RetrogeneDB ID: retro_ptri_24

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 11:15398442..15399402(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0001s41790
• Aliases: None
• Description: None

Sequence

>retro_ptri_24
TGGGTTTTTGTTTGTGAAAATCTAAATTACAATAGTGATGTTCATTAACAACTAAAACAATATGATTACAGGTTCCACCA
GTGTACTTCTCTCCGGTTAAAAGCTGCGTTTGCTCATTCTAGTGAGAGGAGTATGTCTTCAGATTTTGAGTTTAAGGGAC
CATCTTCCCCGAATATTCCATCCTCTGTCTCAAGATCAAGGGGAAAACATTATGCAGGCATGAAATGGGGAGGAGGTGAA
TGTGATCTTTCAATGAATAAGAAGCATCCAGTTAAGGTGTTAAATGATAAGTCTTCAAGGGTGAATTCAGAACCCAGTGA
TGAAATAAAACCAAAACTAAGCTTAGCAAATTCTAAAGGAACTTCTAGGTCAAAATTAAGTATGGTTTCTGGGAAGAGCT
TCACTAGAAATGCTAAGGAAACTGATTTAAAAGCTAAATCCGGTCAAGGTGGTAGTGAAAGTAGTTTGAATTCTGGGATG
GCTATGGTAAGTGATAGCAATACAAGTACTGTTACATTTGGGAGTGATCATCAAGCACGGCAAGGGAACATGGAAGTATT
AAGTCGAGGATTTGATCACACAAGTGGGCTTCTGTCTGCTGTGAGGAATGGTCTTAGGAAAAGCTTTGTTACAAGAAAAG
CATCAAGGGTGGAGATTAAAGATGAGAATAAACAATTAAGAGATCGCAAGTCTTCATCTAGCAAATCTAGTGTTGGATCG
ACTTTGAAACCTGGTCATGATGTCAAGAGCTCAACAATTACATTGATGAGGAACAAAGAACAAACTCCAGATAGCAGAAA
TGTGGCAAGGATGACTGAAGCAGCAAGGAAGAAAAAAAAAGATTCTAACATGTCCAAGACTTCGGATGTTCGAGTTAAGG
AGGTCTTTAATTCTAGGAAGGGAGCTATAAGTAATGTCTCAAAATCAGCTCCCCAAGAAGCTCTGAAATCAAAGGTTAGA

Alignment

ORF - retro_ptri_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.6 %
• Parental protein coverage: 64.9 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WVDFLVEAKSNYQDVDDEWFRTSHPFHQCSSGQLKAAFAYSGEKSTSSDFECKGSFSPNIPSSVSRSRGK
          WV.F..E......DV..........FHQC.S..LKAAFA.S.E.S.SSDFE.KG..SPNIPSSVSRSRGK
Retrocopy WV-FVCENLNYNSDVH*QLKQYDYRFHQCTSLRLKAAFAHSSERSMSSDFEFKGPSSPNIPSSVSRSRGK

Parental  HYASKKWGGGGHDISMNKQHPVKVLS-KSSRVNSEPNDKIKPKLSLVNSKGTSRSKVSVVSGKSFTRNAK
          HYA..KWGGG..D.SMNK.HPVKVL..KSSRVNSEP.D.IKPKLSL.NSKGTSRSK.S.VSGKSFTRNAK
Retrocopy HYAGMKWGGGECDLSMNKKHPVKVLNDKSSRVNSEPSDEIKPKLSLANSKGTSRSKLSMVSGKSFTRNAK

Parental  ETDLEAKSCQGGTESSLNSLVFKAAESNTSTVTSERDHQAKQRNLEVSSRGFDHASGLLSAVRNGLRKSF
          ETDL.AKS.QGG.ESSLNS.......SNTSTVT...DHQA.Q.N.EV.SRGFDH.SGLLSAVRNGLRKSF
Retrocopy ETDLKAKSGQGGSESSLNSGMAMVSDSNTSTVTFGSDHQARQGNMEVLSRGFDHTSGLLSAVRNGLRKSF

Parental  VTRKASRVEINDENKQLRDRKSSSSKSSWGSSSNPGYDAKSSTLAF---KEQTPDSRNVARMTEAARKKT
          VTRKASRVEI.DENKQLRDRKSSSSKSS.GS...PG.D.KSST......KEQTPDSRNVARMTEAARK..
Retrocopy VTRKASRVEIKDENKQLRDRKSSSSKSSVGSTLKPGHDVKSSTITLMRNKEQTPDSRNVARMTEAARKXX

Parental  KDSDMSRASDVRVKEKVFNSRKGGISNVAKSASLEALKSKVQ
          .DS.MS..SDVRVKE.VFNSRKG.ISNV.KSA..EALKSKV.
Retrocopy XDSNMSKTSDVRVKE-VFNSRKGAISNVSKSAPQEALKSKVR

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_24 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_0001s41790	1 retrocopy	retro_ptri_24 ,