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Conserved domains on  [gi|1039765180|ref|XP_017175241|]
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KH homology domain-containing protein 4 isoform X1 [Mus musculus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 231-332 1.09e-59

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


:

Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 194.31  E-value: 1.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 231 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 310
Cdd:cd22386     1 KYYQEKVFVGLEHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSGFIEPASGREADEPLHLLISHPDPEGLQQA 80

                          90       100
                  ....*....|....*....|..
gi 1039765180 311 KKLCENLLQTVHAEYSRFVNQI 332
Cdd:cd22386    81 KKLCEDLLQTVHQEYGEFQQQP 102
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 101-184 7.34e-47

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


:

Pssm-ID: 411813  Cd Length: 84  Bit Score: 159.68  E-value: 7.34e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 101 KDDLVVAEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMTTEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRI 180
Cdd:cd22385     1 GDDLYVAEIEINDLPNTCRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPGERPLYLHVQAPTKEAVDRAVNKI 80


                  ....
gi 1039765180 181 KEII 184
Cdd:cd22385    81 NEII 84
 
Name Accession Description Interval E-value
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 231-332 1.09e-59

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 194.31  E-value: 1.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 231 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 310
Cdd:cd22386     1 KYYQEKVFVGLEHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSGFIEPASGREADEPLHLLISHPDPEGLQQA 80

                          90       100
                  ....*....|....*....|..
gi 1039765180 311 KKLCENLLQTVHAEYSRFVNQI 332
Cdd:cd22386    81 KKLCEDLLQTVHQEYGEFQQQP 102
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 101-184 7.34e-47

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411813  Cd Length: 84  Bit Score: 159.68  E-value: 7.34e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 101 KDDLVVAEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMTTEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRI 180
Cdd:cd22385     1 GDDLYVAEIEINDLPNTCRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPGERPLYLHVQAPTKEAVDRAVNKI 80


                  ....
gi 1039765180 181 KEII 184
Cdd:cd22385    81 NEII 84
 
Name Accession Description Interval E-value
KH-I_KHDC4_rpt2 cd22386
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 231-332 1.09e-59

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411814 [Multi-domain]  Cd Length: 102  Bit Score: 194.31  E-value: 1.09e-59
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 231 HYVQDKLFVGLEHAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGCIEPASGREAFEPMYIYISHPKPEGLAAA 310
Cdd:cd22386     1 KYYQEKVFVGLEHAPPGFNVRGKLIGPGGSNVKHIQQETGAKVQLRGKGSGFIEPASGREADEPLHLLISHPDPEGLQQA 80

                          90       100
                  ....*....|....*....|..
gi 1039765180 311 KKLCENLLQTVHAEYSRFVNQI 332
Cdd:cd22386    81 KKLCEDLLQTVHQEYGEFQQQP 102
KH-I_KHDC4_rpt1 cd22385
first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein ...
 101-184 7.34e-47

first type I K homology (KH) RNA-binding domain found in KH homology domain-containing protein 4 (KHDC4) and similar proteins; KHDC4, also called Brings lots of money 7 (Blom7), or pre-mRNA splicing factor protein KHDC4, is an RNA-binding protein involved in pre-mRNA splicing. It interacts with the PRP19C/Prp19 complex/NTC/Nineteen complex which is part of the spliceosome. KHDC4 binds preferentially RNA with A/C rich sequences and poly-C stretches. KHDC4 contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411813  Cd Length: 84  Bit Score: 159.68  E-value: 7.34e-47
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 101 KDDLVVAEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMTTEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRI 180
Cdd:cd22385     1 GDDLYVAEIEINDLPNTCRNLLTKGSTQEEIQKESGAAVSTRGRYMPPEEKATFNPGERPLYLHVQAPTKEAVDRAVNKI 80


                  ....
gi 1039765180 181 KEII 184
Cdd:cd22385    81 NEII 84
KH-I_RIK_like_rpt2 cd22472
second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and ...
 237-328 4.60e-20

second type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the second one.


Pssm-ID: 411900  Cd Length: 96  Bit Score: 85.19  E-value: 4.60e-20
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 237 LFVGLEhAVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGSGciepaSGREAFEPMYIYISHPKPEGLAAAKKLCEN 316
Cdd:cd22472     7 LYVGIE-APPSFNLAGRIRGPNNSYLQHIASATGATVALRGRGSG-----GAPEGPEPLHLFLSASDPKALEEARGLAEN 80

                          90
                  ....*....|..
gi 1039765180 317 LLQTVHAEYSRF 328
Cdd:cd22472    81 LIDTVRADFKAA 92
KH-I_DDX46_like cd22387
type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); ...
 101-184 2.22e-15

type I K homology (KH) RNA-binding domain found in the family of DEAD box protein 46 (DDX46); The DDX46 family includes DEAD box protein 46 (DDX46), fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5, Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins. DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this family contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411815  Cd Length: 82  Bit Score: 71.54  E-value: 2.22e-15
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 101 KDDLVVAEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMttEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRI 180
Cdd:cd22387     1 NNGNFVEEFEINDYPQIARLKVTSKEVLNSIMEETGATITIKGQYY--PPGKKPKPGERKLYLLIEGATEESVQSARNEI 78


                  ....
gi 1039765180 181 KEII 184
Cdd:cd22387    79 KRVL 82
KH-I_AtRH42_like cd22475
type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana DEAD-box ATP-dependent ...
 107-184 1.51e-14

type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana DEAD-box ATP-dependent RNA helicase RH42 and similar proteins; RH42, also called DEAD-box RNA helicase RCF1, or REGULATOR OF CBF GENE EXPRESSION 1, is a helicase required for pre-mRNA splicing, cold-responsive gene regulation and cold tolerance. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411903  Cd Length: 102  Bit Score: 69.73  E-value: 1.51e-14
                          10        20        30        40        50        60        70
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 1039765180 107 AEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMttEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRIKEII 184
Cdd:cd22475     7 EELEINDFPQHARWKVTHKDTLGQISELTGAAITTRGQYY--PPGRIPGPGERKLYLLIEGPSEASVKEAKAEIKRIL 82
KH-I_RIK_like_rpt1 cd22471
first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and ...
 108-184 2.56e-12

first type I K homology (KH) RNA-binding domain found in Arabidopsis thaliana protein RIK and similar proteins; RIK, also called rough sheath 2-interacting KH domain protein, or RS2-interacting KH domain protein, is a RNA binding protein that acts together with RS2/AS1 in the recruitment of HIRA. RIK contains two type I K homology (KH) RNA-binding domains. The model corresponds to the first one. The KH1 domain is a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411899  Cd Length: 91  Bit Score: 62.87  E-value: 2.56e-12
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 108 EVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMttEEKAKVGPGDRPLYLHV------QGQTREL---VDRAVN 178
Cdd:cd22471     8 EIVINDAPPSVRHHLTKRSTQDEIQSKTGVVVVTRGRYY--PPGTPPPDNEKPLYLHItagaqlPPDDAERqkaVDAAAA 85


                  ....*.
gi 1039765180 179 RIKEII 184
Cdd:cd22471    86 DIQAML 91
KH-I_DDX46 cd22473
type I K homology (KH) RNA-binding domain found in DEAD box protein 46 (DDX46) and similar ...
 108-201 6.49e-10

type I K homology (KH) RNA-binding domain found in DEAD box protein 46 (DDX46) and similar proteins; DDX46, also called PRP5 homolog, is an ATP-dependent RNA helicase that plays an essential role in splicing, either prior to, or during splicing A complex formation. It inhibits antiviral innate responses by entrapping selected antiviral transcripts in the nucleus. It is also involved in the development of several tumors. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411901  Cd Length: 103  Bit Score: 56.56  E-value: 6.49e-10
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 108 EVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMTTEEKAKvgPGDRPLYLHVQGQTRELVDRAVNRIKEIITNG 187
Cdd:cd22473     8 ELEINDFPQTARWKVTSKEALAQISEYSEAGITVRGTYFPPGKEPK--EGERKLYLAIEAASERAVQKAKAEITRLIKEE 85

                          90
                  ....*....|....
gi 1039765180 188 VVKAATGTSPTFNG 201
Cdd:cd22473    86 LLRLQASYQPINKG 99
KH-I_PRP5_like cd22474
type I K homology (KH) RNA-binding domain found in fungal pre-mRNA-processing ATP-dependent ...
 106-189 4.16e-08

type I K homology (KH) RNA-binding domain found in fungal pre-mRNA-processing ATP-dependent RNA helicase PRP5 and similar proteins; PRP5 is an ATP-dependent RNA helicase involved spliceosome assembly and in nuclear splicing. It catalyzes an ATP-dependent conformational change of U2 snRNP. PRP5 interacts with the U2 snRNP and HSH155. Members in this subfamily contain a divergent KH domain that lacks the RNA-binding GXXG motif.


Pssm-ID: 411902  Cd Length: 89  Bit Score: 50.79  E-value: 4.16e-08
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 106 VAEVEINDVPLTCRNLLTRGQTQDEISRLSGAAVSTRGRFMTTEEKAKVGPGDRPLYLHVQGQTRELVDRAVNRIKEIIT 185
Cdd:cd22474     6 HAKVEINDLPQKARWEATNNTSLSKIIEETGCSITNKGNFYPPGKEPQPNNDEPKLYLLIEGTTEKAVRLAIELLRRKLV 85


                  ....
gi 1039765180 186 NGVV 189
Cdd:cd22474    86 EGVV 89
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 124-184 1.55e-05

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 43.84  E-value: 1.55e-05
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 1039765180 124 RGQTQDEISRLSGAAVSTRGRFMTTEEKAKVGPG------DRPLYLHVQGQTRELVDRAVNRIKEII 184
Cdd:cd22382    26 RGNTLKKIEKETGAKIMIRGKGSVKEGKVGRKDGqplpgeDEPLHALVTANTAESVKKAVDKIKEII 92
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 234-319 2.04e-05

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 43.36  E-value: 2.04e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 234 QDKLFVGLEHaVPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGS-----GCIEPASGREAFEPMYIYISHPKPEGLA 308
Cdd:cd02395     3 QRKIYIPVDE-YPDYNFIGLIIGPRGNTQKRMEKESGAKIAIRGKGSvkegkGRSDPQPDPDEEEDLHVLITADTEEKVD 81

                          90
                  ....*....|.
gi 1039765180 309 AAKKLCENLLQ 319
Cdd:cd02395    82 KAAKLIEKLLI 92
KH-I_SF1 cd22382
type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar ...
 233-319 1.11e-03

type I K homology (KH) RNA-binding domain found in splicing factor 1 (SF1) and similar proteins; SF1, also called branch point-binding protein, or BBP, or transcription factor ZFM1, or zinc finger gene in MEN1 locus, or zinc finger protein 162, is necessary for the ATP-dependent first step of spliceosome assembly. Binds to the intron branch point sequence (BPS) 5'-UACUAAC-3' of the pre-mRNA. It may act as transcription repressor.


Pssm-ID: 411810 [Multi-domain]  Cd Length: 93  Bit Score: 38.44  E-value: 1.11e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 1039765180 233 VQDKLFVGLEHAvPTFNVKEKVEGPGCSYLQHIQIETGAKVFLRGKGS--------GCIEPASGREafEPMYIYISHPKP 304
Cdd:cd22382     2 VSDKVMIPQEEY-PDINFVGLLIGPRGNTLKKIEKETGAKIMIRGKGSvkegkvgrKDGQPLPGED--EPLHALVTANTA 78

                          90
                  ....*....|....*
gi 1039765180 305 EGLAAAKKLCENLLQ 319
Cdd:cd22382    79 ESVKKAVDKIKEIIK 93
KH-I_BBP cd02395
type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) ...
 124-184 1.88e-03

type I K homology (KH) RNA-binding domain found in yeast branchpoint-bridging protein (BBP) and similar proteins; Yeast BBP, also called mud synthetic-lethal 5 protein, or splicing factor 1, or zinc finger protein BBP, is a mammalian splicing factor SF1 ortholog. It is involved in protein-protein interactions that bridge the 3' and 5' splice-site ends of the intron during the early steps of yeast pre-mRNA splicing. BBP interacts specifically with the pre-mRNA branchpoint sequence UACUAAC.


Pssm-ID: 411805 [Multi-domain]  Cd Length: 92  Bit Score: 37.97  E-value: 1.88e-03
                          10        20        30        40        50        60
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 1039765180 124 RGQTQDEISRLSGAAVSTRGRFMTTEEK----AKVGPGDR-PLYLHVQGQTRELVDRAVNRIKEII 184
Cdd:cd02395    26 RGNTQKRMEKESGAKIAIRGKGSVKEGKgrsdPQPDPDEEeDLHVLITADTEEKVDKAAKLIEKLL 91
 
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.
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