RetrogeneDB ID: retro_ptri_13

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 2:7562544..7563921(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0002s10480
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0001s06560
• Aliases: None
• Description: None

Sequence

>retro_ptri_13
ATGCACACACAACAACAATCTTACCTTGTCCGCTGTTCCTTCAGCTCAGAGTCCATAGCCATGGACTTCCCTCACTGTGC
TGCTACATTCTTTTTGTTTGCCCTTCTATTCTCGACTACTAAAGCTGTAGATCCTTGTGCCACTCAGTCAGACACCTCTG
ATCTCTCTGTCATTCCCATCTATAGCAAATGCTCACCTTTTGTTCCGCCCAAGCAAGAATCATGGGTTAACACGGTCATC
ACCATGGCCTCAAAAGACCCAGAAAGGCTCAAATATTTATCAACGCTAGCAGACCAAAAGACCACTGCAGTCCCAATTGC
CCCGGGTCAGCAAGTCCTAAAGATTGCTAACTATGTGGTCCGGGTCAAGTTGGGCACCCCGGGTCAACAAATGTTCATGG
TCCTTGACACCAGCAACGATGCTGCATGGGTACCATGCTCAGGGTGCACCGGATGCTCCAGCACCACATTCTTACCCAAT
GCCTCTACGACTCTTGGGTCACTGGACTGTTCTGGAGCCCAATGCTCCCAAGTCCGTGGATTTTCCTGCCCAGCTACCGG
GTCCTCCGCTTGCCTTTTTAACCAATCTTACGGTGGAGACTCCTCCTTAACAGCTACTCTTGTGCAAGATGCAATAACAT
TAGCCAACGATGTAATTCCAGGTTTTACTTTTGGATGCATTAACGCAGTCTCCGGTGGGTCAATACCACCCCAAGGGTTA
TTGGGTCTGGGCCGTGGACCCATCTCGTTAATTTCTCAAGCAGGGGCAATGTACTCGGGTGTCTTCTCTTATTGTCTACC
CAGTTTCAAGAGCTACTACTTCTCAGGTTCTCTCAAGCTCGGCCCTGTTGGTCAACCCAAGTCCATTAGGACCACCCCAC
TTCTACGAAACCCCCACCGCCCATCCCTATACTACGTTAACCTAACTGGAGTTAGCGTGGGCCGGATCAAAGTACCAATT
CCCTCTGAACAACTTGTTTTTGACCCAAATACCGGAGCAGGGACCATAATCGACTCCGGTACAGTCATAACCCGATTTGT
CCAACCCGTTTACTTTGCCATCCGCGATGAGTTTAGAAAGCAAGTGAATGGCCCAATCTCAAGTTTAGGTGCCTTCGACA
CATGCTTTGCTGCAACAAATGAAGCAGAAGCACCTGCAATAACGCTACACTTCGAGGGCTTGAACTTGGTCTTGCCCATG
GAGAACAGCTTGATACATAGCAGTTCTGGCTCACTAGCATGCTTGTCTATGGCTGCAGCACCAAACAATGTGAATTCAGT
GTTGAATGTTATAGCCAATTTGCAGCAGCAGAACCTTAGGATTATGTTTGACACGACCAATTCCCGTTTGGGAATTGCCC
GTGAGCTATGTAACTAG

Alignment

ORF - retro_ptri_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.08 %
• Parental protein coverage: 99.29 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  YLFSLAFLFLSLVQGLNTRGQGTTVKVFHVYSPQSPFRPSKPVSWEDSVLQMLAEDQARLQFLSSLVGRK
          .LF.L.F.....V....T........V...YS..SPF.P.K..SW...V..M...D..RL..LS.L...K
Retrocopy FLFALLFSTTKAVDPCATQSDTSDLSVIPIYSKCSPFVPPKQESWVNTVITMASKDPERLKYLSTLADQK

Parental  SW-VPIASGRQIVQSPTYIVKANVGTPAQTFLMALDTSNDAAWIPCNGCVGCSSTVFNSVTSTTFKTLGC
          ...VPIA.G.Q......Y.V....GTP.Q...M.LDTSNDAAW.PC.GC.GCSST.F....STT...L.C
Retrocopy TTAVPIAPGQQVLKIANYVVRVKLGTPGQQMFMVLDTSNDAAWVPCSGCTGCSSTTFLPNASTTLGSLDC

Parental  DAPQCKQVPNPTC---GGSTCTWNTTYGG-STILSNLTRDTIALSTDIVPGYTFGCIQKTTGSSVPPQGL
          ...QC.QV....C...G.S.C..N..YGG.S.....L..D.I.L..D..PG.TFGCI....G.S.PPQGL
Retrocopy SGAQCSQVRGFSCPATGSSACLFNQSYGGDSSLTATLVQDAITLANDVIPGFTFGCINAVSGGSIPPQGL

Parental  LGLGRGPLSFLSQTQDLYKSTFSYCLPSFRTLNFSGTLRLGPAGQPLRIKTTPLLKNPRRSSLYYVNLIG
          LGLGRGP.S..SQ....Y...FSYCLPSF....FSG.L.LGP.GQP..I.TTPLL.NP.R.SLYYVNL.G
Retrocopy LGLGRGPISLISQAGAMYSGVFSYCLPSFKSYYFSGSLKLGPVGQPKSIRTTPLLRNPHRPSLYYVNLTG

Parental  IRVGRKIVDIPASALAFNPTTGAGTIFDSGTVFTRLVAPVYTAVRDEFRKRVGNAIVSSLGGFDTCY--T
          ..VGR..V.IP...L.F.P.TGAGTI.DSGTV.TR.V.PVY.A.RDEFRK.V.N...SSLG.FDTC...T
Retrocopy VSVGRIKVPIPSEQLVFDPNTGAGTIIDSGTVITRFVQPVYFAIRDEFRKQV-NGPISSLGAFDTCFAAT

Parental  GPIVAPTMTFMFSGMNVTLPPDNLLIRSTAGSTSCLAMAAAPDNVNSVLNVIANMQQQNHRILFDVPNSR
          ....AP..T..F.G.N..LP..N.LI.S..GS..CL.MAAAP.NVNSVLNVIAN.QQQN.RI.FD..NSR
Retrocopy NEAEAPAITLHFEGLNLVLPMENSLIHSSSGSLACLSMAAAPNNVNSVLNVIANLQQQNLRIMFDTTNSR

Parental  IGVAREPCS
          .G.ARE.C.
Retrocopy LGIARELCN

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_13 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g083640	1 retrocopy	retro_bole_10,
Brassica rapa	Bra014819	1 retrocopy	retro_brap_21,
Medicago truncatula	MTR_8g039540	1 retrocopy	retro_mtru_20,
Populus trichocarpa	POPTR_0001s06560	1 retrocopy	retro_ptri_13 ,
Prunus persica	PRUPE_ppa005966mg	1 retrocopy	retro_pper_11,
Theobroma cacao	TCM_045111	1 retrocopy	retro_tcac_5,
Vitis vinifera	VIT_13s0084g00820	1 retrocopy	retro_vvin_28,