Protein Help

TRF5 / YNL299W Protein

Protein abundance data, domains, shared domains with other proteins, protein sequence retrieval for various strains, sequence-based physico-chemical properties, protein modification sites, and external identifiers for the protein.


Protein Product
non-canonical poly(A) polymerase TRF5
Feature Type
ORF , Verified
Paralog
PAP2
EC Number
2.7.7.19

AlphaFold Protein Structure

AlphaFold, developed by DeepMind, is an AI program that accurately predicts protein structures from amino acid sequences, enabling visualization of protein conformations. The predicted structures can be accessed through the Protein Data Bank (PDB) and AlphaFold Protein Structure Database.


Parsing response... [0/0]

Model Confidence

Very high
Confident
Low
Very low

Experimental Data

Contains experimentally-derived protein half-life data obtained using stable isotope labeling by amino acids (SILAC) coupled with mass spectrometry. This section also contains protein abundance data for both untreated and treated cells obtained from over 20 studies. These data have been normalized and converted to a common unit of molecules per cell.


Protein Half Life

No half-life data available for TRF5.

Protein Abundance

Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through its pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1169SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1586SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
2240YEPDuntreatedqualitative western immunoblotting evidenceS288CGhaemmaghami S, et al. (2003)Ho B, et al. (2018)
166YEPDuntreatedquantitative mass spectrometry evidenceS288CKulak NA, et al. (2014)Ho B, et al. (2018)
2424YEPD0.02% methyl methanesulfonate2 hrflow cytometry evidenceS288CLee MW, et al. (2007)Ho B, et al. (2018)
Showing 1 to 5 of 9 entries

Domains and Classification - S288C

Collection of computationally identified domains and motifs, as determined by InterProScan analysis; includes protein coordinates for the domain, a domain Description, a Source and corresponding accession ID, and the number of S. cerevisiae genes that share the same domain.


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through its pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

Gene Protein Coordinates Accession ID Description Source No. of Genes with Domain

Domain Locations

Visual representation of the locations of the domains within the protein, as listed in the Domains and Classification table. Each row displays the domain(s) derived from a different Source, with domains color-coded according to this Source.

Scroll over a domain to view its exact coordinates and its Description.

Shared Domains

This diagram displays domains (colored squares) shared between the given protein (yellow circle) and other proteins (gray circles); the domains are color-coded according to their source, as displayed in the Domain Locations table, above.

Reset

Click on a gene or domain name to go to its specific page within SGD; drag any of the gene or domain objects around within the visualization for easier viewing; click “Reset” to automatically redraw the diagram.

Alleles

Curated mutant alleles for the specified gene, listed alphabetically. Click on the allele name to open the allele page. Click "SGD search" to view all alleles in search results.


trf5-Δ

View all TRF5 alleles in SGD search

Sequence

Protein sequence for the given gene in S288C and other strains, when available. Use the pull-down menu under "Strain" to select the sequence for a specific strain. The displayed sequence can be downloaded in FASTA format as a .txt file. Amino acids displayed in blue represent modification sites. More detailed evidence for these modification sites is presented in the Post-translational Modifications table, located just below the protein sequence.


1 MTRLKAKYSP TKGKRKEDKH TKRMRKSSFT RTQKMLEVFN DNRSHFNKYE SLAIDVEDDD
61 TFGNLVLMEN DKSDVDIPVI EEVTSSEDEQ RAESSKRNNS LEDNQDFIAF SDSSEDETEQ
121 IKEDDDERSS FLLTDEHEVS KLTSQQSLNT ESACNVEYPW IRNHCHSKQR RIADWLTSEI
181 KDFVHYISPS KNEIKCRNRT IDKLRRAVKE LWSDADLHVF GSFATDLYLP GSDIDCVVNS
241 RNRDKEDRNY IYELARHLKN KGLAIRMEVI VKTRVPIIKF IEPQSQLHID VSFERTNGLE
301 AAKLIREWLR DSPGLRELVL IIKQFLHSRR LNNVHTGGLG GFTVICLVYS FLNMHPRIKS
361 NDIDVLDNLG VLLIDFFELY GKNFGYDDVA ISISDGYASY IPKSCWRTLE PSRSKFSLAI
421 QDPGDPNNNI SRGSFNMKDI KKAFAGAFEL LVNKCWELNS ATFKDRVGKS ILGNVIKYRG
481 QKRDFNDERD LVQNKAIIEN ERYHKRRTRI VQEDLFINDT EDLPVEEIYK LDEPAKKKQK
541 AKKDKREGEI KKSAIPSPPP DFGVSRSKLK RKVKKTDQGS LLHQNNLSID DLMGLSENDQ
601 ESDQDQKGRD TPSGQDEKSP LETKTVDAQT RRDYWLSKGQ AL*

* Blue amino acids indicate modification sites. More information below.

Post-translational Modifications - S288C

Modification sites for the protein in the selected strain, based on the presence of a residue in the specific strain, as inferred from experimental evidence.

14 entries for 6 sites

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SiteModificationModifierReference
S9phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S9phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S9phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S28phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S557phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S557phosphorylated residueZhou X, et al. (2021) PMID: 33481703
T611phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T611phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S613phosphorylated residueMacGilvray ME, et al. (2020) PMID: 32597660
S613phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
Showing 1 to 10 of 14 entries

Sequence-Based Physico-chemical Properties - S288C

Calculated protein properties, including amino acid composition, length, coding region calculations, and atomic composition.

Amino Acid Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Amino AcidFrequencyPercentage
A264.05
C71.09
D609.35
E497.63
F264.05
G284.36
H142.18
I426.54
K609.35
L558.57
M81.25
N385.92
P213.27
Q233.58
R467.17
S568.72
T274.21
V335.14
W71.09
Y162.49

Physical Details

Length (a.a): 642
Molecular Weight (Da): 74177.3
Isoelectric Point (pl): 7.03
Formula: C3250H5173N936O1021S15
Aliphatic Index: 72.99
Instability Index: 49.7

Coding Region Translation Calculations

Codon Bias: 0.03
Codon Adaptation Index: 0.14
Frequence of Optimal Codons: 0.45
Hydropathicity of Protein: -0.82
Aromaticity Score: 0.08

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 62715.0
NO Cys residues appear as half cystines: 62340.0

Atomic Composition

Sort table using the arrow to the right of a column header to sort by that column; download all properties as a .txt file using the "Download Properties" button.

Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

List of external identifiers for the protein from various database sources.

22 entries for 8 sources


Increase the total number of rows showing on this page by using the pull-down located below the table, or use the page scroll at the table's top right to browse through its pages; use the arrows to the right of a column header to sort by that column; filter the table using the "Filter" box at the top of the table.

External IDSource
2.7.7.19ExPASy
U47282GenBank/EMBL/DDBJ
Z71575GenBank/EMBL/DDBJ
1050861GenBank/EMBL/DDBJ
81360384GenBank/EMBL/DDBJ
1302392GenBank/EMBL/DDBJ
1493831GenBank/EMBL/DDBJ
1353104GenBank/EMBL/DDBJ
148887014GenBank/EMBL/DDBJ
AAC49099.1GenBank/EMBL/DDBJ
Showing 1 to 10 of 22 entries

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