NCBI Home Page NCBI Site Search page NCBI Guide that lists and describes the NCBI resources
Conserved domains on  [gi|1958802770|ref|XP_038939652|]
View 

nuclear body protein SP140 isoform X18 [Rattus norvegicus]

Protein Classification

nuclear body protein( domain architecture ID 10504717)

nuclear body protein similar to human Sp110 nuclear body protein that may be a nuclear hormone receptor coactivator that enhances transcription of genes with retinoic acid response elements (RARE)

Graphical summary

 Zoom to residue level

show extra options »

Show site features     Horizontal zoom: ×

List of domain hits

 Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 25-122 5.67e-54

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


:

Pssm-ID: 460835  Cd Length: 99  Bit Score: 178.11  E-value: 5.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802770  25 YQLMFKLFKENKVEIASAITKLFPFLMSLRDRDFISEQKYQECQETCKNLVPVDRVVYDILSDIQKKFSRDLLKVIFSNV 104
Cdd:pfam03172   2 EEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDV 81

                          90
                  ....*....|....*...
gi 1958802770 105 HLKAYPDLQEILKHFLSV 122
Cdd:pfam03172  82 NLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 441-517 7.54e-31

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


:

Pssm-ID: 460167  Cd Length: 76  Bit Score: 114.60  E-value: 7.54e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802770 441 NFNAELLPVTCGNLKGVLHKDKFKQGISVMSIQCqDGNWVTPPEFEIMGGHGRSKNWKLSLRCYNWPLKLLIQRNFL 517
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 25-122 5.67e-54

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 460835  Cd Length: 99  Bit Score: 178.11  E-value: 5.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802770  25 YQLMFKLFKENKVEIASAITKLFPFLMSLRDRDFISEQKYQECQETCKNLVPVDRVVYDILSDIQKKFSRDLLKVIFSNV 104
Cdd:pfam03172   2 EEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDV 81

                          90
                  ....*....|....*...
gi 1958802770 105 HLKAYPDLQEILKHFLSV 122
Cdd:pfam03172  82 NLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 441-517 7.54e-31

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 460167  Cd Length: 76  Bit Score: 114.60  E-value: 7.54e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802770 441 NFNAELLPVTCGNLKGVLHKDKFKQGISVMSIQCqDGNWVTPPEFEIMGGHGRSKNWKLSLRCYNWPLKLLIQRNFL 517
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
445-518 8.94e-26

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 100.50  E-value: 8.94e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802770  445 ELLPVTCGNLKGVLHKDKFKQGISVMSIQcQDGNWVTPPEFEIMGGHGRSKNWKLSLRCYNWPLKLLIQRNFLP 518
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQ-YEDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTLD 73
 
Name Accession Description Interval E-value
HSR pfam03172
HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots ...
 25-122 5.67e-54

HSR domain; The Sp100 protein is a constituent of nuclear domains, also known as nuclear dots (NDs). An ND-targeting region that coincides with a homodimerization domain was mapped in Sp100. Sequences similar to the Sp100 homodimerization/ND-targeting region occur in several other proteins and constitute a novel protein motif, termed HSR domain (for homogeneously-staining region). The HSR domain has also been named ASS (AIRE, Sp-100 and Sp140). This domain is usually found at the amino terminus of proteins that contain a SAND domain pfam01342.


Pssm-ID: 460835  Cd Length: 99  Bit Score: 178.11  E-value: 5.67e-54
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1958802770  25 YQLMFKLFKENKVEIASAITKLFPFLMSLRDRDFISEQKYQECQETCKNLVPVDRVVYDILSDIQKKFSRDLLKVIFSNV 104
Cdd:pfam03172   2 EEALFQHFKENKVEIAYAIKKPFPFLEGLRDHSFITEKMYKESLEACRNLVPVQRVVYNVLSELEKTFSLSLLEALFSDV 81

                          90
                  ....*....|....*...
gi 1958802770 105 HLKAYPDLQEILKHFLSV 122
Cdd:pfam03172  82 NLKEYPDLIEILKSFPNV 99
SAND pfam01342
SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The ...
 441-517 7.54e-31

SAND domain; The DNA binding activity of two proteins has been mapped to the SAND domain. The conserved KDWK motif is necessary for DNA binding, and it appears to be important for dimerization. This region is also found in the putative transcription factor RegA from the multicellular green alga Volvox cateri. This region of RegA is known as the VARL domain.


Pssm-ID: 460167  Cd Length: 76  Bit Score: 114.60  E-value: 7.54e-31
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1958802770 441 NFNAELLPVTCGNLKGVLHKDKFKQGISVMSIQCqDGNWVTPPEFEIMGGHGRSKNWKLSLRCYNWPLKLLIQRNFL 517
Cdd:pfam01342   1 DFDSPVLPVTCGAAKGLLHKKKFKQGISGKCIQN-EDSWLTPKEFEIEGGKASSKDWKRSIRCGGKPLRELIEKGLL 76
SAND smart00258
SAND domain;
445-518 8.94e-26

SAND domain;


Pssm-ID: 128554  Cd Length: 73  Bit Score: 100.50  E-value: 8.94e-26
                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 1958802770  445 ELLPVTCGNLKGVLHKDKFKQGISVMSIQcQDGNWVTPPEFEIMGGHGRSKNWKLSLRCYNWPLKLLIQRNFLP 518
Cdd:smart00258   1 SELPVTCGTVKGILYKKKFKCGISVKCIQ-YEDKWFTPKEFEIEGGKGKSKDWKRSIRCGGSSLRTLMENGTLD 73
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
Help | Disclaimer | Write to the Help Desk
NCBI | NLM | NIH