RetrogeneDB ID: retro_ptri_15

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 3:17253222..17254335(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0003s18040
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0015s05560
• Aliases: None
• Description: None

Sequence

>retro_ptri_15
ATGGATTCCTCTCCTCGTTCTTCATTCACTGGAAAAGTAAAACAGACACCATGGTGGATGAAAAGCCTCACTGGGTGGTC
TTATGTAATTTATGAGATGTTATTCCAAAAGATGCAAGCAAGGCATCTGAAAAATCCATTGCCTTTACCTCCGCTCCATG
ATGTTACATGTATTATAACTGGATCCACGAGTGGCATTGGACTTGAAACTGCCAGGCAATTGGCTGTGTCTGGGGCACAT
GTTGTTATGGCTGTACGAAACCAATCTGCAGCCTTTGATTTGATCATGAAGTGGCAGGATGAACGACATGGAACAAGCCT
GCTCAGTGTTGAGGTGATGGAGCTGAATCTTCTCTCCCTCACTTCTGTTGTGAGATTTGCTAGGGCGTGGAACTCGCGCT
CAAAACCTTTGCAAGTTCTTATCAATAATGCTGGAATCTTTTCTATGGGAGAGCCGCAGAAGTTCTCAAAAGATGGGTAC
GAAACACACCAGCAAGTAAATTTTTTGGCTCCTGCATTGCTTTCTATACTGCTTTTGCCATCTCTCGTTAAGGGCTCTCC
CAGCCGAATTATTAACGTGAACTCCATTATGCATTATATGGGCTTTGTCGACACAGATGACATGAATTTTACTTTGAGGA
AAGAGAAATTCAATAGTACAAAGGCATATTCAAGTAGCAAGCTTGCACAGGTCATGTTCAACAGTGTCTTACAGAAACGC
CTGCCTCCTGAAGCTGGCATTAATGTGTTATGTGTATCTCCTGGAACTGTTCACACAAATGTAACAAGGGACCTTCCAAA
ATTGGTGCAAGTTGCTTATAATTTTATACCATTGTTTCTCTTTAGTGCCCAAGAAGGTTCAAGAAGTGCACTTTATGCAG
CTACTGCTCCTGAAATTCCTGAATACTGTAAGGCACTGAAGGCTGATGAATGGCCCACTTGTGCTTATATCTCACATGAT
TGTCGTCCCACACGTGCTGCCAACGAAGCACATAACACAAGAGCTGCTAATGAAGTATGGCAAAAGACATTGGATATGAT
TGGCCTTCCTCTTGATGCTGTAGAGAAGTTGCTCCAAGGGGAAGAAGTCATGTGCAAGTACAAGGATAGCTGA

Alignment

ORF - retro_ptri_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.76 %
• Parental protein coverage: 96.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSTPSTTVPKKKQGLGWVEWLRGWMYILYEMLFQRIMASHLQNPLSLPPINNLTCIVTGSTSGIGLQIAR
          SS..S....K.KQ...W...L.GW.Y..YEMLFQ...A.HL.NPL.LPP....TCI.TGSTSGIGL..AR
Retrocopy SSPRSSFTGKVKQTPWWMKSLTGWSYVIYEMLFQKMQARHLKNPLPLPPLHDVTCIITGSTSGIGLETAR

Parental  QLAESGAHVVMAVRNTKAAHDLIHKWQSEWTGLGLPLNIEVMELDLLSLESVSRFAEAWNARMGPLHVLI
          QLA.SGAHVVMAVRN..AA.DLI.KWQ.E..G..L.L..EVMEL.LLSL.SV.RFA.AWN.R..PL.VLI
Retrocopy QLAVSGAHVVMAVRNQSAAFDLIMKWQDERHGTSL-LSVEVMELNLLSLTSVVRFARAWNSRSKPLQVLI

Parental  NNAGIFSIRGPQKFSKDGYEEHMQVNHLAPALLSILLLPSLIRGSPSRIINVNSVMHYVGFVDTEDMNVI
          NNAGIFS...PQKFSKDGYE.H.QVN.LAPALLSILLLPSL..GSPSRIINVNS.MHY.GFVDT.DMN..
Retrocopy NNAGIFSMGEPQKFSKDGYETHQQVNFLAPALLSILLLPSLVKGSPSRIINVNSIMHYMGFVDTDDMNFT

Parental  SGKRKYTSLVGYTGSKLAQVMFSSVLHRRLPAESGISVLCVSPGVVQTNVARDLPKIVQAGYHLIPYFIF
          ..K.K..S...Y..SKLAQVMF.SVL..RLP.E.GI.VLCVSPG.V.TNV.RDLPK.VQ..Y..IP.F.F
Retrocopy LRKEKFNSTKAYSSSKLAQVMFNSVLQKRLPPEAGINVLCVSPGTVHTNVTRDLPKLVQVAYNFIPLFLF

Parental  NAQEGSRSALFSATDPQIPEYCELLKSDDWPVCAFISQDCRPTNPSEEAHNIDTAYEVWEKTLEMIGLPS
          .AQEGSRSAL..AT.P.IPEYC..LK.D.WP.CA.IS.DCRPT....EAHN...A.EVW.KTL.MIGLP.
Retrocopy SAQEGSRSALYAATAPEIPEYCKALKADEWPTCAYISHDCRPTRAANEAHNTRAANEVWQKTLDMIGLPL

Parental  DAIEKLIEGEEVRCRY
          DA.EKL..GEEV.C.Y
Retrocopy DAVEKLLQGEEVMCKY

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_15 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400010157	1 retrocopy	retro_stub_22,
Populus trichocarpa	POPTR_0015s05560	1 retrocopy	retro_ptri_15 ,
Solanum lycopersicum	Solyc03g098460.2	1 retrocopy	retro_slyc_7,