCGCTGCAGTTTCTCCTCCAATAATAGCCAAGGGAAGATCCCTCACAGGTATCATGA
GCGCATCAGACATTTCTGGTGATTATGGAGAAATTGGATACTTTTACTTCATTGGTTTCGGTTTGTTCAGCCTTGAATCA
ATGCTCAGCATCTGGGTTTTGCACAAAGTTTACAAGTTTTACCGTCACGGTGGTTTAGCTCTGGAGATGGTTTAA

Alignment

ORF - retro_ptri_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.94 %
• Parental protein coverage: 53.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ANEIPVHLQKIQYVAFTTFLGMAFCLFWNVISVTTLWIKGG-GVNIWFLSVIYFIAGVPGAYVLWYRPLY
          A.EI..HLQK.Q.VAF.T.LG...CL.WN..SV...W..GG....I.FL...Y...G.P.A..LW.RPL.
Retrocopy ADEIDGHLQKLQNVAFLTCLGLTQCLMWNCASVAFVWMVGGVETKILFLALAYLVCGLPAANWLWFRPLC

Parental  RAFRTESAMRFGWFFMFYALHIGFCIFAAVAPPIVFKGKSLTGILAAVDVVGKHALAGIFYFIGFGCFCL
          .A.RTE....F..FF.FY.LHI.FC.FAAV.PPI..KG.SLTGI..A.D..G.....G.FYFIGFG.F.L
Retrocopy QALRTENTSMFRYFFLFYQLHIAFCMFAAVSPPIIAKGRSLTGIMSASDISGDYGEIGYFYFIGFGLFSL

Parental  ESLLSIWVIQQVGMYFRGSGKAAEM
          ES.LSIWV...V....R..G.A.EM
Retrocopy ESMLSIWVLHKVYKFYRHGGLALEM

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_7 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0011s04490	1 retrocopy	retro_ptri_7 ,