RetrogeneDB ID: retro_ptri_11

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 1:629788..630502(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0001s00770
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0011s11210
• Aliases: None
• Description: None

Sequence

>retro_ptri_11
ATGGATGTACGTCAAAATTCAGTGTATTCTGCCAAACTTGCTGAACAGGCGAAACGCTACAATGAGATGTTGGATCACAT
GAAGTATATTGCAAAGCTTGACGTTGAGTTGACAACCGAGGAGCGGAATTTGCTGCGTATTGGATGCAAGAATGTAATGG
GCCCAAGAAGAGAATCATGGAGAATGCTTTCATCCATAGAGGAAAAGGAACAAGCCAAAGGGAACCAAGTTAATGCGAAG
AGGATCGAGGAGTATAGACGGAAGATTGAGTCCGAACTCACAAGTATATGCAACGATATCATACAATTGATTGATGATCA
TCTACTCCCTTCAACTTCCCAGTGTGAATCCTGTGTCTTCTATCATAGGATGAAGGGAGATTATTACAGGTATCTAGCAG
AATTCAAGGTTGGCATCGAGATGGAGAAGGCTGCTTCAGAGTCAATGAAAGCATATGATATAGGCATTAAAGCTGCATCC
AAGTTGGCTCCTACAAATTTAGTTCGATTGAGTTTGGCTTTGAATTTCTCAGTGTTATTGTATGATATCATGAAGTTTCC
TGAGAAGGCTTTCTTTCATGCTAAGAATGCTTATGATGAGGCTATCCCAATACTCGACAATTTGAATAAGGAATCACAGA
AAGACAGCATGTTGATATTGGAGATTCTTCTAGACAACGTCAGGTTGTGGAGTTATGACATCTTAGAGAATTGA

Alignment

ORF - retro_ptri_11 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.28 %
• Parental protein coverage: 90.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RENFVYVAKLAEQAERYDEMVDAMKKVAKLDVELTVEERNLLSVGYKNVIGARRASWRILSSIEQKEESK
          R.N.VY.AKLAEQA.RY.EM.D.MK..AKLDVELT.EERNLL..G.KNV.G.RR.SWR.LSSIE.KE..K
Retrocopy RQNSVYSAKLAEQAKRYNEMLDHMKYIAKLDVELTTEERNLLRIGCKNVMGPRRESWRMLSSIEEKEQAK

Parental  GNETNVKRIKEYRKKVEAELTGVCNDIMTVIDEHLIPSSIPGESSVFYHKMKGDYYRYLAEFKSGNERKE
          GN..N.KRI.EYR.K.E.ELT..CNDI...ID.HL.PS....ES.VFYH.MKGDYYRYLAEFK.G.E...
Retrocopy GNQVNAKRIEEYRRKIESELTSICNDIIQLIDDHLLPSTSQCESCVFYHRMKGDYYRYLAEFKVGIEMEK

Parental  AADQSLKAYETATSTAARDLSPTHPIRLGLALNFSVFYYEIMNSPERACHLAKQSFDEAISELDTLSEES
          AA..S.KAY......A...L.PT...RL.LALNFSV..Y.IM..PE.A...AK...DEAI..LD.L..ES
Retrocopy AASESMKAYDIGIKAASK-LAPTNLVRLSLALNFSVLLYDIMKFPEKAFFHAKNAYDEAIPILDNLNKES

Parental  YKDSTLIMQLLRDNLTLWTSDIPED
          .KDS.LI...L.DN..LW..DI.E.
Retrocopy QKDSMLILEILLDNVRLWSYDILEN

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_11 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 ,