Human Gene SSRP1 (uc001njt.3) Description and Page Index
  Description: Homo sapiens structure specific recognition protein 1 (SSRP1), mRNA.
RefSeq Summary (NM_003146): The protein encoded by this gene is a subunit of a heterodimer that, along with SUPT16H, forms chromatin transcriptional elongation factor FACT. FACT interacts specifically with histones H2A/H2B to effect nucleosome disassembly and transcription elongation. FACT and cisplatin-damaged DNA may be crucial to the anticancer mechanism of cisplatin. This encoded protein contains a high mobility group box which most likely constitutes the structure recognition element for cisplatin-modified DNA. This protein also functions as a co-activator of the transcriptional activator p63. An alternatively spliced transcript variant of this gene has been described, but its full-length nature is not known. [provided by RefSeq, Jul 2008]. Publication Note: This RefSeq record includes a subset of the publications that are available for this gene. Please see the Gene record to access additional publications. ##Evidence-Data-START## Transcript exon combination :: SRR3476690.41674.1, M86737.1 [ECO:0000332] RNAseq introns :: mixed/partial sample support SAMEA1965299, SAMEA1966682 [ECO:0000350] ##Evidence-Data-END## ##RefSeq-Attributes-START## MANE Ensembl match :: ENST00000278412.7/ ENSP00000278412.2 RefSeq Select criteria :: based on conservation, expression ##RefSeq-Attributes-END##
Transcript (Including UTRs)
   Position: hg19 chr11:57,093,459-57,103,351 Size: 9,893 Total Exon Count: 17 Strand: -
Coding Region
   Position: hg19 chr11:57,093,881-57,102,595 Size: 8,715 Coding Exon Count: 16 

Page IndexSequence and LinksUniProtKB CommentsCTDGene AllelesRNA-Seq Expression
Microarray ExpressionRNA StructureProtein StructureOther SpeciesGO AnnotationsmRNA Descriptions
PathwaysOther NamesModel InformationMethods
Data last updated: 2013-06-14

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr11:57,093,459-57,103,351)mRNA (may differ from genome)Protein (709 aa)
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UniProtKBWikipedia

-  Comments and Description Text from UniProtKB
  ID: SSRP1_HUMAN
DESCRIPTION: RecName: Full=FACT complex subunit SSRP1; AltName: Full=Chromatin-specific transcription elongation factor 80 kDa subunit; AltName: Full=Facilitates chromatin transcription complex 80 kDa subunit; Short=FACT 80 kDa subunit; Short=FACTp80; AltName: Full=Facilitates chromatin transcription complex subunit SSRP1; AltName: Full=Recombination signal sequence recognition protein 1; AltName: Full=Structure-specific recognition protein 1; Short=hSSRP1; AltName: Full=T160;
FUNCTION: Component of the FACT complex, a general chromatin factor that acts to reorganize nucleosomes. The FACT complex is involved in multiple processes that require DNA as a template such as mRNA elongation, DNA replication and DNA repair. During transcription elongation the FACT complex acts as a histone chaperone that both destabilizes and restores nucleosomal structure. It facilitates the passage of RNA polymerase II and transcription by promoting the dissociation of one histone H2A-H2B dimer from the nucleosome, then subsequently promotes the reestablishment of the nucleosome following the passage of RNA polymerase II. The FACT complex is probably also involved in phosphorylation of 'Ser-392' of p53/TP53 via its association with CK2 (casein kinase II). Binds specifically to double-stranded DNA and at low levels to DNA modified by the antitumor agent cisplatin. May potentiate cisplatin-induced cell death by blocking replication and repair of modified DNA. Also acts as a transcriptional coactivator for p63/TP63.
SUBUNIT: Component of the FACT complex, a stable heterodimer of SSRP1 and SUPT16H. Also component of a CK2-SPT16-SSRP1 complex which forms following UV irradiation, composed of SSRP1, SUPT16H, CSNK2A1, CSNK2A2 and CSNK2B. Binds to histone H3-H4 tetramers, but not to intact nucleosomes. Interacts with isoform gamma of TP63. Interacts with FYTTD1/UIF, SRF and NEK9.
SUBCELLULAR LOCATION: Nucleus. Nucleus, nucleolus. Chromosome. Note=Colocalizes with RNA polymerase II on chromatin. Recruited to actively transcribed loci.
DOMAIN: The HMG box DNA-binding domain mediates DNA-binding. It has both affinity and specificity for DNA damaged globally with cisplatin.
PTM: Phosphorylated by CK2 following UV but not gamma irradiation. Phosphorylation inhibits its DNA-binding activity.
PTM: Ubiquitinated. Polyubiquitinated following caspase cleavage resulting in degradation of the N-terminal ubiquitinated part of the cleaved protein.
PTM: Sumoylated.
MISCELLANEOUS: Autoantibodies against SSRP1 are present in sera from patients with systemic lupus erythematosus, but not other rheumatic diseases.
SIMILARITY: Belongs to the SSRP1 family.
SIMILARITY: Contains 1 HMG box DNA-binding domain.
SEQUENCE CAUTION: Sequence=AAH91486.1; Type=Miscellaneous discrepancy; Note=Contaminating sequence. Potential poly-A sequence;

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
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-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 88.32 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 1995.13 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
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-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -121.94267-0.457 Picture PostScript Text
3' UTR -144.80422-0.343 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR013719 - DUF1747
IPR009071 - HMG_superfamily
IPR000969 - SSrcognition
IPR024954 - SSRP1_dom

Pfam Domains:
PF00505 - HMG (high mobility group) box
PF03531 - Structure-specific recognition protein (SSRP1)
PF08512 - Histone chaperone Rttp106-like
PF09011 - HMG-box domain
PF17292 - POB3-like N-terminal PH domain

SCOP Domains:
47095 - HMG-box

ModBase Predicted Comparative 3D Structure on Q08945
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologGenome BrowserGenome BrowserGenome BrowserGenome BrowserGenome Browser
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 Protein SequenceProtein SequenceProtein SequenceProtein SequenceProtein Sequence
 AlignmentAlignmentAlignmentAlignmentAlignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0003677 DNA binding
GO:0003682 chromatin binding
GO:0003723 RNA binding
GO:0005515 protein binding

Biological Process:
GO:0006260 DNA replication
GO:0006281 DNA repair
GO:0006351 transcription, DNA-templated
GO:0006355 regulation of transcription, DNA-templated
GO:0006357 regulation of transcription from RNA polymerase II promoter
GO:0006366 transcription from RNA polymerase II promoter
GO:0006368 transcription elongation from RNA polymerase II promoter
GO:0006974 cellular response to DNA damage stimulus
GO:1901796 regulation of signal transduction by p53 class mediator

Cellular Component:
GO:0005634 nucleus
GO:0005654 nucleoplasm
GO:0005694 chromosome
GO:0005730 nucleolus


-  Descriptions from all associated GenBank mRNAs
  M86737 - Human high mobility group box (SSRP1) mRNA, complete cds.
AB209132 - Homo sapiens mRNA for structure specific recognition protein 1 variant protein.
BC005116 - Homo sapiens structure specific recognition protein 1, mRNA (cDNA clone MGC:1608 IMAGE:3536048), complete cds.
JD216971 - Sequence 197995 from Patent EP1572962.
JD455422 - Sequence 436446 from Patent EP1572962.
JD277276 - Sequence 258300 from Patent EP1572962.
JD242269 - Sequence 223293 from Patent EP1572962.
JD442207 - Sequence 423231 from Patent EP1572962.
JD294540 - Sequence 275564 from Patent EP1572962.
JD359033 - Sequence 340057 from Patent EP1572962.
JD058224 - Sequence 39248 from Patent EP1572962.
JD274337 - Sequence 255361 from Patent EP1572962.
JD536039 - Sequence 517063 from Patent EP1572962.
JD037188 - Sequence 18212 from Patent EP1572962.
DQ893659 - Synthetic construct clone IMAGE:100006289; FLH188095.01X; RZPDo839G05150D structure specific recognition protein 1 (SSRP1) gene, encodes complete protein.
KJ892206 - Synthetic construct Homo sapiens clone ccsbBroadEn_01600 SSRP1 gene, encodes complete protein.
DQ895832 - Synthetic construct Homo sapiens clone IMAGE:100010292; FLH188091.01L; RZPDo839G05149D structure specific recognition protein 1 (SSRP1) gene, encodes complete protein.
BC091486 - Homo sapiens structure specific recognition protein 1, mRNA (cDNA clone IMAGE:6526385), partial cds.
CU674997 - Synthetic construct Homo sapiens gateway clone IMAGE:100020031 5' read SSRP1 mRNA.
JD115417 - Sequence 96441 from Patent EP1572962.
JD166037 - Sequence 147061 from Patent EP1572962.
JD520105 - Sequence 501129 from Patent EP1572962.
JD286327 - Sequence 267351 from Patent EP1572962.
JD109703 - Sequence 90727 from Patent EP1572962.
JD081679 - Sequence 62703 from Patent EP1572962.
JD484656 - Sequence 465680 from Patent EP1572962.
JD128347 - Sequence 109371 from Patent EP1572962.
JD125011 - Sequence 106035 from Patent EP1572962.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein Q08945 (Reactome details) participates in the following event(s):

R-HSA-112429 Formation of FACT complex
R-HSA-112379 Recruitment of elongation factors to form elongation complex
R-HSA-167077 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-167196 Recruitment of elongation factors to form HIV-1 elongation complex
R-HSA-6805061 CK2 binds FACT
R-HSA-113429 Elongating transcript encounters a lesion in the template
R-HSA-112385 Addition of nucleotides leads to transcript elongation
R-HSA-113411 2-4 nt.backtracking of Pol II complex on the template leading to elongation pausing
R-HSA-113412 Pol II elongation complex moves on the template as transcript elongates
R-HSA-113414 7-14 nt. Backtracking of Pol II complex on the template leading to elongation arrest
R-HSA-112392 Resumption of elongation after recovery from pausing
R-HSA-113413 TFIIS-mediated recovery of elongation from arrest
R-HSA-112395 Abortive termination of elongation after arrest
R-HSA-112396 Separation of elongating transcript from template
R-HSA-167150 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167076 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167282 2-4 nt.backtracking of Pol II complex on the HIV-1 template leading to elongation pausing
R-HSA-167284 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-167288 TFIIS-mediated recovery of HIV-1 elongation from arrest
R-HSA-167292 Resumption of elongation of HIV-1 transcript after recovery from pausing
R-HSA-167148 TFIIS-mediated recovery of elongation from arrest
R-HSA-167459 Abortive termination of HIV-1 elongation after arrest (Tat-containing elongation complex)
R-HSA-167090 7-14 nt. Backtracking of Pol II complex on the HIV-1 template leading to elongation arrest
R-HSA-167192 Pol II elongation complex moves on the HIV-1 template as transcript elongates
R-HSA-167181 Addition of nucleotides leads to HIV-1 transcript elongation
R-HSA-167197 Separation of elongating HIV-1 transcript from template
R-HSA-167481 Abortive termination of HIV-1 elongation after arrest
R-HSA-6797616 CCNK:CDK12 binds RNA Pol II at DNA repair genes
R-HSA-6797606 CDK12 phosphorylates RNA Pol II CTD at DNA repair genes
R-HSA-6805059 CK2:FACT phosphorylates TP53
R-HSA-674695 RNA Polymerase II Pre-transcription Events
R-HSA-112382 Formation of RNA Pol II elongation complex
R-HSA-167152 Formation of HIV elongation complex in the absence of HIV Tat
R-HSA-167200 Formation of HIV-1 elongation complex containing HIV-1 Tat
R-HSA-6804756 Regulation of TP53 Activity through Phosphorylation
R-HSA-73857 RNA Polymerase II Transcription
R-HSA-75955 RNA Polymerase II Transcription Elongation
R-HSA-167238 Pausing and recovery of Tat-mediated HIV elongation
R-HSA-167290 Pausing and recovery of HIV elongation
R-HSA-167287 HIV elongation arrest and recovery
R-HSA-167243 Tat-mediated HIV elongation arrest and recovery
R-HSA-167246 Tat-mediated elongation of the HIV-1 transcript
R-HSA-6796648 TP53 Regulates Transcription of DNA Repair Genes
R-HSA-167172 Transcription of the HIV genome
R-HSA-5633007 Regulation of TP53 Activity
R-HSA-74160 Gene expression (Transcription)
R-HSA-167169 HIV Transcription Elongation
R-HSA-3700989 Transcriptional Regulation by TP53
R-HSA-162599 Late Phase of HIV Life Cycle
R-HSA-212436 Generic Transcription Pathway
R-HSA-162587 HIV Life Cycle
R-HSA-162906 HIV Infection
R-HSA-5663205 Infectious disease
R-HSA-1643685 Disease

-  Other Names for This Gene
  Alternate Gene Symbols: FACT80, NM_003146, NP_003137, Q08945, Q5BJG8, SSRP1_HUMAN
UCSC ID: uc001njt.3
RefSeq Accession: NM_003146
Protein: Q08945 (aka SSRP1_HUMAN)
CCDS: CCDS7952.1

-  Gene Model Information
 
category: coding nonsense-mediated-decay: no RNA accession: NM_003146.2
exon count: 17CDS single in 3' UTR: no RNA size: 2825
ORF size: 2130CDS single in intron: no Alignment % ID: 100.00
txCdsPredict score: 4460.00frame shift in genome: no % Coverage: 99.79
has start codon: yes stop codon in genome: no # of Alignments: 1
has end codon: yes retained intron: no # AT/AC introns 0
selenocysteine: no end bleed into intron: 0# strange splices: 0
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-  Methods, Credits, and Use Restrictions
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