WORKLIST ENTRIES (1):
HUDSXLRNA View alignment View Structure Paraneoplastic encephalomyelitis antigen family signature
Type of fingerprint: COMPOUND with 6 elements
Links:
INTERPRO; IPR002343
PROSITE; PS00030 RNP_1
PDB; 1SXL 3Dinfo
SCOP; 1SXL
CATH; 1SXL
Creation date 15-AUG-1998; UPDATE 10-JUN-1999
1. BANDZIULIS, R.J., SWANSON, M.S. AND DREYFUSS, G.
RNA-binding proteins as developmental regulators.
GENES DEV. 3 431-437 (1989).
2. DREYFUSS, G., SWANSON, M.S. AND PINOL-ROMA, S.
Heterogeneous nuclear ribonucleoprotein particles and the pathway of
mRNA formation.
TRENDS BIOCHEM.SCI. 13 86-91 (1988).
3. LEE, A.L., KANAAR, R., RIO, D.C. AND WEMMER, D.E.
Resonance assignments and solution structure of the second RNA-binding
domain of sex-lethal determined by multidimensional heteronuclear magnetic
resonance.
BIOCHEMISTRY 33 13775-13786 (1994).
Many eukaryotic proteins that are either known or thought to bind single-
stranded RNA contain one or more copies of a putative RNA-binding domain
of about 90 amino acids [1,2]. This region has been found in, for example,
heterogeneous nuclear ribonucleoproteins, small nuclear ribonucleoproteins,
pre-RNA and mRNA associated proteins, Drosophila sex determination and elav
proteins, human paraneoplastic encephalomyelitis antigen HuD, and many
others.
The structure of an RNA-binding domain of Drosophila Sex-lethal (Sxl)
protein has been determined using multi-dimensional hetero-nuclear NMR [3].
Sxl contains two RNP consensus-type RNA-binding domains (RBDs) - the
determined structure represents the second of these (RBD-2) [3]. The
calculated intermediate-resolution family of structures exhibits the beta-
alpha-beta/beta-alpha-beta tertiary fold found in other RBD-containing
proteins [3].
HUDSXLRNA is a 6-element fingerprint that provides a signature for the
HuD/Elav/Sxl family of RNA-binding proteins. The fingerprint was derived
from an initial alignment of 11 sequences: the motifs were drawn from
conserved regions spanning the N-terminal half of the alignment - motif 3
encodes strand 1; motif 4 includes helix 1; and motif 5 includes strand 2.
Two iterations on OWL30.2 were required to reach convergence, at which point
a true set comprising 30 sequences was identified. Several partial matches
were also found, all of which are fragments or ribonucleoprotein homologues
that fail to match one or more motifs.
An update on SPTR37_9f identified a true set of 30 sequences, and 4
partial matches.
SUMMARY INFORMATION
30 codes involving 6 elements
0 codes involving 5 elements
0 codes involving 4 elements
0 codes involving 3 elements
4 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
6| 30 30 30 30 30 30
5| 0 0 0 0 0 0
4| 0 0 0 0 0 0
3| 0 0 0 0 0 0
2| 0 0 0 0 4 4
--+-------------------------------
| 1 2 3 4 5 6
True positives..
HUD_HUMAN O55010 HUD_RAT HUD_MOUSE
Q91583 Q60899 Q13235 Q12926
Q90409 Q91585 Q91903 HUC_MOUSE
HUC_HUMAN P79736 Q91584 Q24473
Q24474 Q15717 Q91582 P70372
ELAV_DROME ELAV_DROVI Q20084 O17310
O61374 Q24668 Q99141 SXLF_DROME
O01671 O76876
Subfamily: Codes involving 2 elements
Subfamily True positives..
Q92950 P70055 O88756 O57406
PROTEIN TITLES
HUD_HUMAN PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD (HU-ANTIGEN D)
O55010 HU-ANTIGEN D (RNA BINDING PROTEIN ELAVL4) - MUS MUSCULUS (MO
HUD_RAT PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD HOMOLOG (HU-ANT
HUD_MOUSE PARANEOPLASTIC ENCEPHALOMYELITIS ANTIGEN HUD HOMOLOG (HU-ANT
Q91583 RIBONUCLEOPROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q60899 HU-ANTIGEN D (NERVOUS SYSTEM-SPECIFIC RNA BINDING PROTEIN ME
Q13235 ELAV-LIKE NEURONAL PROTEIN 2 HEL-N2 - HOMO SAPIENS (HUMAN).
Q12926 ELAV-LIKE NEURONAL PROTEIN 1 - HOMO SAPIENS (HUMAN).
Q90409 RIBONUCLEOPROTEIN - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DAN
Q91585 RIBONUCLEOPROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q91903 XEL-1 - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
HUC_MOUSE HU-ANTIGEN C - MUS MUSCULUS (MOUSE).
HUC_HUMAN HU-ANTIGEN C (PARANEOPLASTIC CEREBELLAR DEGENERATION-ASSOCIA
P79736 ELAV/HUC HOMOLOG - BRACHYDANIO RERIO (ZEBRAFISH) (ZEBRA DANI
Q91584 RIBONUCLEOPROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
Q24473 RNA-BINDING PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q24474 RNA-BINDING PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q15717 HUR RNA BINDING PROTEIN - HOMO SAPIENS (HUMAN).
Q91582 RIBONUCLEOPROTEIN - XENOPUS LAEVIS (AFRICAN CLAWED FROG).
P70372 ELAV G HOMOLOG (RIBONUCLEOPROTEIN) - MUS MUSCULUS (MOUSE).
ELAV_DROME ELAV PROTEIN (EMBRYONIC LETHAL ABNORMAL VISUAL PROTEIN) - DR
ELAV_DROVI ELAV PROTEIN - DROSOPHILA VIRILIS (FRUIT FLY).
Q20084 F35H8.5 PROTEIN - CAENORHABDITIS ELEGANS.
O17310 SEX-LETHAL PROTEIN - MUSCA DOMESTICA (HOUSE FLY).
O61374 SEX-LETHAL HOMOLOG CCSXL - CERATITIS CAPITATA (MEDITERRANEAN
Q24668 SEX-LETHAL GENE - DROSOPHILA SUBOBSCURA (FRUIT FLY).
Q99141 SEX-LETHAL PROTEIN, ALTERNATIVELY SPLICED PRODUCT - DROSOPHI
SXLF_DROME SEX-LETHAL PROTEIN, FEMALE-SPECIFIC - DROSOPHILA MELANOGASTE
O01671 SEX-LETHAL PROTEIN - MEGASELIA SCALARIS.
O76876 EG:132E8.1 PROTEIN - DROSOPHILA MELANOGASTER (FRUIT FLY).
Q92950 ETR-3 - HOMO SAPIENS (HUMAN).
P70055 RNA BINDING PROTEIN ETR-3 - XENOPUS LAEVIS (AFRICAN CLAWED F
O88756 ETR-R3B PROTEIN (ETR-R3A PROTEIN) - RATTUS NORVEGICUS (RAT).
O57406 EMBRYO DEADENYLATION ELEMENT BINDING PROTEIN - XENOPUS LAEVI
SCAN HISTORY
OWL30_2 2 100 NSINGLE
SPTR37_9f 2 44 NSINGLE
INITIAL MOTIF SETS
HUDSXLRNA1 Length of motif = 16 Motif number = 1
HU-antigen D motif I - 1
PCODE ST INT
TNLIVNYLPQNMTQEE HUD_HUMAN 46 46
TNLIVNYLPQNMTQEE HUD_MOUSE 51 51
TNLIVNYLPQNMTQEE HUD_RAT 39 39
TNLIVNYLPQNMTQEE I50513 44 44
TNLIVNYLPQNMTQEE I51676 66 66
TNLIVNYLPQNMTQEE I51678 46 46
TNLIVNYLPQNMTQEE I38726 39 39
TNLIVNYLPQNMTQEE I39077 39 39
TNLIVNYLPQNMTQEE JC6057 39 39
TNLIVNYLPQTMTEDE ELAV_DROME 149 149
TNLIVNYLPQTMTEDE ELAV_DROVI 185 185
HUDSXLRNA2 Length of motif = 16 Motif number = 2
HU-antigen D motif II - 1
PCODE ST INT
AINTLNGLRLQTKTIK HUD_HUMAN 103 41
AINTLNGLRLQTKTIK HUD_MOUSE 108 41
AINTLNGLRLQTKTIK HUD_RAT 96 41
AINTLNGLRLQTKTIK I50513 101 41
AINTLNGLRLQTKTIK I51676 124 42
AINTLNGLRLQTKTIK I51678 103 41
AINTLNGLRLQTKTIK I38726 96 41
AINTLNGLRLQTKTIK I39077 96 41
AINTLNGLRLQTKTIK JC6057 96 41
AVNVLNGLRLQNKTIK ELAV_DROME 219 54
AVNVLNGLRLQNKTIK ELAV_DROVI 255 54
HUDSXLRNA3 Length of motif = 18 Motif number = 3
HU-antigen D motif III - 1
PCODE ST INT
VSYARPSSASIRDANLYV HUD_HUMAN 119 0
VSYARPSSASIRDANLYV HUD_MOUSE 124 0
VSYARPSSASIRDANLYV HUD_RAT 112 0
VSYARPSSASIRDANLYV I50513 117 0
VSYARPSSASIRDANLYV I51676 140 0
VSYARPSSASIRDANLYV I51678 119 0
VSYARPSSASIRDANLYV I38726 112 0
VSYARPSSASIRDANLYV I39077 112 0
VSYARPSSASIRDANLYV JC6057 112 0
VSFARPSSDAIKGANLYV ELAV_DROME 235 0
VSFARPSSDAIKGANLYV ELAV_DROVI 271 0
HUDSXLRNA4 Length of motif = 16 Motif number = 4
HU-antigen D motif IV - 1
PCODE ST INT
SGLPKTMTQKELEQLF HUD_HUMAN 137 0
SGLPKTMTQKELEQLF HUD_MOUSE 142 0
SGLPKTMTQKELEQLF HUD_RAT 130 0
SGLPKTMTQKELEQLF I50513 135 0
SGLPKTMTQKELEQLF I51676 158 0
SGLPKTMTQKELEQLF I51678 137 0
SGLPKTMTQKELEQLF I38726 130 0
SGLPKTMTQKELEQLF I39077 130 0
SGLPKTMTQKELEQLF JC6057 130 0
SGLPKTMTQQELEAIF ELAV_DROME 253 0
SGLPKTMTQQELEAIF ELAV_DROVI 289 0
HUDSXLRNA5 Length of motif = 13 Motif number = 5
HU-antigen D motif V - 1
PCODE ST INT
FSQYGRIITSRIL HUD_HUMAN 152 -1
FSQYGRIITSRIL HUD_MOUSE 157 -1
FSQYGRIITSRIL HUD_RAT 145 -1
FSQYGRIITSRIL I50513 150 -1
FSQYGRIITSRIL I51676 173 -1
FSQYGRIITSRIL I51678 152 -1
FSQYGRIITSRIL I38726 145 -1
FSQYGRIITSRIL I39077 145 -1
FSQYGRIITSRIL JC6057 145 -1
FAPFGAIITSRIL ELAV_DROME 268 -1
FAPFGAIITSRIL ELAV_DROVI 304 -1
HUDSXLRNA6 Length of motif = 18 Motif number = 6
HU-antigen D motif VI - 1
PCODE ST INT
LNGQKPSGATEPITVKFA HUD_HUMAN 193 28
LNGQKPSGATEPITVKFA HUD_MOUSE 198 28
LNGQKPSGATEPITVKFA HUD_RAT 186 28
LNGQKPSGAAEPITVKFA I50513 194 31
LNGQKPPGATEPITVKFA I51676 214 28
LNGQKPSGAAEPITVKFA I51678 193 28
LNGQKPPGATEPITVKFA I38726 186 28
LNGQKPPGATEPITVKFA I39077 186 28
LNGQKPPGATEPITVKFA JC6057 186 28
LNGTTPSSCTDPIVVKFS ELAV_DROME 310 29
LNGTTPSSCTDPIVVKFS ELAV_DROVI 346 29
FINAL MOTIF SETS
HUDSXLRNA1 Length of motif = 16 Motif number = 1
HU-antigen D motif I - 2
PCODE ST INT
TNLIVNYLPQNMTQEE HUD_HUMAN 46 46
TNLIVNYLPQNMTQEE O55010 39 39
TNLIVNYLPQNMTQEE HUD_RAT 39 39
TNLIVNYLPQNMTQEE HUD_MOUSE 51 51
TNLIVNYLPQNMTQEE Q12926 39 39
TNLIVNYLPQNMTQEE Q13235 39 39
TNLIVNYLPQNMTQEE Q60899 39 39
TNLIVNYLPQNMTQEE Q91583 66 66
TNLIVNYLPQNMTQEE Q90409 44 44
TNLIVNYLPQNMTQEE Q91585 46 46
TNLIVNYLPQNMTQEE Q91903 66 66
TNLIVNYLPQNMTQDE HUC_HUMAN 39 39
TNLIVNYLPQNMTQDE HUC_MOUSE 39 39
TNLIVNYLPQNMTQEE P79736 38 38
TNLIVNYLPQNMTQEE Q91584 34 34
TNLIVNYLPQTMSQDE Q24473 110 110
TNLIVNYLPQTMSQDE Q24474 110 110
TNLIVNYLPQNMTQDE Q15717 20 20
TNLIVNYLPQNMTQDE Q91582 20 20
TNLIVNYLPQNMTQEE P70372 20 20
TNLIVNYLPQTMTEDE ELAV_DROME 149 149
TNLIVNYLPQTMTEDE ELAV_DROVI 185 185
TNLIINYLPQGMTQEE Q20084 42 42
TNLIVNYLPQDMTDRE O17310 102 102
TNLIVNYLPQDMTDRE O61374 102 102
TNLIVNYLPQDMTDRE Q24668 119 119
TNLIVNYLPQDMTDRE Q99141 117 117
TNLIVNYLPQDMTDRE SXLF_DROME 125 125
TNLIVNYLPQDMQDRE O01671 64 64
TNLIINYLPQDMTDRE O76876 93 93
HUDSXLRNA2 Length of motif = 16 Motif number = 2
HU-antigen D motif II - 2
PCODE ST INT
AINTLNGLRLQTKTIK HUD_HUMAN 103 41
AINTLNGLRLQTKTIK O55010 96 41
AINTLNGLRLQTKTIK HUD_RAT 96 41
AINTLNGLRLQTKTIK HUD_MOUSE 108 41
AINTLNGLRLQTKTIK Q12926 96 41
AINTLNGLRLQTKTIK Q13235 96 41
AINTLNGLRLQTKTIK Q60899 96 41
AINTLNGLRLQTKTIK Q91583 124 42
AINTLNGLRLQTKTIK Q90409 101 41
AINTLNGLRLQTKTIK Q91585 103 41
AINTVNGLRLQTKTIK Q91903 124 42
AINTLNGLKLQTKTIK HUC_HUMAN 96 41
AINTLNGLKLQTKTIK HUC_MOUSE 96 41
AINTLNGLKLQTKTIK P79736 95 41
AINTLNGLKLQTKTIK Q91584 91 41
AINALNGLRLQNKTIK Q24473 167 41
AINALNGLRLQNKTIK Q24474 167 41
AINTLNGLRLQSKTIK Q15717 77 41
AINTLNGLRLQSKTIK Q91582 77 41
AISTLNGLRLQSKTIK P70372 77 41
AVNVLNGLRLQNKTIK ELAV_DROME 219 54
AVNVLNGLRLQNKTIK ELAV_DROVI 255 54
AVSSFNGLRLQNKTIK Q20084 99 41
AIKTVNGITVRNKRLK O17310 159 41
AIKSLNGITVRNKRLK O61374 159 41
AIKVLNGITVRNKRLK Q24668 176 41
AIKVLNGITVRNKRLK Q99141 174 41
AIKVLNGITVRNKRLK SXLF_DROME 182 41
AINNLNGITVRNKRIK O01671 121 41
AIQKLNGFYVRNKRLK O76876 150 41
HUDSXLRNA3 Length of motif = 18 Motif number = 3
HU-antigen D motif III - 2
PCODE ST INT
VSYARPSSASIRDANLYV HUD_HUMAN 119 0
VSYARPSSASIRDANLYV O55010 112 0
VSYARPSSASIRDANLYV HUD_RAT 112 0
VSYARPSSASIRDANLYV HUD_MOUSE 124 0
VSYARPSSASIRDANLYV Q12926 112 0
VSYARPSSASIRDANLYV Q13235 112 0
VSYARPSSASIRDANLYV Q60899 112 0
VSYARPSSASIRDANLYV Q91583 140 0
VSYARPSSASIRDANLYV Q90409 117 0
VSYARPSSASIRDANLYV Q91585 119 0
VSYARPSSASIRDANLYV Q91903 140 0
VSYARPSSASIRDANLYV HUC_HUMAN 112 0
VSYARPSSASIRDANLYV HUC_MOUSE 112 0
VSYARPSSASIRDANLYV P79736 111 0
VSYARPSSASIRDANLYV Q91584 107 0
VSIARPSSESIKGANLYV Q24473 183 0
VSIARPSSESIKGANLYV Q24474 183 0
VSYARPSSEVIKDANLYI Q15717 93 0
VSFARPSSESIKDANLYI Q91582 93 0
VSYARPSSEVIKDANLYI P70372 93 0
VSFARPSSDAIKGANLYV ELAV_DROME 235 0
VSFARPSSDAIKGANLYV ELAV_DROVI 271 0
VSYARPSNDQIKGSNLYV Q20084 115 0
VSYARPGGESIKDTNLYV O17310 175 0
VSYARPGGESIKDTNLYV O61374 175 0
VSYARPGGESIKDTNLYV Q24668 192 0
VSYARPGGESIKDTNLYV Q99141 190 0
VSYARPGGESIKDTNLYV SXLF_DROME 198 0
VSFARPGGEQLRDTNLYV O01671 137 0
VSYARPGGQSIKDTNLYV O76876 166 0
HUDSXLRNA4 Length of motif = 16 Motif number = 4
HU-antigen D motif IV - 2
PCODE ST INT
SGLPKTMTQKELEQLF HUD_HUMAN 137 0
SGLPKTMTQKELEQLF O55010 130 0
SGLPKTMTQKELEQLF HUD_RAT 130 0
SGLPKTMTQKELEQLF HUD_MOUSE 142 0
SGLPKTMTQKELEQLF Q12926 130 0
SGLPKTMTQKELEQLF Q13235 130 0
SGLPKTMTQKELEQLF Q60899 130 0
SGLPKTMTQKELEQLF Q91583 158 0
SGLPKTMTQKELEQLF Q90409 135 0
SGLPKTMTQKELEQLF Q91585 137 0
SGLPKTMTQKELEQLF Q91903 158 0
SGLPKTMSQKEMEQLF HUC_HUMAN 130 0
SGLPKTMSQKEMEQLF HUC_MOUSE 130 0
SGLPKTMSQKDMEQLF P79736 129 0
SSLPKTMNQKEMEQLF Q91584 125 0
SGLPKNMTQSDLESLF Q24473 201 0
SGLPKNMTQSDLESLF Q24474 201 0
SGLPRTMTQKDVEDMF Q15717 111 0
SGLPRTMTQKDVEDMF Q91582 111 0
SGLPRTMTQKDVEDMF P70372 111 0
SGLPKTMTQQELEAIF ELAV_DROME 253 0
SGLPKTMTQQELEAIF ELAV_DROVI 289 0
SGIPKSMTLHELESIF Q20084 133 0
TNLPRTITDDELEKIF O17310 193 0
TNLPRTITDDQLDTIF O61374 193 0
TNLPRTITDDQLDTIF Q24668 210 0
TNLPRTITDDQLDTIF Q99141 208 0
TNLPRTITDDQLDTIF SXLF_DROME 216 0
TNLSRSITDEQLETIF O01671 155 0
INLSRNINDDMLDRIF O76876 184 0
HUDSXLRNA5 Length of motif = 13 Motif number = 5
HU-antigen D motif V - 2
PCODE ST INT
FSQYGRIITSRIL HUD_HUMAN 152 -1
FSQYGRIITSRIL O55010 145 -1
FSQYGRIITSRIL HUD_RAT 145 -1
FSQYGRIITSRIL HUD_MOUSE 157 -1
FSQYGRIITSRIL Q12926 145 -1
FSQYGRIITSRIL Q13235 145 -1
FSQYGRIITSRIL Q60899 145 -1
FSQYGRIITSRIL Q91583 173 -1
FSQYGRIITSRIL Q90409 150 -1
FSQYGRIITSRIL Q91585 152 -1
FSQYGRIITSRIL Q91903 173 -1
FSQYGRIITSRIL HUC_HUMAN 145 -1
FSQYGRIITSRIL HUC_MOUSE 145 -1
FSQYGRIITSRIL P79736 144 -1
FSQYGRIITSRIL Q91584 140 -1
FSPYGKIITSRIL Q24473 216 -1
FSPYGKIITSRIL Q24474 216 -1
FSRFGRIINSRVL Q15717 126 -1
FLPFGHIINSRVL Q91582 126 -1
FSRFGRIINSRVL P70372 126 -1
FAPFGAIITSRIL ELAV_DROME 268 -1
FAPFGAIITSRIL ELAV_DROVI 304 -1
FRPFGQIITSRIL Q20084 148 -1
FGKYGNIVQKNIL O17310 208 -1
FGKYGMIVQKNIL O61374 208 -1
FGKYGSIVQKNIL Q24668 225 -1
FGKYGSIVQKNIL Q99141 223 -1
FGKYGSIVQKNIL SXLF_DROME 231 -1
FGKYGQIVQKNIL O01671 170 -1
FSPYGLIVQRNIL O76876 199 -1
HUDSXLRNA6 Length of motif = 18 Motif number = 6
HU-antigen D motif VI - 2
PCODE ST INT
LNGQKPSGATEPITVKFA HUD_HUMAN 193 28
LNGQKPSGATEPITVKFA O55010 186 28
LNGQKPSGATEPITVKFA HUD_RAT 186 28
LNGQKPSGATEPITVKFA HUD_MOUSE 198 28
LNGQKPPGATEPITVKFA Q12926 186 28
LNGQKPPGATEPITVKFA Q13235 186 28
LNGQKPPGATEPITVKFA Q60899 186 28
LNGQKPPGATEPITVKFA Q91583 214 28
LNGQKPSGAAEPITVKFA Q90409 194 31
LNGQKPSGAAEPITVKFA Q91585 193 28
LNGQKPPGATEPITVKFA Q91903 214 28
LNGQKPLGAAEPITVKFA HUC_HUMAN 186 28
LNGQKPLGAAEPITVKFA HUC_MOUSE 186 28
LNGQKPLGAAEPITVKFA P79736 185 28
LNGQKPLGASEPITVKFA Q91584 181 28
LNGTTPKNSTEPITVKFA Q24473 262 33
LNGTTPKNSTEPITVKFA Q24474 257 28
FNGHKPPGSSEPIAVKFA Q15717 167 28
FNGHKPPGSSEPITVKFA Q91582 167 28
FIGHKPPGSSEPITVKFA P70372 167 28
LNGTTPSSCTDPIVVKFS ELAV_DROME 310 29
LNGTTPSSCTDPIVVKFS ELAV_DROVI 346 29
LNGSIPSGCSEQITVKFA Q20084 189 28
LNNVIPEGASQPLTVRLA O17310 249 28
LNNVIPEGASQPLTVRLA O61374 249 28
LNNVIPEGGSQPLSVRLA Q24668 266 28
LNNVIPEGGSQPLSVRLA Q99141 264 28
LNNVIPEGGSQPLSVRLA SXLF_DROME 272 28
LNNVIPEGGTQPLTVRVA O01671 211 28
LNNTVPEGGSQPIWVRLA O76876 240 28
User query: Display/Full Code "HUDSXLRNA"