Protein Overview: YJR028W

General Information:
Name(s) found:	YJR028W [SGD]
Description(s) found: SHOW ONLY BEST	gi\|6322488\|ref\|NP_012563.1\| Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yjr [NCBI NR] gi\|1353063\|sp\|P47099.1\|YJ12A_YEAST RecName: Full=Transposon Ty1-JR2 Gag polyprotein; AltName: Full=Gag-p49; AltName: Full=Transposon Ty1 protein A; Short=TY1A; Short=TYA; AltName: Full=p58; Contains: RecName: Full=Capsid protein; Short=CA; AltName: Full=G [NCBI NR] gi\|1129163\|emb\|CAA60722.1\| Ty1A [Saccharomyces cerevisiae] [NCBI NR] pir\|\|S57046 TyA protein - yeast (Saccharomyces cerevisiae) retrotransposon Ty1.JR [NCBI NR] gi\|1015670\|emb\|CAA89555.1\| TY1A [Saccharomyces cerevisiae] [NCBI NR] (P47099) Transposon Ty1 protein A [Swiss-Prot] Transposon Ty1-JR2 Gag polyprotein OS=Saccharomyces cerevisiae GN=TY1A-JR2 PE=1 SV=1 [Swiss-Prot] TY1A TY1A protein [mips] - TY1A - TY1A protein [mips] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag [SGD] YJR028W, Chr X from 478036-479358 [yeast_orfs2] Chr X from 478036-479358 [yeastorf3.fasta] Chr X from 478037-479359 [yeastorf4.fasta] Chr X from 478038-479360 [yeastorf5.fasta] YJR028W SGDID:S0003789, Chr X from 478258-479580, Ty ORF [yeastflysequest.fasta] Ty ORF [Saccharomyces cerevisiae]gi\|1015670\|emb\|CAA89555.1\| TY1A [Saccharomyces cerevisiae]gi\|1129163\|emb\|CAA60722.1\| Ty1A [Saccharomyces cerevisiae]gi\|1353063\|sp\|P47099\|YJZ8_YEAST Transposon Ty1 protein Agi\|1078433\|pir\|\|S57046 TyA protein - yeast (Sa [nrdb_11152004_Chlamydomonas] YJR028W SGDID:S000003789, Chr X from 478258-479580, transposable_element_gene, "Ty ORF" [SGD_S-cerevisiae_na_12-16-2005_con_reversed.fasta] YJR028W SGDID:S000003789, Chr X from 478337-479659, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-l [yeast-contam.fasta] YJR028W SGDID:S000003789, Chr X from 478336-479658, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-l [yeast-200209-contam.fasta] Transposon Ty1 protein A [nr-271106-contam.fasta] Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag; Yjr028wp [Saccharomyces cerevis [nr-271106-contam.fasta] TY1A [Saccharomyces cerevisiae] [nr-271106-contam.fasta] Ty1A [Saccharomyces cerevisiae] [nr-271106-contam.fasta] YJR028W SGDID:S000003789, Chr X from 478336-479658, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-bovrabprots.fasta] YJR028W SGDID:S000003789, Chr X from 478337-479659, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-contam_custom.fasta] [chemostatdb.fasta] Transposon Ty1-JR2 Gag polyprotein OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) GN=TY1A-JR2 PE=2 SV=1 [UniProt_S_cerevisiae_20120516_05-16-2012_reversed.fasta] YJR028W SGDID:S000003789, Chr X from 478344-479666, Genome Release 64-1-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [yeast-030211-contam.fasta] YJR028W SGDID:S000003789, Chr X from 478344-479666, Genome Release 64-2-1, transposable_element_gene, "Retrotransposon TYA Gag gene co-transcribed with TYB Pol; translated as TYA or TYA-TYB polyprotein; Gag is a nucleocapsid protein that is the structural constituent of virus-like particles (VLPs); similar to retroviral Gag" [20141208_orf_trans.fasta]
Organism:	Saccharomyces cerevisiae
Length:	440 amino acids
Gene Ontology:
Cellular Component:	retrotransposon nucleocapsid [ISS]
Biological Process:	transposition, RNA-mediated [ISS]
Molecular Function:	RNA binding [ISS] protein binding [ISS]

Sequence:

Sequence:
[PDR BLAST]
[ProtParam]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MESQQLSQHS HISHGSACAS VTSKEVHTNQ DPLDVSASKT EECEKASTKA NSQQTTTPAS  60
   61 SAVPENPHHA SPQTAQSHSP QNGPYPQQCM MTQNQANPSG WSFYGHPSMI PYTPYQMSPM 120
  121 YFPPGPQSQF PQYPSSVGTP LSTPSPESGN TFTDSSSADS DMTSTKKYVR PPPMLTSPND 180
  181 FPNWVKTYIK FLQNSNLGGI IPTVNGKPVR QITDDELTFL YNTFQIFAPS QFLPTWVKDI 240
  241 LSVDYTDIMK ILSKSIEKMQ SDTQEANDIV TLANLQYNGS TPADAFETKV TNIIDRLNNN 300
  301 GIHINNKVAC QLIMRGLSGE YKFLRYTRHR HLNMTVAELF LDIHAIYEEQ QGSRNSKPNY 360
  361 RRNPSDEKND SRSYTNTTKP KVIARNPQKT NNSKSKTARA HNVSTSNNSP STDNDSISKS 420
  421 TTEPIQLNNK HDLHLRPETY

Protein Complex Data

	PUBLICATION	TOPOLOGY	COCOMPLEXED PROTEINS
View Details	Ho Y, et al. (2002)		CDC25 CKI1 GCR2 GIN4 HOM3 IRA1 IRA2 MYO2 MYO4 NAP1 PMD1 PRS2 PRS3 PRS5 RIM11 TPS1 TSL1 YDR170W-A YER138C YER160C YJR027W YJR028W
View Details	Qiu et al. (2008)		YDR210C-C YDR210C-D YJR028W YLR227W-A, YML04... YOR343W-A YOR343W-B YPR137C-A, YAR010C

Mass Spectrometry Data

The following runs contain data for this protein:

	BAIT	COMMENTS	PUBLICATION
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	RPA135	his-HA tag on RPA135	Schneider, DA, et al. (2006)
View Run	CEP3	sample cbf3 from feb 2005	Sandall S, et all (2006)
View Run	ZDS1	Sample 2- cpn2 from june 2005	McCusker D, et al (2007)
View Run	ZDS1	Sample 3 - cpn + atp, from june 2005	McCusker D, et al (2007)
View Run	BOI1	Sample boi 1 with ha tag from october 2005	McCusker D, et al (2007)
View Run	BOI1	Sample boi1 with gst from october 2005	McCusker D, et al (2007)
View Run	BOI1	Sample bob1 (2nd set) from october 2005	McCusker D, et al (2007)

Yeast Two-Hybrid Data

The following interactions contain this protein:

SHOWING SINGLE HITS. [ Hide Single Hits ]

[View our yeast two-hybrid interpretation guidelines.]

	BAIT	PREY	HITS	PUBLICATION
View Screen	CMD1	YJR028W	1	Unpublished Fields Lab Data
View Screen	TWF1	YJR028W	1	Unpublished Fields Lab Data
View Screen	PGA1	YJR028W	1	Unpublished Fields Lab Data

Microscopy / Localization Data

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No microscopy data found in the PDR for this protein.

Protein Structure Data

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[View Top Sequence Alignments] [Show Ginzu Version Information]

Domains predicted:

#		Region(s)	Method	Confidence	Match Description
1	View Details	[1..113]	Pfam	67.244125	No description for PF01021.10 was found. No confident structure predictions are available.
2	View Details	[114..176]	MSA	1.160992	View MSA. No confident structure predictions are available.
3	View Details	[177..333]	deduced	N/A	No confident structure predictions are available.
4	View Details	[334..440]	MSA	1.006973	View MSA. No confident structure predictions are available.

Reference: Malmström L, et al. (2007) Superfamily assignments for the yeast proteome through integration of structure prediction with the gene ontology. PLoS Biol 5(4): e76. doi:10.1371/journal.pbio.0050076

Philius Transmembrane Prediction:

Protein predicted to be:	GLOBULAR (No transmembrane regions or signal peptide)
Confidence of classification:	0.98

Source: Reynolds et al. (2008)

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2