Protein Help

RIF1 / YBR275C 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
DNA-binding protein RIF1
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.


Downloading... 1.00 MB

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-life6.5 hrChristiano R, et al. (2014)

Protein Abundance

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Abundance (molecules/cell)MediaTreatmentTreatment timeFold ChangeVisualizationStrain backgroundOriginal ReferenceReference
1315SDuntreatedconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1240SD1 mM hydrogen peroxide1 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
1128SD minus nitrogencellular response to nitrogen starvation15 hrconfocal microscopy evidenceS288CBreker M, et al. (2013)Ho B, et al. (2018)
3890SDuntreatedquantitative mass spectrometry evidenceS288Cde Godoy LM, et al. (2008)Ho B, et al. (2018)
91YEPDuntreatedquantitative mass spectrometry evidenceS288CKulak NA, et al. (2014)Ho B, et al. (2018)
Showing 1 to 5 of 11 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.


rif1-C466A | rif1-C466A,C473A | rif1-C473A | rif1-M436A,T564A,R565A,W572A | rif1-N560S | rif1-R299A,Q303A,R306A | rif1-RVxF,SILK | ... Show all

View all RIF1 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 MSKDFSDKKK HTIDRIDQHI LRRSQHDNYS NGSSPWMKTN LPPPSPQAHM HIQSDLSPTP
61 KRRKLASSSD CENKQFDLSA INKNLYPEDT GSRLMQSLPE LSASNSDNVS PVTKSVAFSD
121 RIESSPIYRI PGSSPKPSPS SKPGKSILRN RLPSVRTVSD LSYNKLQYTQ HKLHNGNIFT
181 SPYKETRVNP RALEYWVSGE IHGLVDNESV SEFKEIIEGG LGILRQESED YVARRFEVYA
241 TFNNIIPILT TKNVNEVDQK FNILIVNIES IIEICIPHLQ IAQDTLLSSS EKKNPFVIRL
301 YVQIVRFFSA IMSNFKIVKW LTKRPDLVNK LKVIYRWTTG ALRNENSNKI IITAQVSFLR
361 DEKFGTFFLS NEEIKPIIST FTEIMEINSH NLIYEKLLLI RGFLSKYPKL MIETVTSWLP
421 GEVLPRIIIG DEIYSMKILI TSIVVLLELL KKCLDFVDEH ERIYQCIMLS PVCETIPEKF
481 LSKLPLNSYD SANLDKVTIG HLLTQQIKNY IVVKNDNKIA MDLWLSMTGL LYDSGKRVYD
541 LTSESNKVWF DLNNLCFINN HPKTRLMSIK VWRIITYCIC TKISQKNQEG NKSLLSLLRT
601 PFQMTLPYVN DPSAREGIIY HLLGVVYTAF TSNKNLSTDM FELFWDHLIT PIYEDYVFKY
661 DSIHLQNVLF TVLHLLIGGK NADVALERKY KKHIHPMSVI ASEGVKLKDI SSLPPQIIKR
721 EYDKIMKVVF QAVEVAISNV NLAHDLILTS LKHLPEDRKD QTHLESFSSL ILKVTQNNKD
781 TPIFRDFFGA VTSSFVYTFL DLFLRKNDSS LVNFNIQISK VGISQGNMTL DLLKDVIRKA
841 RNETSEFLII EKFLELDDKK TEVYAQNWVG STLLPPNISF REFQSLANIV NKVPNENSIE
901 NFLDLCLKLS FPVNLFTLLH VSMWSNNNFI YFIQSYVSKN ENKLNVDLIT LLKTSLPGNP
961 ELFSGLLPFL RRNKFMDILE YCIHSNPNLL NSIPDLNSDL LLKLLPRSRA SYFAANIKLF
1021 KCSEQLTLVR WLLKGQQLEQ LNQNFSEIEN VLQNASDSEL EKSEIIRELL HLAMANPIEP
1081 LFSGLLNFCI KNNMADHLDE FCGNMTSEVL FKISPELLLK LLTYKEKPNG KLLAAVIEKI
1141 ENGDDDYILE LLEKIIIQKE IQILEKLKEP LLVFFLNPVS SNMQKHKKST NMLRELVLLY
1201 LTKPLSRSAA KKFFSMLISI LPPNPNYQTI DMVNLLIDLI KSHNRKFKDK RTYNATLKTI
1261 GKWIQESGVV HQGDSSKEIE AIPDTKSMYI PCEGSENKLS NLQRKVDSQD IQVPATQGMK
1321 EPPSSIQISS QISAKDSDSI SLKNTAIMNS SQQESHANRS RSIDDETLEE VDNESIREID
1381 QQMKSTQLDK NVANHSNICS TKSDEVDVTE LHESIDTQSS EVNAYQPIEV LTSELKAVTN
1441 RSIKTNPDHN VVNSDNPLKR PSKETPTSEN KRSKGHETMV DVLVSEEQAV SPSSDVICTN
1501 IKSIANEESS LALRNSIKVE TNCNENSLNV TLDLDQQTIT KEDGKGQVEH VQRQENQESM
1561 NKINSKSFTQ DNIAQYKSVK KARPNNEGEN NDYACNVEQA SPVRNEVPGD GIQIPSGTIL
1621 LNSSKQTEKS KVDDLRSDED EHGTVAQEKH QVGAINSRNK NNDRMDSTPI QGTEEESREV
1681 VMTEEGINVR LEDSGTCELN KNLKGPLKGD KDANINDDFV PVEENVRDEG FLKSMEHAVS
1741 KETGLEEQPE VADISVLPEI RIPIFNSLKM QGSKSQIKEK LKKRLQRNEL MPPDSPPRMT
1801 ENTNINAQNG LDTVPKTIGG KEKHHEIQLG QAHTEADGEP LLGGDGNEDA TSREATPSLK
1861 VHFFSKKSRR LVARLRGFTP GDLNGISVEE RRNLRIELLD FMMRLEYYSN RDNDMN*

* 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.

116 entries for 55 sites

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SiteModificationModifierReference
S6phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
K38ubiquitinylated lysineSwaney DL, et al. (2013) PMID: 23749301
S45phosphorylated residueCDC28Holt LJ, et al. (2009) PMID: 19779198
S45phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S45phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
S54phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S57phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S57phosphorylated residueLanz MC, et al. (2021) PMID: 33491328
T59phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
S67phosphorylated residueSwaney DL, et al. (2013) PMID: 23749301
Showing 1 to 10 of 116 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
A643.34
C190.99
D1075.58
E1457.57
F693.60
G683.55
H422.19
I1548.04
K1527.93
L20810.86
M412.14
N1517.88
P894.65
Q774.02
R794.12
S1869.71
T965.01
V1115.79
W130.68
Y452.35

Physical Details

Length (a.a): 1916
Molecular Weight (Da): 217911.8
Isoelectric Point (pl): 6.52
Formula: C9653H15469N2630O2976S60
Aliphatic Index: 90.04
Instability Index: 47.33

Coding Region Translation Calculations

Codon Bias: -0.02
Codon Adaptation Index: 0.12
Frequence of Optimal Codons: 0.42
Hydropathicity of Protein: -0.44
Aromaticity Score: 0.07

Extinction Coefficients at 280nm

ALL Cys residues appear as half cystines: 139675.0
NO Cys residues appear as half cystines: 138550.0

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.

42 entries for 10 sources


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External IDSource
orf19.427CGD
801DIP
X76053GenBank/EMBL/DDBJ
513137167GenBank/EMBL/DDBJ
513137164GenBank/EMBL/DDBJ
Z36144GenBank/EMBL/DDBJ
X66501GenBank/EMBL/DDBJ
CAA85240.1GenBank/EMBL/DDBJ
CAA53638.1GenBank/EMBL/DDBJ
CAA47121.1GenBank/EMBL/DDBJ
Showing 1 to 10 of 42 entries

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