SMYD5 (SMYD family member 5) - Rat Genome Database

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Gene: SMYD5 (SMYD family member 5) Homo sapiens
Analyze
Symbol: SMYD5
Name: SMYD family member 5
RGD ID: 1319335
HGNC Page HGNC:16258
Description: Predicted to enable histone H4K20 methyltransferase activity. Involved in negative regulation of transposition and regulation of stem cell differentiation.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: [histone H4]-lysine20 N-trimethyltransferase SMYD5; histone-lysine N-trimethyltransferase SMYD5; NN8-4AG; RAI15; retinoic acid induced 15; retinoic acid responsive; retinoic acid-induced protein 15; RRG1; SET and MYND domain-containing protein 5; ZMYND23
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38273,214,245 - 73,227,221 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl273,214,222 - 73,227,221 (+)EnsemblGRCh38hg38GRCh38
GRCh37273,441,373 - 73,454,349 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36273,294,874 - 73,307,863 (+)NCBINCBI36Build 36hg18NCBI36
Build 34273,353,044 - 73,366,010NCBI
Celera273,292,193 - 73,305,182 (+)NCBICelera
Cytogenetic Map2p13.2NCBI
HuRef273,177,028 - 73,190,017 (+)NCBIHuRef
CHM1_1273,372,172 - 73,385,162 (+)NCBICHM1_1
T2T-CHM13v2.0273,227,234 - 73,240,210 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8754834   PMID:12477932   PMID:15489334   PMID:21873635   PMID:22658674   PMID:24981860   PMID:26496610   PMID:28951459   PMID:29117863   PMID:30021884   PMID:32296183   PMID:32344865  
PMID:32416067   PMID:33545068   PMID:33676231   PMID:33961781   PMID:35256949   PMID:35831314  


Genomics

Comparative Map Data
SMYD5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38273,214,245 - 73,227,221 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl273,214,222 - 73,227,221 (+)EnsemblGRCh38hg38GRCh38
GRCh37273,441,373 - 73,454,349 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36273,294,874 - 73,307,863 (+)NCBINCBI36Build 36hg18NCBI36
Build 34273,353,044 - 73,366,010NCBI
Celera273,292,193 - 73,305,182 (+)NCBICelera
Cytogenetic Map2p13.2NCBI
HuRef273,177,028 - 73,190,017 (+)NCBIHuRef
CHM1_1273,372,172 - 73,385,162 (+)NCBICHM1_1
T2T-CHM13v2.0273,227,234 - 73,240,210 (+)NCBIT2T-CHM13v2.0
Smyd5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39685,408,958 - 85,423,411 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl685,408,971 - 85,423,417 (+)EnsemblGRCm39 Ensembl
GRCm38685,431,976 - 85,446,429 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl685,431,989 - 85,446,435 (+)EnsemblGRCm38mm10GRCm38
MGSCv37685,381,970 - 85,396,423 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36685,397,647 - 85,411,441 (+)NCBIMGSCv36mm8
Celera687,403,922 - 87,418,368 (+)NCBICelera
Cytogenetic Map6C3NCBI
cM Map637.44NCBI
Smyd5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.24117,969,615 - 117,984,082 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl4117,969,626 - 117,984,347 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx4123,450,999 - 123,465,446 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.04119,226,113 - 119,240,550 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.04117,839,478 - 117,853,906 (+)NCBIRnor_WKY
Rnor_6.04117,215,064 - 117,229,873 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl4117,215,064 - 117,229,873 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.04181,792,679 - 181,807,488 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.44119,686,587 - 119,701,588 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.14119,931,087 - 119,945,151 (+)NCBI
Celera4106,951,724 - 106,966,117 (+)NCBICelera
Cytogenetic Map4q34NCBI
Smyd5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542412,408,059 - 12,423,164 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495542412,408,059 - 12,422,424 (-)NCBIChiLan1.0ChiLan1.0
SMYD5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12A74,755,794 - 74,768,776 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2A74,755,794 - 74,768,776 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02A73,267,007 - 73,280,006 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
SMYD5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11749,638,436 - 49,650,231 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1749,639,765 - 49,650,182 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1749,285,049 - 49,296,844 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01750,504,369 - 50,516,165 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1750,504,370 - 50,516,117 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11749,520,653 - 49,532,448 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01749,587,525 - 49,599,320 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01750,146,500 - 50,158,285 (-)NCBIUU_Cfam_GSD_1.0
Smyd5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440629211,559,385 - 11,573,364 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493649116,997,962 - 17,011,551 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493649116,997,962 - 17,011,470 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SMYD5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl369,552,738 - 69,565,978 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1369,552,731 - 69,566,013 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2372,756,041 - 72,769,307 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SMYD5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11433,946,154 - 33,959,571 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1433,946,108 - 33,959,285 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604578,123,381 - 78,136,576 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Smyd5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_004624762416,229 - 429,741 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_004624762416,229 - 429,763 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in SMYD5
2 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:2816
Count of miRNA genes:983
Interacting mature miRNAs:1221
Transcripts:ENST00000258100, ENST00000389501, ENST00000413491, ENST00000443900, ENST00000474652, ENST00000477038, ENST00000486518, ENST00000491204
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.

Markers in Region
RH70659  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37273,453,133 - 73,453,274UniSTSGRCh37
Build 36273,306,641 - 73,306,782RGDNCBI36
Celera273,303,960 - 73,304,101RGD
Cytogenetic Map2p13.2UniSTS
HuRef273,188,795 - 73,188,936UniSTS
GeneMap99-GB4 RH Map2227.43UniSTS


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 visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 2097 1687 1439 323 1170 190 3901 1415 3263 378 1454 1537 148 1 1160 2344 4 1
Low 342 1291 287 301 767 275 456 781 471 41 6 76 27 44 444 2 1
Below cutoff 13 14 1

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000258100   ⟹   ENSP00000258100
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,238 - 73,223,106 (+)Ensembl
RefSeq Acc Id: ENST00000389501   ⟹   ENSP00000374152
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,245 - 73,227,221 (+)Ensembl
RefSeq Acc Id: ENST00000413491   ⟹   ENSP00000388195
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,222 - 73,221,213 (+)Ensembl
RefSeq Acc Id: ENST00000443900   ⟹   ENSP00000412587
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,567 - 73,221,194 (+)Ensembl
RefSeq Acc Id: ENST00000474652
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,590 - 73,221,922 (+)Ensembl
RefSeq Acc Id: ENST00000477038
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,221,176 - 73,223,167 (+)Ensembl
RefSeq Acc Id: ENST00000486518
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,225,222 - 73,225,881 (+)Ensembl
RefSeq Acc Id: ENST00000491204
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,219,917 - 73,220,721 (+)Ensembl
RefSeq Acc Id: ENST00000629411   ⟹   ENSP00000485790
RefSeq Status:
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p13 Ensembl273,214,267 - 73,219,992 (+)Ensembl
RefSeq Acc Id: NM_006062   ⟹   NP_006053
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38273,214,245 - 73,227,221 (+)NCBI
GRCh37273,441,366 - 73,454,355 (+)RGD
Build 36273,294,874 - 73,307,863 (+)NCBI Archive
Celera273,292,193 - 73,305,182 (+)RGD
HuRef273,177,028 - 73,190,017 (+)RGD
CHM1_1273,372,172 - 73,385,162 (+)NCBI
T2T-CHM13v2.0273,227,234 - 73,240,210 (+)NCBI
Sequence:
Reference Sequences
RefSeq Acc Id: NP_006053   ⟸   NM_006062
- UniProtKB: Q13558 (UniProtKB/Swiss-Prot),   Q6GMV2 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000388195   ⟸   ENST00000413491
RefSeq Acc Id: ENSP00000374152   ⟸   ENST00000389501
RefSeq Acc Id: ENSP00000258100   ⟸   ENST00000258100
RefSeq Acc Id: ENSP00000485790   ⟸   ENST00000629411
RefSeq Acc Id: ENSP00000412587   ⟸   ENST00000443900
Protein Domains
SET

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6GMV2-F1-model_v2 AlphaFold Q6GMV2 1-418 view protein structure

Promoters
RGD ID:6860676
Promoter ID:EPDNEW_H3503
Type:initiation region
Name:SMYD5_2
Description:SMYD family member 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3504  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38273,213,356 - 73,213,416EPDNEW
RGD ID:6860678
Promoter ID:EPDNEW_H3504
Type:initiation region
Name:SMYD5_1
Description:SMYD family member 5
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_H3503  
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38273,214,245 - 73,214,305EPDNEW
RGD ID:6798200
Promoter ID:HG_KWN:33242
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000318301,   OTTHUMT00000318302,   OTTHUMT00000318303,   OTTHUMT00000318304,   OTTHUMT00000318305
Position:
Human AssemblyChrPosition (strand)Source
Build 36273,294,684 - 73,295,184 (+)MPROMDB
RGD ID:6798201
Promoter ID:HG_KWN:33246
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:Jurkat
Transcripts:OTTHUMT00000318308
Position:
Human AssemblyChrPosition (strand)Source
Build 36273,305,471 - 73,305,971 (+)MPROMDB

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 2p16.1-11.2(chr2:58279519-83586962)x3 copy number gain See cases [RCV000136053] Chr2:58279519..83586962 [GRCh38]
Chr2:58506654..83814086 [GRCh37]
Chr2:58360158..83667597 [NCBI36]
Chr2:2p16.1-11.2
pathogenic
GRCh38/hg38 2p16.3-11.2(chr2:47620388-86702722)x3 copy number gain See cases [RCV000137586] Chr2:47620388..86702722 [GRCh38]
Chr2:47847527..86929845 [GRCh37]
Chr2:47701031..86783356 [NCBI36]
Chr2:2p16.3-11.2
uncertain significance
GRCh38/hg38 2p25.1-11.2(chr2:7495123-87705899)x3 copy number gain See cases [RCV000141494] Chr2:7495123..87705899 [GRCh38]
Chr2:7635254..88005418 [GRCh37]
Chr2:7552705..87786533 [NCBI36]
Chr2:2p25.1-11.2
benign
GRCh37/hg19 2p25.3-q37.3(chr2:14238-243048760)x3 copy number gain not provided [RCV000752802] Chr2:14238..243048760 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
GRCh37/hg19 2p15-11.2(chr2:62245236-86978895)x3 copy number gain See cases [RCV000448688] Chr2:62245236..86978895 [GRCh37]
Chr2:2p15-11.2
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384) copy number gain See cases [RCV000512056] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
Single allele deletion not provided [RCV000714264] Chr2:40608411..146900718 [GRCh37]
Chr2:2p22.1-q22.3
likely pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:12771-242783384)x3 copy number gain See cases [RCV000511212] Chr2:12771..242783384 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
Single allele duplication not provided [RCV000677942] Chr2:63671346..85698002 [GRCh37]
Chr2:2p15-11.2
pathogenic
GRCh37/hg19 2p25.3-q37.3(chr2:15672-243101834)x3 copy number gain not provided [RCV000752804] Chr2:15672..243101834 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NM_006062.3(SMYD5):c.585C>T (p.Asn195=) single nucleotide variant not provided [RCV000955943] Chr2:73221873 [GRCh38]
Chr2:73449001 [GRCh37]
Chr2:2p13.2
benign
NM_006062.3(SMYD5):c.460G>A (p.Ala154Thr) single nucleotide variant not provided [RCV000911469] Chr2:73220775 [GRCh38]
Chr2:73447903 [GRCh37]
Chr2:2p13.2
benign
GRCh37/hg19 2p25.3-q37.3(chr2:1-243199373) copy number gain Mosaic trisomy 2 [RCV002280628] Chr2:1..243199373 [GRCh37]
Chr2:2p25.3-q37.3
pathogenic
NC_000002.11:g.(?_73114549)_(73836749_?)dup duplication Alstrom syndrome [RCV001365067] Chr2:73114549..73836749 [GRCh37]
Chr2:2p13.2-13.1
uncertain significance
GRCh37/hg19 2p25.1-q13(chr2:11504318-111365996)x1 copy number loss See cases [RCV002287563] Chr2:11504318..111365996 [GRCh37]
Chr2:2p25.1-q13
pathogenic

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:16258 AgrOrtholog
COSMIC SMYD5 COSMIC
Ensembl Genes ENSG00000135632 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Protein ENSP00000258100.4 UniProtKB/TrEMBL
  ENSP00000374152 ENTREZGENE
  ENSP00000374152.4 UniProtKB/Swiss-Prot
  ENSP00000388195.1 UniProtKB/TrEMBL
  ENSP00000412587.1 UniProtKB/TrEMBL
  ENSP00000485790.1 UniProtKB/TrEMBL
Ensembl Transcript ENST00000258100.8 UniProtKB/TrEMBL
  ENST00000389501 ENTREZGENE
  ENST00000389501.9 UniProtKB/Swiss-Prot
  ENST00000413491.5 UniProtKB/TrEMBL
  ENST00000443900.1 UniProtKB/TrEMBL
  ENST00000629411.2 UniProtKB/TrEMBL
Gene3D-CATH 2.170.270.10 UniProtKB/Swiss-Prot
GTEx ENSG00000135632 GTEx
HGNC ID HGNC:16258 ENTREZGENE
Human Proteome Map SMYD5 Human Proteome Map
InterPro SET_dom UniProtKB/Swiss-Prot
  SET_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SMYD5_SET UniProtKB/Swiss-Prot
KEGG Report hsa:10322 UniProtKB/Swiss-Prot
NCBI Gene 10322 ENTREZGENE
OMIM 619114 OMIM
Pfam SET UniProtKB/Swiss-Prot
PharmGKB PA34190 PharmGKB
PROSITE SET UniProtKB/Swiss-Prot
SMART SET UniProtKB/Swiss-Prot
Superfamily-SCOP SSF82199 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt C9IYN9_HUMAN UniProtKB/TrEMBL
  E2QRN5_HUMAN UniProtKB/TrEMBL
  F8WEJ9_HUMAN UniProtKB/TrEMBL
  Q13558 ENTREZGENE
  Q6GMV2 ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary D6W5H3 UniProtKB/Swiss-Prot
  Q13558 UniProtKB/Swiss-Prot