WORKLIST ENTRIES (1):
LNOTCHREPEAT View alignment LIN-12/notch repeat (LNR) signature
Type of fingerprint: COMPOUND with 3 elements
Links:
PRINTS; PR01983 NOTCH
PFAM; PF00066 notch
INTERPRO; IPR000800
Creation date 01-DEC-2000
1. KIMBLE, J., HENDERSON, S. AND CRITTENDEN, S.
Notch/LIN-12 signalling: transduction by regulated protein splicing.
TRENDS BIOCHEM.SCI. 23 353-357 (1998).
2. BRAY, S.
Notch.
CURR.BIOL. 10 R433-R435 (2000).
3. KIMBLE, J. AND SIMPSON, P.
The LIN-12/Notch signalling pathway and its regulation.
ANNU.REV.CELL DEV.BIOL. 13 333-361 (1997).
LIN-12/notch proteins function as receptors for intercellular signals during
development in a diverse range of species, from human through to C.elegans.
The LIN-12/notch family is characterised by a repeat region (termed LNR),
and members also share a number of other features, such as extracellular EGF
repeats and intracellular ankyrin repeats. Notch is involved in many
developmental processes, including limb and appendage development, lymphoid
lineage selection, axon pathfinding and dendritic sprouting. Dysfunction of
the notch/LIN-12 signalling pathway has been implicated in several human
diseases, including leukaemia, cervical and colon cancer, Alzheimer's
disease, cerebral ischaemia and alagille syndrome [1].
The notch protein can be divided into 3 main regions: a large extracellular
domain (ECD), which is composed largely of EGF repeats (between 10 and 36)
and also contains the triplet cysteine-rich LIN-12/Notch repeat; a single
transmembrane (TM) domain; and an intracellular domain (ICD), which contains
6 ankyrin repeats that form the binding site for cytoplasmic regulators of
notch activity [2]. Three components appear to be essential for LIN-12/notch
signalling: the Delta/Serrate/LAG-2 (DSL) ligand; the LIN-12/notch receptor
itself; and the CBF1/Su(H)/LAG-1 (CSL) transcription factor. While 2 EGF-
like repeats (11 and 12 in Drosophila) appear to be sufficient and necessary
for DSL ligand binding, the LNR region appears to be involved in receptor
regulation. Currently, 2 possible methods of CSL factor regulation are
proposed: receptor-mediated transport of the CSL factor from cytoplasm
to nucleus; and cleavage of the ICD upon receptor activation, followed by
entry of the ICD into the nucleus, where it acts as a co-activator of
transcription with the CSL factor [3].
LNOTCHREPEAT is a 3-element fingerprint that provides a signature for the
LIN-12/notch (LNR) repeat. The fingerprint was derived from an initial alignment
of 10 sequences: the motifs were drawn from conserved regions within the
repeat, successively encoding the C-termini of repeats 1, 2 and 3
respectively. Two iterations on SPTR39_14f were required to reach
convergence, at which point a true set comprising 23 sequences was identified.
SUMMARY INFORMATION
23 codes involving 3 elements
0 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
3| 23 23 23
2| 0 0 0
--+----------------
| 1 2 3
True positives..
NTC1_MOUSE NTC1_RAT NOTC_XENLA NOTC_BRARE
Q9QW58 NTC3_MOUSE Q9R172 Q9UM47
Q9Y6L8 Q25253 Q9QW30 O35516
NOTC_DROME O97458 Q9W4T8 O00306
Q99940 NTC4_MOUSE O35442 O61240
LI12_CAEEL O16004 GLP1_CAEEL
PROTEIN TITLES
NTC1_MOUSE NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 PRECURSOR (MOTCH PR
NTC1_RAT NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 1 PRECURSOR - Rattus
NOTC_XENLA NEUROGENIC LOCUS NOTCH PROTEIN HOMOLOG PRECURSOR (XOTCH PROT
NOTC_BRARE NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN PRECURSOR - Brachydan
Q9QW58 MOTCH=NOTCH PRODUCT HOMOLOG - Mus sp.
NTC3_MOUSE NEUROGENIC LOCUS NOTCH 3 PROTEIN - Mus musculus (Mouse).
Q9R172 NOTCH 3 PROTEIN - Rattus norvegicus (Rat).
Q9UM47 NOTCH3 - Homo sapiens (Human).
Q9Y6L8 NOTCH3 - Homo sapiens (Human).
Q25253 NOTCH HOMOLOG SCALLOPED WINGS (SCL) - Lucilia cuprina (Green
Q9QW30 NOTCH2 PROTEIN - Rattus sp.
O35516 CELL SURFACE PROTEIN - Mus musculus (Mouse).
NOTC_DROME NEUROGENIC LOCUS NOTCH PROTEIN PRECURSOR - Drosophila melano
O97458 EG:163A10.2 PROTEIN - Drosophila melanogaster (Fruit fly).
Q9W4T8 N GENE PRODUCT - Drosophila melanogaster (Fruit fly).
O00306 NOTCH4 - Homo sapiens (Human).
Q99940 NOTCH4 - Homo sapiens (Human).
NTC4_MOUSE NEUROGENIC LOCUS NOTCH HOMOLOG PROTEIN 4 PRECURSOR (TRANSFOR
O35442 NOTCH4 - Mus musculus (Mouse).
O61240 HRNOTCH PROTEIN - Halocynthia roretzi (Sea squirt).
LI12_CAEEL LIN-12 PROTEIN PRECURSOR - Caenorhabditis elegans.
O16004 NOTCH HOMOLOG - Lytechinus variegatus (Sea urchin).
GLP1_CAEEL GLP-1 PROTEIN PRECURSOR - Caenorhabditis elegans.
SCAN HISTORY
SPTR39_14f 2 50 NSINGLE
INITIAL MOTIF SETS
LNOTCHREPEAT1 Length of motif = 14 Motif number = 1
LIN-12/notch repeat (LNR) motif I - 1
PCODE ST INT
CNTYACNFDGNDCS NOTC_DROME 1500 1500
CNNHACGWDGGDCS NOTC_XENLA 1465 1465
CNNHACGWDGGDCS NTC1_RAT 1467 1467
CNTHLCEWDGKDCS O16004 1458 1458
CNSHACQWDGGDCS O35516 1441 1441
CNTPGCGWDGGDCS NTC3_MOUSE 1406 1406
CSGPGGDWDGGDCS NTC4_MOUSE 1187 1187
CNVHECEFDGGDCS O61240 1327 1327
CNYAACKFDGGDCS LI12_CAEEL 656 656
CNLEECNFDGGDCS GLP1_CAEEL 514 514
LNOTCHREPEAT2 Length of motif = 13 Motif number = 2
LIN-12/notch repeat (LNR) motif II - 1
PCODE ST INT
CNNAACHYDGHDC NOTC_DROME 1540 26
CNNTGCLYDGFDC NOTC_XENLA 1507 28
CNSAGCLFDGFDC NTC1_RAT 1509 28
CNNHGCLFDGFDC O16004 1500 28
CNTAECLFDNFEC O35516 1482 27
CSSPACLYDNFDC NTC3_MOUSE 1447 27
CDSEECLFDGYDC NTC4_MOUSE 1229 28
CNNEDCLHDGMDC O61240 1369 28
CNNEECLYDGMDC LI12_CAEEL 697 27
CNNEECLYDGLDC GLP1_CAEEL 555 27
LNOTCHREPEAT3 Length of motif = 13 Motif number = 3
LIN-12/notch repeat (LNR) motif III - 1
PCODE ST INT
CNNAECSWDGLDC NOTC_DROME 1580 27
CNNAECEWDGLDC NOTC_XENLA 1547 27
CNSAECEWDGLDC NTC1_RAT 1549 27
CNNIGCLYDGLDC O16004 1539 26
CNSEECGWDGLDC O35516 1520 25
CNTEECGWDGLDC NTC3_MOUSE 1489 29
CNNAECGWDGGDC NTC4_MOUSE 1268 26
CNNANCGWDGADC O61240 1409 27
CNTNGCGFDGGDC LI12_CAEEL 737 27
CSFIGCGFDGGDC GLP1_CAEEL 595 27
FINAL MOTIF SETS
LNOTCHREPEAT1 Length of motif = 14 Motif number = 1
LIN-12/notch repeat (LNR) motif I - 2
PCODE ST INT
CNNHACGWDGGDCS NTC1_MOUSE 1467 1467
CNNHACGWDGGDCS NTC1_RAT 1467 1467
CNNHACGWDGGDCS NOTC_XENLA 1465 1465
CNNHACGWDGGDCS NOTC_BRARE 1465 1465
CNNHACGWDGGDCS Q9QW58 648 648
CNTPGCGWDGGDCS NTC3_MOUSE 1406 1406
CNSPGCGWDGGDCS Q9R172 1407 1407
CNSPGCGWDGGDCS Q9UM47 1405 1405
CNSPGCGWDGGDCS Q9Y6L8 1405 1405
CNTYACNFDGNDCS Q25253 1481 1481
CNSHACQWDGGDCS Q9QW30 1443 1443
CNSHACQWDGGDCS O35516 1441 1441
CNTYACNFDGNDCS NOTC_DROME 1500 1500
CNTYACNFDGNDCS O97458 1500 1500
CNTYACNFDGNDCS Q9W4T8 1500 1500
CSGPGGNWDGGDCS O00306 1191 1191
CSGPGGNWDGGDCS Q99940 1190 1190
CSGPGGDWDGGDCS NTC4_MOUSE 1187 1187
CSGPGGDWDGGDCS O35442 1187 1187
CNVHECEFDGGDCS O61240 1327 1327
CNYAACKFDGGDCS LI12_CAEEL 656 656
CNTHLCEWDGKDCS O16004 1458 1458
CNLEECNFDGGDCS GLP1_CAEEL 514 514
LNOTCHREPEAT2 Length of motif = 13 Motif number = 2
LIN-12/notch repeat (LNR) motif II - 2
PCODE ST INT
CNSAGCLFDGFDC NTC1_MOUSE 1509 28
CNSAGCLFDGFDC NTC1_RAT 1509 28
CNNTGCLYDGFDC NOTC_XENLA 1507 28
CATAGCLYDGFDC NOTC_BRARE 1507 28
CNSAGCLFDGFDC Q9QW58 690 28
CSSPACLYDNFDC NTC3_MOUSE 1447 27
CSSPACLYDNFDC Q9R172 1448 27
CSSPACLYDNFDC Q9UM47 1446 27
CSSPACLYDNFDC Q9Y6L8 1446 27
CNNAACLFDGRDC Q25253 1522 27
CNTAECLFDNFEC Q9QW30 1484 27
CNTAECLFDNFEC O35516 1482 27
CNNAACHYDGHDC NOTC_DROME 1540 26
CNNAACHYDGHDC O97458 1540 26
CNNAACHYDGHDC Q9W4T8 1540 26
CDSEECLFDGYDC O00306 1233 28
CDSEECLFDGYDC Q99940 1232 28
CDSEECLFDGYDC NTC4_MOUSE 1229 28
CDSEECLFDGYDC O35442 1229 28
CNNEDCLHDGMDC O61240 1369 28
CNNEECLYDGMDC LI12_CAEEL 697 27
CNNHGCLFDGFDC O16004 1500 28
CNNEECLYDGLDC GLP1_CAEEL 555 27
LNOTCHREPEAT3 Length of motif = 13 Motif number = 3
LIN-12/notch repeat (LNR) motif III - 2
PCODE ST INT
CNSAECEWDGLDC NTC1_MOUSE 1549 27
CNSAECEWDGLDC NTC1_RAT 1549 27
CNNAECEWDGLDC NOTC_XENLA 1547 27
CNNAECEWDGLDC NOTC_BRARE 1547 27
CNSAECERDGLDC Q9QW58 730 27
CNTEECGWDGLDC NTC3_MOUSE 1489 29
CNTEECGWDGLDC Q9R172 1490 29
CNTEECGWDGLDC Q9UM47 1488 29
CNTEECGWDGLDC Q9Y6L8 1488 29
CNNAECNWDGLDC Q25253 1562 27
CNNEECGWDGLDC Q9QW30 1522 25
CNSEECGWDGLDC O35516 1520 25
CNNAECSWDGLDC NOTC_DROME 1580 27
CNNAECSWDGLDC O97458 1580 27
CNNAECSWDGLDC Q9W4T8 1580 27
CNTAECGWDGGDC O00306 1272 26
CNTAECGWDGGDC Q99940 1271 26
CNNAECGWDGGDC NTC4_MOUSE 1268 26
CNNAECGWDGGDC O35442 1268 26
CNNANCGWDGADC O61240 1409 27
CNTNGCGFDGGDC LI12_CAEEL 737 27
CNNIGCLYDGLDC O16004 1539 26
CSFIGCGFDGGDC GLP1_CAEEL 595 27
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