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Protein

SET domain-containing protein 4

Gene

SETD4

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 3 out of 5-Experimental evidence at transcript leveli

Functioni

GO - Molecular functioni

  1. methyltransferase activity Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Ligandi

S-adenosyl-L-methionine

Names & Taxonomyi

Protein namesi
Recommended name:
SET domain-containing protein 4 (EC:2.1.1.-)
Gene namesi
Name:SETD4
Synonyms:C21orf18, C21orf27
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
ProteomesiUP000005640 Componenti: Chromosome 21

Organism-specific databases

HGNCiHGNC:1258. SETD4.

Pathology & Biotechi

Organism-specific databases

PharmGKBiPA25814.

Polymorphism and mutation databases

DMDMi12229715.

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 440440SET domain-containing protein 4PRO_0000079509Add
BLAST

Proteomic databases

PaxDbiQ9NVD3.
PRIDEiQ9NVD3.

PTM databases

PhosphoSiteiQ9NVD3.

Expressioni

Gene expression databases

BgeeiQ9NVD3.
CleanExiHS_SETD4.
ExpressionAtlasiQ9NVD3. baseline and differential.
GenevestigatoriQ9NVD3.

Organism-specific databases

HPAiHPA024073.
HPA035405.

Interactioni

Protein-protein interaction databases

BioGridi119892. 3 interactions.
STRINGi9606.ENSP00000329189.

Structurei

3D structure databases

ProteinModelPortaliQ9NVD3.
SMRiQ9NVD3. Positions 59-332.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini48 – 273226SETPROSITE-ProRule annotationAdd
BLAST

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Phylogenomic databases

eggNOGiNOG239522.
GeneTreeiENSGT00730000110866.
HOGENOMiHOG000010303.
HOVERGENiHBG051225.
InParanoidiQ9NVD3.
OMAiLWKPYLE.
PhylomeDBiQ9NVD3.
TreeFamiTF106421.

Family and domain databases

InterProiIPR015353. Rubisco_LSMT_subst-bd.
IPR001214. SET_dom.
IPR016852. SET_MeTrfase.
[Graphical view]
PfamiPF09273. Rubis-subs-bind. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF027158. Lys_MTase_YDR198C_prd. 1 hit.
PROSITEiPS50280. SET. 1 hit.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform A (identifier: Q9NVD3-1) [UniParc]FASTAAdd to basket

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MQKGKGRTSR IRRRKLCGSS ESRGVNESHK SEFIELRKWL KARKFQDSNL
60 70 80 90 100
APACFPGTGR GLMSQTSLQE GQMIISLPES CLLTTDTVIR SYLGAYITKW
110 120 130 140 150
KPPPSPLLAL CTFLVSEKHA GHRSLWKPYL EILPKAYTCP VCLEPEVVNL
160 170 180 190 200
LPKSLKAKAE EQRAHVQEFF ASSRDFFSSL QPLFAEAVDS IFSYSALLWA
210 220 230 240 250
WCTVNTRAVY LRPRQRECLS AEPDTCALAP YLDLLNHSPH VQVKAAFNEE
260 270 280 290 300
THSYEIRTTS RWRKHEEVFI CYGPHDNQRL FLEYGFVSVH NPHACVYVSR
310 320 330 340 350
EILVKYLPST DKQMDKKISI LKDHGYIENL TFGWDGPSWR LLTALKLLCL
360 370 380 390 400
EAEKFTCWKK VLLGEVISDT NEKTSLDIAQ KICYYFIEET NAVLQKVSHM
410 420 430 440
KDEKEALINQ LTLVESLWTE ELKILRASAE TLHSLQTAFT
Length:440
Mass (Da):50,416
Last modified:October 1, 2000 - v1
Checksum:i9EBCAA05397BE287
GO
Isoform B (identifier: Q9NVD3-2) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     70-440: EGQMIISLPE...TLHSLQTAFT → VEASSISSAG...PSSQIFKSKG

Note: May be produced at very low levels due to a premature stop codon in the mRNA, leading to nonsense-mediated mRNA decay. No experimental confirmation available.

Show »
Length:129
Mass (Da):14,013
Checksum:iA1FDB90CB2CE8420
GO
Isoform 3 (identifier: Q9NVD3-3) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     1-25: MQKGKGRTSRIRRRKLCGSSESRGV → M

Note: No experimental confirmation available.

Show »
Length:416
Mass (Da):47,731
Checksum:i63539282EE060837
GO
Isoform 4 (identifier: Q9NVD3-4) [UniParc]FASTAAdd to basket

The sequence of this isoform differs from the canonical sequence as follows:
     301-307: EILVKYL → GWNQLCS
     308-440: Missing.

Show »
Length:307
Mass (Da):35,086
Checksum:i4B7520151BA3D9E6
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti301 – 440140EILVK…QTAFT → GWNQLCS in AAH02898 (PubMed:15489334).CuratedAdd
BLAST

Natural variant

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Natural varianti387 – 3871I → V.
Corresponds to variant rs2835239 [ dbSNP | Ensembl ].
VAR_021948
Natural varianti420 – 4201E → G in a colorectal cancer sample; somatic mutation. 1 Publication
VAR_035988

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei1 – 2525MQKGK…ESRGV → M in isoform 3. 1 PublicationVSP_026578Add
BLAST
Alternative sequencei70 – 440371EGQMI…QTAFT → VEASSISSAGAVHLFSFRKA CWAPISLEALPGDFTQGVYL PCLFGAGSGEPSSQIFKSKG in isoform B. 2 PublicationsVSP_004146Add
BLAST
Alternative sequencei301 – 3077EILVKYL → GWNQLCS in isoform 4. 1 PublicationVSP_054087
Alternative sequencei308 – 440133Missing in isoform 4. 1 PublicationVSP_054088Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF391112 mRNA. Translation: AAL34503.1.
AK001660 mRNA. Translation: BAA91819.1.
AK300009 mRNA. Translation: BAG61826.1.
AP000688 Genomic DNA. No translation available.
CH471079 Genomic DNA. Translation: EAX09757.1.
CH471079 Genomic DNA. Translation: EAX09758.1.
CH471079 Genomic DNA. Translation: EAX09759.1.
CH471079 Genomic DNA. Translation: EAX09760.1.
CH471079 Genomic DNA. Translation: EAX09762.1.
BC002898 mRNA. Translation: AAH02898.1.
BC036556 mRNA. Translation: AAH36556.1.
CCDSiCCDS13640.1. [Q9NVD3-1]
CCDS42923.1. [Q9NVD3-4]
CCDS74792.1. [Q9NVD3-3]
RefSeqiNP_001007260.1. NM_001007259.2. [Q9NVD3-4]
NP_001007262.1. NM_001007261.2.
NP_001273681.1. NM_001286752.1.
NP_059134.1. NM_017438.4. [Q9NVD3-1]
UniGeneiHs.606200.

Genome annotation databases

EnsembliENST00000332131; ENSP00000329189; ENSG00000185917. [Q9NVD3-1]
ENST00000399207; ENSP00000382158; ENSG00000185917. [Q9NVD3-4]
ENST00000399208; ENSP00000382159; ENSG00000185917. [Q9NVD3-4]
ENST00000399212; ENSP00000382161; ENSG00000185917. [Q9NVD3-3]
ENST00000399215; ENSP00000382163; ENSG00000185917. [Q9NVD3-1]
GeneIDi54093.
KEGGihsa:54093.
UCSCiuc002yuw.2. human. [Q9NVD3-1]
uc002yux.2. human. [Q9NVD3-3]

Keywords - Coding sequence diversityi

Alternative splicing, Polymorphism

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF391112 mRNA. Translation: AAL34503.1.
AK001660 mRNA. Translation: BAA91819.1.
AK300009 mRNA. Translation: BAG61826.1.
AP000688 Genomic DNA. No translation available.
CH471079 Genomic DNA. Translation: EAX09757.1.
CH471079 Genomic DNA. Translation: EAX09758.1.
CH471079 Genomic DNA. Translation: EAX09759.1.
CH471079 Genomic DNA. Translation: EAX09760.1.
CH471079 Genomic DNA. Translation: EAX09762.1.
BC002898 mRNA. Translation: AAH02898.1.
BC036556 mRNA. Translation: AAH36556.1.
CCDSiCCDS13640.1. [Q9NVD3-1]
CCDS42923.1. [Q9NVD3-4]
CCDS74792.1. [Q9NVD3-3]
RefSeqiNP_001007260.1. NM_001007259.2. [Q9NVD3-4]
NP_001007262.1. NM_001007261.2.
NP_001273681.1. NM_001286752.1.
NP_059134.1. NM_017438.4. [Q9NVD3-1]
UniGeneiHs.606200.

3D structure databases

ProteinModelPortaliQ9NVD3.
SMRiQ9NVD3. Positions 59-332.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

BioGridi119892. 3 interactions.
STRINGi9606.ENSP00000329189.

PTM databases

PhosphoSiteiQ9NVD3.

Polymorphism and mutation databases

DMDMi12229715.

Proteomic databases

PaxDbiQ9NVD3.
PRIDEiQ9NVD3.

Protocols and materials databases

DNASUi54093.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000332131; ENSP00000329189; ENSG00000185917. [Q9NVD3-1]
ENST00000399207; ENSP00000382158; ENSG00000185917. [Q9NVD3-4]
ENST00000399208; ENSP00000382159; ENSG00000185917. [Q9NVD3-4]
ENST00000399212; ENSP00000382161; ENSG00000185917. [Q9NVD3-3]
ENST00000399215; ENSP00000382163; ENSG00000185917. [Q9NVD3-1]
GeneIDi54093.
KEGGihsa:54093.
UCSCiuc002yuw.2. human. [Q9NVD3-1]
uc002yux.2. human. [Q9NVD3-3]

Organism-specific databases

CTDi54093.
GeneCardsiGC21M037406.
H-InvDBHIX0019923.
HIX0138443.
HGNCiHGNC:1258. SETD4.
HPAiHPA024073.
HPA035405.
neXtProtiNX_Q9NVD3.
PharmGKBiPA25814.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiNOG239522.
GeneTreeiENSGT00730000110866.
HOGENOMiHOG000010303.
HOVERGENiHBG051225.
InParanoidiQ9NVD3.
OMAiLWKPYLE.
PhylomeDBiQ9NVD3.
TreeFamiTF106421.

Miscellaneous databases

ChiTaRSiSETD4. human.
GenomeRNAii54093.
NextBioi56432.
PROiQ9NVD3.

Gene expression databases

BgeeiQ9NVD3.
CleanExiHS_SETD4.
ExpressionAtlasiQ9NVD3. baseline and differential.
GenevestigatoriQ9NVD3.

Family and domain databases

InterProiIPR015353. Rubisco_LSMT_subst-bd.
IPR001214. SET_dom.
IPR016852. SET_MeTrfase.
[Graphical view]
PfamiPF09273. Rubis-subs-bind. 1 hit.
PF00856. SET. 1 hit.
[Graphical view]
PIRSFiPIRSF027158. Lys_MTase_YDR198C_prd. 1 hit.
PROSITEiPS50280. SET. 1 hit.
[Graphical view]
ProtoNetiSearch...

Publicationsi

« Hide 'large scale' publications
  1. "From PREDs and open reading frames to cDNA isolation: revisiting the human chromosome 21 transcription map."
    Reymond A., Friedli M., Neergaard Henrichsen C., Chapot F., Deutsch S., Ucla C., Rossier C., Lyle R., Guipponi M., Antonarakis S.E.
    Genomics 78:46-54(2001) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM B).
  2. "Complete sequencing and characterization of 21,243 full-length human cDNAs."
    Ota T., Suzuki Y., Nishikawa T., Otsuki T., Sugiyama T., Irie R., Wakamatsu A., Hayashi K., Sato H., Nagai K., Kimura K., Makita H., Sekine M., Obayashi M., Nishi T., Shibahara T., Tanaka T., Ishii S.
    , Yamamoto J., Saito K., Kawai Y., Isono Y., Nakamura Y., Nagahari K., Murakami K., Yasuda T., Iwayanagi T., Wagatsuma M., Shiratori A., Sudo H., Hosoiri T., Kaku Y., Kodaira H., Kondo H., Sugawara M., Takahashi M., Kanda K., Yokoi T., Furuya T., Kikkawa E., Omura Y., Abe K., Kamihara K., Katsuta N., Sato K., Tanikawa M., Yamazaki M., Ninomiya K., Ishibashi T., Yamashita H., Murakawa K., Fujimori K., Tanai H., Kimata M., Watanabe M., Hiraoka S., Chiba Y., Ishida S., Ono Y., Takiguchi S., Watanabe S., Yosida M., Hotuta T., Kusano J., Kanehori K., Takahashi-Fujii A., Hara H., Tanase T.-O., Nomura Y., Togiya S., Komai F., Hara R., Takeuchi K., Arita M., Imose N., Musashino K., Yuuki H., Oshima A., Sasaki N., Aotsuka S., Yoshikawa Y., Matsunawa H., Ichihara T., Shiohata N., Sano S., Moriya S., Momiyama H., Satoh N., Takami S., Terashima Y., Suzuki O., Nakagawa S., Senoh A., Mizoguchi H., Goto Y., Shimizu F., Wakebe H., Hishigaki H., Watanabe T., Sugiyama A., Takemoto M., Kawakami B., Yamazaki M., Watanabe K., Kumagai A., Itakura S., Fukuzumi Y., Fujimori Y., Komiyama M., Tashiro H., Tanigami A., Fujiwara T., Ono T., Yamada K., Fujii Y., Ozaki K., Hirao M., Ohmori Y., Kawabata A., Hikiji T., Kobatake N., Inagaki H., Ikema Y., Okamoto S., Okitani R., Kawakami T., Noguchi S., Itoh T., Shigeta K., Senba T., Matsumura K., Nakajima Y., Mizuno T., Morinaga M., Sasaki M., Togashi T., Oyama M., Hata H., Watanabe M., Komatsu T., Mizushima-Sugano J., Satoh T., Shirai Y., Takahashi Y., Nakagawa K., Okumura K., Nagase T., Nomura N., Kikuchi H., Masuho Y., Yamashita R., Nakai K., Yada T., Nakamura Y., Ohara O., Isogai T., Sugano S.
    Nat. Genet. 36:40-45(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS A AND B).
  3. "The DNA sequence of human chromosome 21."
    Hattori M., Fujiyama A., Taylor T.D., Watanabe H., Yada T., Park H.-S., Toyoda A., Ishii K., Totoki Y., Choi D.-K., Groner Y., Soeda E., Ohki M., Takagi T., Sakaki Y., Taudien S., Blechschmidt K., Polley A.
    , Menzel U., Delabar J., Kumpf K., Lehmann R., Patterson D., Reichwald K., Rump A., Schillhabel M., Schudy A., Zimmermann W., Rosenthal A., Kudoh J., Shibuya K., Kawasaki K., Asakawa S., Shintani A., Sasaki T., Nagamine K., Mitsuyama S., Antonarakis S.E., Minoshima S., Shimizu N., Nordsiek G., Hornischer K., Brandt P., Scharfe M., Schoen O., Desario A., Reichelt J., Kauer G., Bloecker H., Ramser J., Beck A., Klages S., Hennig S., Riesselmann L., Dagand E., Wehrmeyer S., Borzym K., Gardiner K., Nizetic D., Francis F., Lehrach H., Reinhardt R., Yaspo M.-L.
    Nature 405:311-319(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  4. Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
  5. "The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC)."
    The MGC Project Team
    Genome Res. 14:2121-2127(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [LARGE SCALE MRNA] (ISOFORMS A; 3 AND 4).
    Tissue: Lung and Testis.
  6. Cited for: SPLICE ISOFORM(S) THAT ARE POTENTIAL NMD TARGET(S).
  7. Cited for: VARIANT [LARGE SCALE ANALYSIS] GLY-420.

Entry informationi

Entry nameiSETD4_HUMAN
AccessioniPrimary (citable) accession number: Q9NVD3
Secondary accession number(s): B4DT14
, D3DSG2, D3DSG4, Q8NE19, Q9BU46
Entry historyi
Integrated into UniProtKB/Swiss-Prot: January 11, 2001
Last sequence update: October 1, 2000
Last modified: April 29, 2015
This is version 119 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

Complete proteome, Reference proteome

Documents

  1. Human chromosome 21
    Human chromosome 21: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. SIMILARITY comments
    Index of protein domains and families

External Data

Dasty 3

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into Uniref entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.