H3Y1 (H3.Y histone 1) - Rat Genome Database

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Gene: H3Y1 (H3.Y histone 1) Homo sapiens
Analyze
Symbol: H3Y1
Name: H3.Y histone 1
RGD ID: 14700602
HGNC Page HGNC:43735
Description: Enables nucleosomal DNA binding activity. Located in nucleoplasm. Part of nucleosome.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: H3 histone, family 3B (H3.3B) pseudogene; H3.Y; H3.Y.1; histone cluster 2, H3c pseudogene; Histone H3.Y; histone H3.Y1
RGD Orthologs
Rat
Alliance Orthologs
More Info more info ...
Related Pseudogenes: H3P19   H3P22  
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38517,654,868 - 17,655,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl517,654,868 - 17,655,849 (-)EnsemblGRCh38hg38GRCh38
GRCh37517,654,977 - 17,655,958 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p15.1NCBI
HuRef517,554,383 - 17,554,793 (-)NCBIHuRef
CHM1_1517,655,081 - 17,655,491 (-)NCBICHM1_1
T2T-CHM13v2.0517,655,075 - 17,656,048 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
chromosome  (IEA)
intracellular organelle  (IEA)
nucleoplasm  (IDA)
nucleosome  (IDA,IEA)
nucleus  (IBA,IEA)

Molecular Function

References
Additional References at PubMed
PMID:20819935   PMID:21263457   PMID:21873635   PMID:25362550   PMID:27016736   PMID:28334823   PMID:31722199   PMID:36180920  


Genomics

Comparative Map Data
H3Y1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38517,654,868 - 17,655,849 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl517,654,868 - 17,655,849 (-)EnsemblGRCh38hg38GRCh38
GRCh37517,654,977 - 17,655,958 (-)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map5p15.1NCBI
HuRef517,554,383 - 17,554,793 (-)NCBIHuRef
CHM1_1517,655,081 - 17,655,491 (-)NCBICHM1_1
T2T-CHM13v2.0517,655,075 - 17,656,048 (-)NCBIT2T-CHM13v2.0
H3cl
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21741,372,194 - 41,378,877 (-)NCBImRatBN7.2mRatBN7.2
Rnor_6.01743,626,081 - 43,626,568 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01745,480,466 - 45,481,037 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Celera1741,009,446 - 41,009,933 (-)NCBICelera
Cytogenetic Map17p11NCBI


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 5p15.2-14.3(chr5:13609772-21930280)x1 copy number loss See cases [RCV000053447] Chr5:13609772..21930280 [GRCh38]
Chr5:13609881..21930389 [GRCh37]
Chr5:13662881..21966146 [NCBI36]
Chr5:5p15.2-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27788616)x1 copy number loss See cases [RCV000134873] Chr5:22149..27788616 [GRCh38]
Chr5:22149..27788723 [GRCh37]
Chr5:75149..27824480 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28075106)x3 copy number gain See cases [RCV000137682] Chr5:22149..28075106 [GRCh38]
Chr5:22149..28075213 [GRCh37]
Chr5:75149..28110970 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic|uncertain significance
GRCh38/hg38 5p15.33-14.1(chr5:22149-26593891)x1 copy number loss See cases [RCV000142645] Chr5:22149..26593891 [GRCh38]
Chr5:22149..26594000 [GRCh37]
Chr5:75149..26629757 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.1-14.3(chr5:16456444-18561765)x1 copy number loss See cases [RCV000143153] Chr5:16456444..18561765 [GRCh38]
Chr5:16456553..18561874 [GRCh37]
Chr5:16509553..18597631 [NCBI36]
Chr5:5p15.1-14.3		 uncertain significance
GRCh38/hg38 5p15.33-11(chr5:49978-46114984)x3 copy number gain See cases [RCV000135453] Chr5:49978..46114984 [GRCh38]
Chr5:50093..46115086 [GRCh37]
Chr5:103093..46150843 [NCBI36]
Chr5:5p15.33-11		 pathogenic
GRCh38/hg38 5p15.2-15.1(chr5:12572563-17965988)x1 copy number loss See cases [RCV000136041] Chr5:12572563..17965988 [GRCh38]
Chr5:12572675..17966097 [GRCh37]
Chr5:12625675..18001854 [NCBI36]
Chr5:5p15.2-15.1		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27187950)x1 copy number loss See cases [RCV000138099] Chr5:22149..27187950 [GRCh38]
Chr5:22149..27188057 [GRCh37]
Chr5:75149..27223814 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21217120)x1 copy number loss See cases [RCV000138553] Chr5:22149..21217120 [GRCh38]
Chr5:22149..21217229 [GRCh37]
Chr5:75149..21252986 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.32-14.3(chr5:4932707-18465361)x1 copy number loss See cases [RCV000141795] Chr5:4932707..18465361 [GRCh38]
Chr5:4932820..18465470 [GRCh37]
Chr5:4985820..18501227 [NCBI36]
Chr5:5p15.32-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:49778-19125522)x1 copy number loss See cases [RCV000053424] Chr5:49778..19125522 [GRCh38]
Chr5:49893..19125631 [GRCh37]
Chr5:102893..19161388 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-25699605)x1 copy number loss See cases [RCV000133768] Chr5:22149..25699605 [GRCh38]
Chr5:22149..25699714 [GRCh37]
Chr5:75149..25735471 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:22149-35831538)x1 copy number loss See cases [RCV000138888] Chr5:22149..35831538 [GRCh38]
Chr5:22149..35831640 [GRCh37]
Chr5:75149..35867397 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28589192)x1 copy number loss See cases [RCV000141225] Chr5:22149..28589192 [GRCh38]
Chr5:22149..28589299 [GRCh37]
Chr5:75149..28625056 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-12(chr5:54839-45649861)x3 copy number gain See cases [RCV000051810] Chr5:54839..45649861 [GRCh38]
Chr5:54954..45649963 [GRCh37]
Chr5:107954..45685720 [NCBI36]
Chr5:5p15.33-12		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22419-19280892)x1 copy number loss See cases [RCV000053419] Chr5:22419..19280892 [GRCh38]
Chr5:22419..19281001 [GRCh37]
Chr5:75419..19316758 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27485619)x1 copy number loss See cases [RCV000137072] Chr5:22149..27485619 [GRCh38]
Chr5:22149..27485726 [GRCh37]
Chr5:75149..27521483 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.32-13.2(chr5:4849498-36818719)x3 copy number gain See cases [RCV000141246] Chr5:4849498..36818719 [GRCh38]
Chr5:4849611..36818821 [GRCh37]
Chr5:4902611..36854578 [NCBI36]
Chr5:5p15.32-13.2		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:113461-33998289)x1 copy number loss See cases [RCV000141844] Chr5:113461..33998289 [GRCh38]
Chr5:113576..33998394 [GRCh37]
Chr5:166576..34034151 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-27611163)x1 copy number loss See cases [RCV000142934] Chr5:22149..27611163 [GRCh38]
Chr5:22149..27611270 [GRCh37]
Chr5:75149..27647027 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-13.2(chr5:54839-35680845)x3 copy number gain See cases [RCV000051811] Chr5:54839..35680845 [GRCh38]
Chr5:54954..35680947 [GRCh37]
Chr5:107954..35716704 [NCBI36]
Chr5:5p15.33-13.2		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-32248010)x1 copy number loss See cases [RCV000135668] Chr5:22149..32248010 [GRCh38]
Chr5:22149..32248116 [GRCh37]
Chr5:75149..32283873 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-22775295)x1 copy number loss See cases [RCV000138116] Chr5:22149..22775295 [GRCh38]
Chr5:22149..22775404 [GRCh37]
Chr5:75149..22811161 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-q13.3(chr5:22149-74412725)x3 copy number gain See cases [RCV000138780] Chr5:22149..74412725 [GRCh38]
Chr5:22149..73708550 [GRCh37]
Chr5:75149..73744306 [NCBI36]
Chr5:5p15.33-q13.3		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:49978-30112535)x1 copy number loss See cases [RCV000135878] Chr5:49978..30112535 [GRCh38]
Chr5:50093..30112642 [GRCh37]
Chr5:103093..30148399 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-14.1(chr5:22149-28429241)x1 copy number loss See cases [RCV000137165] Chr5:22149..28429241 [GRCh38]
Chr5:22149..28429348 [GRCh37]
Chr5:75149..28465105 [NCBI36]
Chr5:5p15.33-14.1		 pathogenic
GRCh38/hg38 5p15.33-14.2(chr5:22149-23607053)x3 copy number gain See cases [RCV000137806] Chr5:22149..23607053 [GRCh38]
Chr5:22149..23607162 [GRCh37]
Chr5:75149..23642919 [NCBI36]
Chr5:5p15.33-14.2		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-23132046)x1 copy number loss See cases [RCV000053398] Chr5:22149..23132046 [GRCh38]
Chr5:22149..23132155 [GRCh37]
Chr5:75149..23167912 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
GRCh38/hg38 5p15.33-13.3(chr5:22149-33418188)x3 copy number gain See cases [RCV000133788] Chr5:22149..33418188 [GRCh38]
Chr5:22149..33418294 [GRCh37]
Chr5:75149..33454051 [NCBI36]
Chr5:5p15.33-13.3		 pathogenic
GRCh38/hg38 5p15.33-14.3(chr5:22149-21726360)x1 copy number loss See cases [RCV000143022] Chr5:22149..21726360 [GRCh38]
Chr5:22149..21726469 [GRCh37]
Chr5:75149..21762226 [NCBI36]
Chr5:5p15.33-14.3		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:208
Count of miRNA genes:105
Interacting mature miRNAs:106
Transcripts:ENST00000509027, ENST00000598383
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1 2 3 4
Low 1 102 4 2 36 3 75 10 13 7 177 27 10 40 1
Below cutoff 80 407 55 17 84 16 397 122 116 30 276 82 3 98 273 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000598383   ⟹   ENSP00000496014
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl517,654,868 - 17,655,849 (-)Ensembl
RefSeq Acc Id: NM_001355258   ⟹   NP_001342187
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38517,654,868 - 17,655,849 (-)NCBI
T2T-CHM13v2.0517,655,075 - 17,656,048 (-)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001342187 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000496014
  ENSP00000496014.2
GenBank Protein P0DPK2 (Get FASTA)   NCBI Sequence Viewer  
Reference Protein Sequences
RefSeq Acc Id: NP_001342187   ⟸   NM_001355258
- UniProtKB: P0DPK2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000496014   ⟸   ENST00000598383

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-P0DPK2-F1-model_v2 AlphaFold P0DPK2 1-136 view protein structure


Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:43735 AgrOrtholog
COSMIC H3Y1 COSMIC
Ensembl Genes ENSG00000269466 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000598383 ENTREZGENE
  ENST00000598383.3 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.10 UniProtKB/Swiss-Prot
GTEx ENSG00000269466 GTEx
HGNC ID HGNC:43735 ENTREZGENE
Human Proteome Map H3Y1 Human Proteome Map
InterPro Histone-fold UniProtKB/Swiss-Prot
  Histone_H2A/H2B/H3 UniProtKB/Swiss-Prot
  Histone_H3/CENP-A UniProtKB/Swiss-Prot
NCBI Gene H3Y1 ENTREZGENE
PANTHER HISTONE H3.X-RELATED UniProtKB/Swiss-Prot
  PTHR11426 UniProtKB/Swiss-Prot
Pfam Histone UniProtKB/Swiss-Prot
PRINTS HISTONEH3 UniProtKB/Swiss-Prot
PROSITE HISTONE_H3_2 UniProtKB/Swiss-Prot
SMART SM00428 UniProtKB/Swiss-Prot
Superfamily-SCOP SSF47113 UniProtKB/Swiss-Prot
UniProt H3Y1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE