RetrogeneDB ID: retro_ptri_2

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 1:30404056..30404971(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0001s31970
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0009s05010
• Aliases: None
• Description: None

Sequence

>retro_ptri_2
ATGCTTTCGTTGCGCCTCCGCTCCTCAGTTTGCAAGACCCTTCCTCCTCAAAAATTCTTTCAATTCTTTAGCCATCAAAA
GACCAGTGATGACCAAACACACGGCTTTCCTCCACTTCCCGCAACGAAAACGAACTCCGGTCTCAAAGAAGAGGAGAAAG
GAGGAATAGAGCAAGCTATGCAGTTGCCGGAGGGATTACGCAGAGAGTCCATGCCCCGGCATGTTGCTGTAATCATGGAC
GGAAATTCCAGGTGGGCTCGGCAACGAGGGATGCTCACACCTTCTGGTCATGAAGCTGGCGTGAGGTCATTGAAAGAGTT
TATAAGGCTTTGCCTTCAATGGGGTATTAAGGTTGTCACCGTTTTTGCATTTTCTATAGATAATTGGACTAGGCCTAAGG
AGGAGGTTGATATCGTCATGACTATGATTGAGAATCTGTTAAAGTCTGGTTTGGATGATTTTATCAGGGAAGGTACTCGA
GTCTCTATAATAGGTGATACCTCAAGGGTCCCAAAGTCTTTGCAGAGAACGATATGTGACATAGAAGAGATGACAAGAGA
GAACTCAAAATTCCATTTCATCATGGCTATCAGCTATAGCGGGACATATGATGTTGTACAAGCATGCAAAAGTGTTGCTC
AAAAGGTAAAGGATGGTGTTATTCAAGTGGAGGACATCAATGAAAGTGCAGTTCAACAGGAATTAGAAACCAAGTGTTGC
GAGTTTCCTTGTCCTGATTTGTTAATAAGAACAAGTGGTGAACTTAGAATTAGCAATTTTTTGCTGTGGCAGTCAGCCTA
TAGTGAGCTTTTCTTCGCAAAAGCACTATGGCCTGATTTTGGAAAGGCTGATTTTGTAGAGGCCTTAACTTCATATCAGC
ATAGGCAGAGACGTTATGGTGGTCGATATTCATAA

Alignment

ORF - retro_ptri_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.99 %
• Parental protein coverage: 91.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RNTRDQTHRFPTLLLAAKHDLDLKEEEDKGVA-AVPLPEGLLREAMPRHVAVIMDGNARWARQRGFIALS
          ....DQTH.FP.L..A.K....LKEEE..G...A..LPEGL.RE.MPRHVAVIMDGN.RWARQRG....S
Retrocopy KTSDDQTHGFPPLP-ATKTNSGLKEEEKGGIEQAMQLPEGLRRESMPRHVAVIMDGNSRWARQRGMLTPS

Parental  AGHEAGARSLRELVELCCDWGVRVLTVFAFSYDNWIRPKVEVDFLMSLFERMLKSELDNFVRQGARVSTI
          .GHEAG.RSL.E...LC..WG..V.TVFAFS.DNW.RPK.EVD..M...E..LKS.LD.F.R.G.RVS.I
Retrocopy -GHEAGVRSLKEFIRLCLQWGIKVVTVFAFSIDNWTRPKEEVDIVMTMIENLLKSGLDDFIREGTRVSII

Parental  GDSSRLSESLKKLISDVEEKTKDNSRLHLIVAVSYSGKYDVTQACKSIAQKVKDGTVQLEDIDESLLEQE
          GD.SR...SL...I.D.EE.T..NS..H.I.A.SYSG.YDV.QACKS.AQKVKDG..Q.EDI.ES...QE
Retrocopy GDTSRVPKSLQRTICDIEEMTRENSKFHFIMAISYSGTYDVVQACKSVAQKVKDGVIQVEDINESAVQQE

Parental  LETNCAEYPCPDLLIRTSGELRISNFLLWQLAYTELFFAEALWPDFGKAEFVEALTSYQQRQRRYGGR
          LET.C.E.PCPDLLIRTSGELRISNFLLWQ.AY.ELFFA.ALWPDFGKA.FVEALTSYQ.RQRRYGGR
Retrocopy LETKCCEFPCPDLLIRTSGELRISNFLLWQSAYSELFFAKALWPDFGKADFVEALTSYQHRQRRYGGR

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_2 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0009s05010	1 retrocopy	retro_ptri_2 ,