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Entry version 139 (29 Sep 2021)
Sequence version 1 (04 Apr 2006)
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Protein

Histone H2B

Gene

hist2h2bf

Organism
Xenopus tropicalis (Western clawed frog) (Silurana tropicalis)
Status
Unreviewed-Annotation score:

Annotation score:2 out of 5

<p>The annotation score provides a heuristic measure of the annotation content of a UniProtKB entry or proteome. This score <strong>cannot</strong> be used as a measure of the accuracy of the annotation as we cannot define the 'correct annotation' for any given protein.<p><a href='/help/annotation_score' target='_top'>More...</a></p>
-Experimental evidence at protein leveli <p>This indicates the type of evidence that supports the existence of the protein. Note that the 'protein existence' evidence does not give information on the accuracy or correctness of the sequence(s) displayed.<p><a href='/help/protein_existence' target='_top'>More...</a></p>

<p>This section provides any useful information about the protein, mostly biological knowledge.<p><a href='/help/function_section' target='_top'>More...</a></p>Functioni

<p>The <a href="http://www.geneontology.org/">Gene Ontology (GO)</a> project provides a set of hierarchical controlled vocabulary split into 3 categories:<p><a href='/help/gene_ontology' target='_top'>More...</a></p>GO - Molecular functioni

GO - Biological processi

<p>UniProtKB Keywords constitute a <a href="http://www.uniprot.org/keywords">controlled vocabulary</a> with a hierarchical structure. Keywords summarise the content of a UniProtKB entry and facilitate the search for proteins of interest.<p><a href='/help/keywords' target='_top'>More...</a></p>Keywordsi

Molecular functionDNA-binding

Enzyme and pathway databases

Reactome - a knowledgebase of biological pathways and processes

More...
Reactomei
R-XTR-110330, Recognition and association of DNA glycosylase with site containing an affected purine
R-XTR-110331, Cleavage of the damaged purine
R-XTR-212300, PRC2 methylates histones and DNA
R-XTR-2299718, Condensation of Prophase Chromosomes
R-XTR-2559580, Oxidative Stress Induced Senescence
R-XTR-3214815, HDACs deacetylate histones
R-XTR-5625886, Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-XTR-8936459, RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function

<p>This section provides information about the protein and gene name(s) and synonym(s) and about the organism that is the source of the protein sequence.<p><a href='/help/names_and_taxonomy_section' target='_top'>More...</a></p>Names & Taxonomyi

<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides an exhaustive list of all names of the protein, from commonly used to obsolete, to allow unambiguous identification of a protein.<p><a href='/help/protein_names' target='_top'>More...</a></p>Protein namesi
Recommended name:
Histone H2BUniRule annotation
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section indicates the name(s) of the gene(s) that code for the protein sequence(s) described in the entry. Four distinct tokens exist: 'Name', 'Synonyms', 'Ordered locus names' and 'ORF names'.<p><a href='/help/gene_name' target='_top'>More...</a></p>Gene namesi
Name:hist2h2bfImported
Synonyms:LOC116407592Imported
ORF Names:TGas058p09.1-001Imported, XENTR_v90029327mgImported, XENTR_v90029353mgImported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section provides information on the name(s) of the organism that is the source of the protein sequence.<p><a href='/help/organism-name' target='_top'>More...</a></p>OrganismiXenopus tropicalis (Western clawed frog) (Silurana tropicalis)Imported
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section shows the unique identifier assigned by the NCBI to the source organism of the protein. This is known as the 'taxonomic identifier' or 'taxid'.<p><a href='/help/taxonomic_identifier' target='_top'>More...</a></p>Taxonomic identifieri8364 [NCBI]
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section contains the taxonomic hierarchical classification lineage of the source organism. It lists the nodes as they appear top-down in the taxonomic tree, with the more general grouping listed first.<p><a href='/help/taxonomic_lineage' target='_top'>More...</a></p>Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiAmphibiaBatrachiaAnuraPipoideaPipidaeXenopodinaeXenopusSilurana
<p>This subsection of the <a href="http://www.uniprot.org/help/names_and_taxonomy_section">Names and taxonomy</a> section is present for entries that are part of a <a href="http://www.uniprot.org/proteomes">proteome</a>, i.e. of a set of proteins thought to be expressed by organisms whose genomes have been completely sequenced.<p><a href='/help/proteomes_manual' target='_top'>More...</a></p>Proteomesi
  • UP000008143 <p>A UniProt <a href="http://www.uniprot.org/manual/proteomes_manual">proteome</a> can consist of several components.<br></br>The component name refers to the genomic component encoding a set of proteins.<p><a href='/help/proteome_component' target='_top'>More...</a></p> Componenti: Unassembled WGS sequence

<p>This section provides information on the location and the topology of the mature protein in the cell.<p><a href='/help/subcellular_location_section' target='_top'>More...</a></p>Subcellular locationi

Keywords - Cellular componenti

Chromosome, Nucleosome coreUniRule annotation, NucleusUniRule annotation

<p>This section provides information on the expression of a gene at the mRNA or protein level in cells or in tissues of multicellular organisms.<p><a href='/help/expression_section' target='_top'>More...</a></p>Expressioni

Gene expression databases

Bgee dataBase for Gene Expression Evolution

More...
Bgeei
ENSXETG00000026113, Expressed in blastula and 5 other tissues

ExpressionAtlas, Differential and Baseline Expression

More...
ExpressionAtlasi
Q28D68, baseline

<p>This section provides information on the quaternary structure of a protein and on interaction(s) with other proteins or protein complexes.<p><a href='/help/interaction_section' target='_top'>More...</a></p>Interactioni

<p>This subsection of the <a href="http://www.uniprot.org/help/interaction_section">'Interaction'</a> section provides information about the protein quaternary structure and interaction(s) with other proteins or protein complexes (with the exception of physiological receptor-ligand interactions which are annotated in the <a href="http://www.uniprot.org/help/function_section">'Function'</a> section).<p><a href='/help/subunit_structure' target='_top'>More...</a></p>Subunit structurei

The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA.

UniRule annotation

GO - Molecular functioni

Protein-protein interaction databases

Database of interacting proteins

More...
DIPi
DIP-46362N

Protein interaction database and analysis system

More...
IntActi
Q28D68, 1 interactor

<p>This section provides information on the tertiary and secondary structure of a protein.<p><a href='/help/structure_section' target='_top'>More...</a></p>Structurei

3D structure databases

SWISS-MODEL Repository - a database of annotated 3D protein structure models

More...
SMRi
Q28D68

Database of comparative protein structure models

More...
ModBasei
Search...

Protein Data Bank in Europe - Knowledge Base

More...
PDBe-KBi
Search...

<p>This section provides information on sequence similarities with other proteins and the domain(s) present in a protein.<p><a href='/help/family_and_domains_section' target='_top'>More...</a></p>Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the <a href="http://www.uniprot.org/help/family_and_domains_section">Family and Domains</a> section describes the position and type of a domain, which is defined as a specific combination of secondary structures organized into a characteristic three-dimensional structure or fold.<p><a href='/help/domain' target='_top'>More...</a></p>Domaini9 – 101HistoneInterPro annotationAdd BLAST93

Region

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes a region of interest that cannot be described in other subsections.<p><a href='/help/region' target='_top'>More...</a></p>Regioni1 – 34DisorderedSequence analysisAdd BLAST34

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
<p>This subsection of the 'Family and Domains' section describes the position of regions of compositional bias within the protein and the particular type of amino acids that are over-represented within those regions.<p><a href='/help/compbias' target='_top'>More...</a></p>Compositional biasi17 – 34Basic residuesSequence analysisAdd BLAST18

<p>This subsection of the 'Family and domains' section provides information about the sequence similarity with other proteins.<p><a href='/help/sequence_similarities' target='_top'>More...</a></p>Sequence similaritiesi

Belongs to the histone H2B family.UniRule annotationARBA annotation

Phylogenomic databases

Ensembl GeneTree

More...
GeneTreei
ENSGT01030000234632

The HOGENOM Database of Homologous Genes from Fully Sequenced Organisms

More...
HOGENOMi
CLU_075666_2_1_1

Identification of Orthologs from Complete Genome Data

More...
OMAi
KXSTITS

Database of Orthologous Groups

More...
OrthoDBi
1536672at2759

Database for complete collections of gene phylogenies

More...
PhylomeDBi
Q28D68

TreeFam database of animal gene trees

More...
TreeFami
TF300212

Family and domain databases

Gene3D Structural and Functional Annotation of Protein Families

More...
Gene3Di
1.10.20.10, 1 hit

Integrated resource of protein families, domains and functional sites

More...
InterProi
View protein in InterPro
IPR009072, Histone-fold
IPR007125, Histone_H2A/H2B/H3
IPR000558, Histone_H2B

The PANTHER Classification System

More...
PANTHERi
PTHR23428, PTHR23428, 1 hit

Pfam protein domain database

More...
Pfami
View protein in Pfam
PF00125, Histone, 1 hit

Protein Motif fingerprint database; a protein domain database

More...
PRINTSi
PR00621, HISTONEH2B

Simple Modular Architecture Research Tool; a protein domain database

More...
SMARTi
View protein in SMART
SM00427, H2B, 1 hit

Superfamily database of structural and functional annotation

More...
SUPFAMi
SSF47113, SSF47113, 1 hit

PROSITE; a protein domain and family database

More...
PROSITEi
View protein in PROSITE
PS00357, HISTONE_H2B, 1 hit

<p>This section displays by default the canonical protein sequence and upon request all isoforms described in the entry. It also includes information pertinent to the sequence(s), including <a href="http://www.uniprot.org/help/sequence_length">length</a> and <a href="http://www.uniprot.org/help/sequences">molecular weight</a>. The information is filed in different subsections. The current subsections and their content are listed below:<p><a href='/help/sequences_section' target='_top'>More...</a></p>Sequencei

<p>This subsection of the <a href="http://www.uniprot.org/help/sequences_section">Sequence</a> section indicates if the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> displayed by default in the entry is complete or not.<p><a href='/help/sequence_status' target='_top'>More...</a></p>Sequence statusi: Complete.

Q28D68-1 [UniParc]FASTAAdd to basket
« Hide
        10         20         30         40         50
MPDPAKSAPA AKKGSKKAVT KTQKKDGKKR RKTRKESYAI YVYKVLKQVH
60 70 80 90 100
PDTGISSKAM SIMNSFVNDV FERIAGEASR LAHYNKRSTI TSREIQTAVR
110 120
LLLPGELAKH AVSEGTKAVT KYTSAK
Length:126
Mass (Da):13,908
Last modified:April 4, 2006 - v1
<p>The checksum is a form of redundancy check that is calculated from the sequence. It is useful for tracking sequence updates.</p> <p>It should be noted that while, in theory, two different sequences could have the same checksum value, the likelihood that this would happen is extremely low.</p> <p>However UniProtKB may contain entries with identical sequences in case of multiple genes (paralogs).</p> <p>The checksum is computed as the sequence 64-bit Cyclic Redundancy Check value (CRC64) using the generator polynomial: x<sup>64</sup> + x<sup>4</sup> + x<sup>3</sup> + x + 1. The algorithm is described in the ISO 3309 standard. </p> <p class="publication">Press W.H., Flannery B.P., Teukolsky S.A. and Vetterling W.T.<br /> <strong>Cyclic redundancy and other checksums</strong><br /> <a href="http://www.nrbook.com/b/bookcpdf.php">Numerical recipes in C 2nd ed., pp896-902, Cambridge University Press (1993)</a>)</p> Checksum:i6B39B677DEF533B3
GO

Sequence databases

Select the link destinations:

EMBL nucleotide sequence database

More...
EMBLi

GenBank nucleotide sequence database

More...
GenBanki

DNA Data Bank of Japan; a nucleotide sequence database

More...
DDBJi
Links Updated
CR855675 mRNA Translation: CAJ82556.1
KV460383 Genomic DNA Translation: OCA19274.1
KV460383 Genomic DNA Translation: OCA19304.1

NCBI Reference Sequences

More...
RefSeqi
NP_001297031.1, NM_001310102.1
XP_002943313.1, XM_002943267.4
XP_004913866.1, XM_004913809.3
XP_017952909.1, XM_018097420.1
XP_017952910.1, XM_018097421.1
XP_017952911.1, XM_018097422.1
XP_017952912.1, XM_018097423.1
XP_017952914.1, XM_018097425.1

Genome annotation databases

Ensembl eukaryotic genome annotation project

More...
Ensembli
ENSXETT00000065266; ENSXETP00000063108; ENSXETG00000036199
ENSXETT00000106048; ENSXETP00000107115; ENSXETG00000042082
ENSXETT00000106187; ENSXETP00000111661; ENSXETG00000041947
ENSXETT00000107096; ENSXETP00000117225; ENSXETG00000046250
ENSXETT00000109894; ENSXETP00000110625; ENSXETG00000046804
ENSXETT00000119758; ENSXETP00000119459; ENSXETG00000048855
ENSXETT00000121072; ENSXETP00000102924; ENSXETG00000042082
ENSXETT00000122418; ENSXETP00000108106; ENSXETG00000043427

Database of genes from NCBI RefSeq genomes

More...
GeneIDi
100495396
101731959
101733171
108648861
108648862
108648863
108648864

KEGG: Kyoto Encyclopedia of Genes and Genomes

More...
KEGGi
xtr:100495396
xtr:101731959
xtr:101733171
xtr:108648861
xtr:108648862
xtr:108648863
xtr:108648864

<p>This section provides links to proteins that are similar to the protein sequence(s) described in this entry at different levels of sequence identity thresholds (100%, 90% and 50%) based on their membership in UniProt Reference Clusters (<a href="http://www.uniprot.org/help/uniref">UniRef</a>).<p><a href='/help/similar_proteins_section' target='_top'>More...</a></p>Similar proteinsi

<p>This section is used to point to information related to entries and found in data collections other than UniProtKB.<p><a href='/help/cross_references_section' target='_top'>More...</a></p>Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
CR855675 mRNA Translation: CAJ82556.1
KV460383 Genomic DNA Translation: OCA19274.1
KV460383 Genomic DNA Translation: OCA19304.1
RefSeqiNP_001297031.1, NM_001310102.1
XP_002943313.1, XM_002943267.4
XP_004913866.1, XM_004913809.3
XP_017952909.1, XM_018097420.1
XP_017952910.1, XM_018097421.1
XP_017952911.1, XM_018097422.1
XP_017952912.1, XM_018097423.1
XP_017952914.1, XM_018097425.1

3D structure databases

Select the link destinations:

Protein Data Bank Europe

More...
PDBei

Protein Data Bank RCSB

More...
RCSB PDBi

Protein Data Bank Japan

More...
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3C1BX-ray2.20D/H2-126[»]
3C1CX-ray3.15D/H2-126[»]
6FTXelectron microscopy4.50D/H1-126[»]
SMRiQ28D68
ModBaseiSearch...
PDBe-KBiSearch...

Protein-protein interaction databases

DIPiDIP-46362N
IntActiQ28D68, 1 interactor

Genome annotation databases

EnsembliENSXETT00000065266; ENSXETP00000063108; ENSXETG00000036199
ENSXETT00000106048; ENSXETP00000107115; ENSXETG00000042082
ENSXETT00000106187; ENSXETP00000111661; ENSXETG00000041947
ENSXETT00000107096; ENSXETP00000117225; ENSXETG00000046250
ENSXETT00000109894; ENSXETP00000110625; ENSXETG00000046804
ENSXETT00000119758; ENSXETP00000119459; ENSXETG00000048855
ENSXETT00000121072; ENSXETP00000102924; ENSXETG00000042082
ENSXETT00000122418; ENSXETP00000108106; ENSXETG00000043427
GeneIDi100495396
101731959
101733171
108648861
108648862
108648863
108648864
KEGGixtr:100495396
xtr:101731959
xtr:101733171
xtr:108648861
xtr:108648862
xtr:108648863
xtr:108648864

Phylogenomic databases

GeneTreeiENSGT01030000234632
HOGENOMiCLU_075666_2_1_1
OMAiKXSTITS
OrthoDBi1536672at2759
PhylomeDBiQ28D68
TreeFamiTF300212

Enzyme and pathway databases

ReactomeiR-XTR-110330, Recognition and association of DNA glycosylase with site containing an affected purine
R-XTR-110331, Cleavage of the damaged purine
R-XTR-212300, PRC2 methylates histones and DNA
R-XTR-2299718, Condensation of Prophase Chromosomes
R-XTR-2559580, Oxidative Stress Induced Senescence
R-XTR-3214815, HDACs deacetylate histones
R-XTR-5625886, Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3
R-XTR-8936459, RUNX1 regulates genes involved in megakaryocyte differentiation and platelet function

Gene expression databases

BgeeiENSXETG00000026113, Expressed in blastula and 5 other tissues
ExpressionAtlasiQ28D68, baseline

Family and domain databases

Gene3Di1.10.20.10, 1 hit
InterProiView protein in InterPro
IPR009072, Histone-fold
IPR007125, Histone_H2A/H2B/H3
IPR000558, Histone_H2B
PANTHERiPTHR23428, PTHR23428, 1 hit
PfamiView protein in Pfam
PF00125, Histone, 1 hit
PRINTSiPR00621, HISTONEH2B
SMARTiView protein in SMART
SM00427, H2B, 1 hit
SUPFAMiSSF47113, SSF47113, 1 hit
PROSITEiView protein in PROSITE
PS00357, HISTONE_H2B, 1 hit

MobiDB: a database of protein disorder and mobility annotations

More...
MobiDBi
Search...

<p>This section provides general information on the entry.<p><a href='/help/entry_information_section' target='_top'>More...</a></p>Entry informationi

<p>This subsection of the 'Entry information' section provides a mnemonic identifier for a UniProtKB entry, but it is not a stable identifier. Each reviewed entry is assigned a unique entry name upon integration into UniProtKB/Swiss-Prot.<p><a href='/help/entry_name' target='_top'>More...</a></p>Entry nameiQ28D68_XENTR
<p>This subsection of the 'Entry information' section provides one or more accession number(s). These are stable identifiers and should be used to cite UniProtKB entries. Upon integration into UniProtKB, each entry is assigned a unique accession number, which is called 'Primary (citable) accession number'.<p><a href='/help/accession_numbers' target='_top'>More...</a></p>AccessioniPrimary (citable) accession number: Q28D68
Secondary accession number(s): F6RFK5, F6VR03, F7B3A0
<p>This subsection of the 'Entry information' section shows the date of integration of the entry into UniProtKB, the date of the last sequence update and the date of the last annotation modification ('Last modified'). The version number for both the entry and the <a href="http://www.uniprot.org/help/canonical_and_isoforms">canonical sequence</a> are also displayed.<p><a href='/help/entry_history' target='_top'>More...</a></p>Entry historyiIntegrated into UniProtKB/TrEMBL: April 4, 2006
Last sequence update: April 4, 2006
Last modified: September 29, 2021
This is version 139 of the entry and version 1 of the sequence. See complete history.
<p>This subsection of the 'Entry information' section indicates whether the entry has been manually annotated and reviewed by UniProtKB curators or not, in other words, if the entry belongs to the Swiss-Prot section of UniProtKB (<strong>reviewed</strong>) or to the computer-annotated TrEMBL section (<strong>unreviewed</strong>).<p><a href='/help/entry_status' target='_top'>More...</a></p>Entry statusiUnreviewed (UniProtKB/TrEMBL)

<p>This section contains any relevant information that doesn't fit in any other defined sections<p><a href='/help/miscellaneous_section' target='_top'>More...</a></p>Miscellaneousi

Keywords - Technical termi

3D-structureCombined sources, Reference proteomeImported
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