Protein Help

DIP2 / YLR129W 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.


Aliases
UTP12 2
Protein Product
snoRNA-binding rRNA-processing protein DIP2
Feature Type
ORF , Verified

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.


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

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ExperimentResultReference
half-life9.4 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1645SDuntreatedconfocal microscopy evidenceS288CChong YT, et al. (2015)Ho B, et al. (2018)
4857SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
9620YEPDuntreatedqualitative western immunoblotting evidenceS288CGhaemmaghami S, et al. (2003)Ho B, et al. (2018)
3007YEPDuntreatedquantitative mass spectrometry evidenceS288CKulak NA, et al. (2014)Ho B, et al. (2018)
504SDuntreatedquantitative mass spectrometry evidenceCEN.PKLahtvee PJ, et al. (2017)Ho B, et al. (2018)
Showing 1 to 5 of 13 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.


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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.


dip2-5001 | dip2-ts | dip2-Δ | ylr129w-DAmP

View all DIP2 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 MVKSYQRFEQ AAAFGVIASN ANCVWIPASS GNSNGSGPGQ LITSALEDVN IWDIKTGDLV
61 SKLSDGLPPG ASDARGAKPA ECTYLEAHKD TDLLAVGYAD GVIKVWDLMS KTVLLNFNGH
121 KAAITLLQFD GTGTRLISGS KDSNIIVWDL VGEVGLYKLR SHKDSITGFW CQGEDWLIST
181 SKDGMIKLWD LKTHQCIETH IAHTGECWGL AVKDDLLITT GTDSQVKIWK LDIENDKMGG
241 KLTEMGIFEK QSKQRGLKIE FITNSSDKTS FFYIQNADKT IETFRIRKEE EIARGLKKRE
301 KRLKEKGLTE EEIAKSIKES YSSFILHPFQ TIRSLYKIKS ASWTTVSSSK LELVLTTSSN
361 TIEYYSIPYE KRDPTSPAPL KTHTIELQGQ RTDVRSIDIS DDNKLLATAS NGSLKIWNIK
421 THKCIRTFEC GYALTCKFLP GGLLVILGTR NGELQLFDLA SSSLLDTIED AHDAAIWSLD
481 LTSDGKRLVT GSADKTVKFW DFKVENSLVP GTKNKFLPVL KLHHDTTLEL TDDILCVRVS
541 PDDRYLAISL LDNTVKVFFL DSMKFYLSLY GHKLPVLSID ISFDSKMIIT SSADKNIKIW
601 GLDFGDCHKS LFAHQDSIMN VKFLPQSHNF FSCSKDAVVK YWDGEKFECI QKLYAHQSEV
661 WALAVATDGG FVVSSSHDHS IRIWEETEDQ VFLEEEKEKE LEEQYEDTLL TSLEEGNGDD
721 AFKADASGEG VEDEASGVHK QTLESLKAGE RLMEALDLGI AEIEGLEAYN RDMKLWQRKK
781 LGEAPIKPQG NAVLIAVNKT PEQYIMDTLL RIRMSQLEDA LMVMPFSYVL KFLKFIDTVM
841 QNKTLLHSHL PLICKNLFFI IKFNHKELVS QKNEELKLQI NRVKTELRSA LKSTEDDLGF
901 NVQGLKFVKQ QWNLRHNYEF VDEYDQQEKE SNSARKRVFG TVI*

* 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.

8 entries for 4 sites

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SiteModificationModifierReference
K237monoacetylated residueHenriksen P, et al. (2012) PMID: 22865919
S727phosphorylated residueZhou X, et al. (2021) PMID: 33481703
S727phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S727phosphorylated residueHolt LJ, et al. (2009) PMID: 19779198
S727phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S736phosphorylated residueZhou X, et al. (2021) PMID: 33481703
S736phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S933phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
Showing 1 to 8 of 8 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
A535.62
C131.38
D687.21
E687.21
F414.35
G586.15
H242.55
I656.89
K859.01
L10511.13
M151.59
N353.71
P212.23
Q333.50
R303.18
S798.38
T596.26
V505.30
W192.01
Y222.33

Physical Details

Length (a.a): 943
Molecular Weight (Da): 106322.1
Isoelectric Point (pl): 5.89
Formula: C4764H7490N1253O1444S28
Aliphatic Index: 87.63
Instability Index: 40.97

Coding Region Translation Calculations

Codon Bias: 0.07
Codon Adaptation Index: 0.17
Frequence of Optimal Codons: 0.47
Hydropathicity of Protein: -0.31
Aromaticity Score: 0.09

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 138030.0
NO Cys residues appear as half cystines: 137280.0

Atomic Composition

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Atom Frequency Percentage

Data not found or not available for  S288C

External Identifiers

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

31 entries for 9 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
AN0305AspGD
orf19.5106CGD
6494DIP
6323158GenBank/EMBL/DDBJ
CAA97699.1GenBank/EMBL/DDBJ
CAA62640.1GenBank/EMBL/DDBJ
AAB82375.1GenBank/EMBL/DDBJ
AAB82402.1GenBank/EMBL/DDBJ
CAA61707.1GenBank/EMBL/DDBJ
CAA97700.1GenBank/EMBL/DDBJ
Showing 1 to 10 of 31 entries

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