Putative ALternative Splicing Database 
(PALS db)

[Introduction] [Rationale] [History] [Statistics]

[User's Guide] [AS Lists] [Text Info] [All Seq Info] [Hyperlinks] [Related db]

User's Guide


  1. Rationale
  2. Audience of PALS db
  3. Steps to use PALS db
  4. Release note
  5. Statistics
  6. Abbreviations
  7. For updates, see User's guide
  8. Disclaimer

Audience of PALS db

This database is designed for biologists, who are interested in

  • Discovering biological phenomenon
  • Solving a biological problem

PALS db is NOT designed to collect splicing site information for gene prediction programs.

Steps to use PALS db

  1. Select search field [next step] [top]

wpe3.jpg (7437 bytes)

  • "Gene description + Gene name": the gene symbol and gene name approved by The Human Genome Organisation (HUGO)
  • "Literature aliases": other gene symbols used in literatures (known as aliases), see HUGO help
  • Ug_id: the UniGene Cluster ID
  • Gb_id: the GenBank accession number
  • Human and Mouse Cytoband: the cytogenetic location of a gene
  1. Enter keyword [next step] [previous step] [top]
  • All the search is case insensitive. 
  • Partial word is also acceptable. 
  • Logic operations "and" and "not" are not available.
  • Logic operation "or", i.e. "|", can ONLY be used in "Gene description + Gene name". For example, "smn|eif4g" will find records that contains "smn", or "eif4g", or "smn, eif4g".
  • Query against Ug_id must be exact, e.g. "hs.2" or "Hs.2" can only retrieve Hs.2, but not Hs.22, Hs.222, Hs.2222, etc.
  • Query against cytogenetic locations
  • Human: use the "n[p|q]n" format (e.g. 1p36, 1q20, etc)
  • Mouse: e.g. "1 40" means position 40 cM on chromosome #1
  1. Set the optional parameters [search results] [previous step] [top]

The default species is human. The search speed will be slowing down by selecting both human and mouse.  In order to perform the AS comparison between human and mouse, users can also use the hyperlinks "homologs" or "similarities" in the graphical output of "AS lists" and "All seq info".

PALS db saves all the predicted AS sites and marked those sites that pass the threshold criteria. The default setting is 95% identity on both ends of alignment at least 50-bp in length (See rationale for details). Hopefully, the users can take advantage of the unmarked information to 

  • to enhance the confidence on prediction 
  • to recover false negatives

[previous step] [top]

Search Results

The results are displayed in an eight-column table (not the six-cloumn table shown below)

  1. Ug_id: The UniGene cluster id will hyperlink to NCBI's UniGene database
    • Green background: UniGene clusters that have at least one predicted AS site at the given threshold in the query interface
    • Gray background: UniGene clusters that don't have any predicted AS site at the given threshold in the query interface
  2. Gene: Will hyperlink to alias list of the given gene name
  3. UniGene member: List the number of all sequences in a given UniGene cluster
  4. AS lists: Will hyperlink to non-redundant AS information in graphics
  5. Text Info: Will hyperlink to text information for those UniGene clusters that pass the filtering criteria
  6. All seq info: Will hyperlink to a graphical display that have ALL the AS sites regardless of their quality
  7. Description: An one-sentence description of a given UniGene cluster
  8. Cytoband: List the cytogenetic location of a given UniGene cluster



Genes with more than 20 putative ASSPs (Release 7, 2005/01/24)

Ug_id Gene UniGene member AS lists(pic) Text_Info All seq info Descriptions Cytoband
Hs.75431 FGG 2062 20 text pic Fibrinogen, gamma polypeptide 4q28
Hs.523628 DAP3 801 20 text pic Death associated protein 3 1q21-q22
Hs.235873 PAQR6 230 20 text pic Progestin and adipoQ receptor family member VI 1q22
Hs.25647 FOS 1003 20 text pic V-fos FBJ murine osteosarcoma viral oncogene homolog 14q24.3
Hs.334841 SELENBP1 543 20 text pic Selenium binding protein 1 1q21-q22
Hs.520640 ACTB 15679 20 text pic Actin, beta 7p15-p12
Hs.370581 CAP1 1813 20 text pic CAP, adenylate cyclase-associated protein 1 (yeast) 1p34.2
Hs.26593 HDAC10 268 20 text pic Histone deacetylase 10 22q13.31
Hs.180877 H3F3B 3655 20 text pic H3 histone, family 3B (H3.3B) 17q25
Hs.491359 LMNA 1988 20 text pic Lamin A/C 1q21.2-q21.3
Hs.522373 GSN 1399 20 text pic Gelsolin (amyloidosis, Finnish type) 9q33
Hs.512629 EIF4B 2012 20 text pic Eukaryotic translation initiation factor 4B 12q13.13
Hs.470477 PTP4A2 863 20 text pic Protein tyrosine phosphatase type IVA, member 2 1p35
Hs.183684 EIF4G2 2905 20 text pic Eukaryotic translation initiation factor 4 gamma, 2 11p15
Hs.461200 DKFZp434K1323 276 20 text pic CXYorf1-related protein Yq12
Hs.515947 LOC376745 347 20 text pic AG1 1q21.2
Hs.514941 MOV10 503 20 text pic Mov10, Moloney leukemia virus 10, homolog (mouse) 1p13.2
Hs.516111 DCTN1 789 20 text pic Dynactin 1 (p150, glued homolog, Drosophila) 2p13
Hs.518525 GLUL 1676 20 text pic Glutamate-ammonia ligase (glutamine synthase) 1q31
Hs.90107 ADRM1 683 20 text pic Adhesion regulating molecule 1 20q13.33
Hs.522500 KIAA0310 557 20 text pic KIAA0310 9q34.3
Hs.375001 TLN1 980 20 text pic Talin 1 9p13
Hs.136905 UREB1 1086 20 text pic Upstream regulatory element binding protein 1 Xp11.22
Hs.535597 @ 481 21 text pic Anti-HIV-1 gp120 V3 loop antibody DO142-10 light chain variable region @
Hs.274772 C15orf15 1616 21 text pic Chromosome 15 open reading frame 15 15q21
Hs.411480 AUP1 698 21 text pic Ancient ubiquitous protein 1 2p13
Hs.449070 RPL13A 6429 21 text pic Ribosomal protein L13a 19q13.3
Hs.821 BGN 863 21 text pic Biglycan Xq28
Hs.533282 NONO 2561 21 text pic Non-POU domain containing, octamer-binding Xq13.1
Hs.495985 TCIRG1 267 21 text pic T-cell, immune regulator 1, ATPase, H+ transporting, lysosomal V0 protein a isoform 3 11q13.4-q13.5
Hs.517969 APEH 687 21 text pic N-acylaminoacyl-peptide hydrolase 3p21.31
Hs.497599 WARS 1390 21 text pic Tryptophanyl-tRNA synthetase 14q32.31
Hs.369397 TGFBI 2077 21 text pic Transforming growth factor, beta-induced, 68kDa 5q31
Hs.279806 DDX5 2459 21 text pic DEAD (Asp-Glu-Ala-Asp) box polypeptide 5 17q21
Hs.524599 NAP1L1 1910 21 text pic Nucleosome assembly protein 1-like 1 12q21.2
Hs.270869 ZNF410 448 21 text pic Zinc finger protein 410 14q24.3
Hs.218362 FLJ34283 143 21 text pic Hypothetical protein FLJ34283 11p15.5
Hs.411501 KRT7 1393 21 text pic Keratin 7 12q12-q13
Hs.183706 ADD1 1003 21 text pic Adducin 1 (alpha) 4p16.3
Hs.517782 TTLL3 353 21 text pic Tubulin tyrosine ligase-like family, member 3 3p25.3
Hs.514474 KIAA0195 332 21 text pic KIAA0195 gene product 17q25.1
Hs.15744 SH2B 283 21 text pic SH2-B homolog 16p11.2
Hs.369646 MUC4 333 21 text pic Mucin 4, tracheobronchial 3q29
Hs.33538 RP1L1 31 21 text pic Retinitis pigmentosa 1-like 1 8p23
Hs.437043 KIAA0540 368 21 text pic KIAA0540 protein 3p21.31
Hs.433343 SRRM2 1562 21 text pic Serine/arginine repetitive matrix 2 16p13.3
Hs.518460 AP2M1 2222 22 text pic Adaptor-related protein complex 2, mu 1 subunit 3q28
Hs.512640 PRKCSH 1152 22 text pic Protein kinase C substrate 80K-H 19p13.2
Hs.514535 LGALS3BP 1709 22 text pic Lectin, galactoside-binding, soluble, 3 binding protein 17q25
Hs.414579 SCOTIN 1228 22 text pic Scotin 3p21.31
Hs.517438 ASCC2 409 22 text pic Activating signal cointegrator 1 complex subunit 2 22q12.1
Hs.515876 NRBP 645 22 text pic Nuclear receptor binding protein 2p23
Hs.118983 GSDMDC1 366 22 text pic Gasdermin domain containing 1 8q24.3
Hs.387804 PABPC1 3460 22 text pic Poly(A) binding protein, cytoplasmic 1 8q22.2-q23
Hs.511525 PRSS1 2047 22 text pic Protease, serine, 1 (trypsin 1) 7q32-qter
Hs.527861 OS-9 1215 22 text pic Amplified in osteosarcoma 12q13
Hs.460499 ATXN2L 509 22 text pic Ataxin 2-like 16p11
Hs.173716 ADAM33 84 22 text pic A disintegrin and metalloproteinase domain 33 20p13
Hs.531664 LOC23117 867 22 text pic KIAA0220-like protein 16p12.2
Hs.380021 MLL5 447 22 text pic Myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila) 7q22.1
Hs.279881 MAN1B1 335 22 text pic Mannosidase, alpha, class 1B, member 1 9q34
Hs.137510 NCOR2 642 22 text pic Nuclear receptor co-repressor 2 12q24
Hs.496487 ATF4 2465 23 text pic Activating transcription factor 4 (tax-responsive enhancer element B67) 22q13.1
Hs.433845 KRT5 1637 23 text pic Keratin 5 (epidermolysis bullosa simplex, Dowling-Meara/Kobner/Weber-Cockayne types) 12q12-q13
Hs.129959 IL17RC 260 23 text pic Interleukin 17 receptor C 3p25.3
Hs.62886 SPARCL1 1413 23 text pic SPARC-like 1 (mast9, hevin) 4q22.1
Hs.522257 HNRPK 1732 23 text pic Heterogeneous nuclear ribonucleoprotein K 9q21.32-q21.33
Hs.533782 KRT8 4148 23 text pic Keratin 8 12q13
Hs.437388 PIGT 723 23 text pic Phosphatidylinositol glycan, class T 20q12-q13.12
Hs.446747 CLN3 483 23 text pic Ceroid-lipofuscinosis, neuronal 3, juvenile (Batten, Spielmeyer-Vogt disease) 16p12.1
Hs.172550 PTBP1 1606 23 text pic Polypyrimidine tract binding protein 1 19p13.3
Hs.525647 IGHM 1537 23 text pic Immunoglobulin heavy constant mu 14q32.33
Hs.437351 CIRBP 1246 23 text pic Cold inducible RNA binding protein 19p13.3
Hs.258111 RNF123 241 23 text pic Ring finger protein 123 3p24.3
Hs.515371 CAPNS1 1266 24 text pic Calpain, small subunit 1 19q13.12
Hs.89603 MUC1 356 24 text pic Mucin 1, transmembrane 1q21
Hs.433615 TUBB2 2391 24 text pic Tubulin, beta, 2 @
Hs.502876 RHOB 1150 24 text pic Ras homolog gene family, member B 2p24
Hs.534293 SERPINA3 1631 24 text pic Serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 3 14q32.1
Hs.336916 DAXX 444 24 text pic Death-associated protein 6 6p21.3
Hs.436204 ZNF289 702 24 text pic Zinc finger protein 289, ID1 regulated 11p11.2-p11.12
Hs.73965 SFRS2 1289 24 text pic Splicing factor, arginine/serine-rich 2 17q25.1
Hs.500721 MMS19L 527 24 text pic MMS19-like (MET18 homolog, S. cerevisiae) 10q24-q25
Hs.533273 UBE1 1582 24 text pic Ubiquitin-activating enzyme E1 (A1S9T and BN75 temperature sensitivity complementing) Xp11.23
Hs.530084 PILRB 450 24 text pic Paired immunoglobin-like type 2 receptor beta 7q22.1
Hs.443134 GBA2 450 24 text pic Glucosidase, beta (bile acid) 2 9p13.3
Hs.513984 FLII 851 24 text pic Flightless I homolog (Drosophila) 17p11.2
Hs.513242 RHOT2 392 24 text pic Ras homolog gene family, member T2 16p13.3
Hs.282901 RNPC2 838 24 text pic RNA-binding region (RNP1, RRM) containing 2 20q11.22
Hs.429581 RTN4 1968 24 text pic Reticulon 4 2p16.3
Hs.119598 RPL3 10856 24 text pic Ribosomal protein L3 22q13
Hs.448583 DKFZP434B061 24 24 text pic DKFZP434B061 protein 13p13
Hs.390817 MYO15B 113 24 text pic Similar to KIAA1783 protein 17q25.1
Hs.280978 FLJ10496 287 25 text pic Hypothetical protein FLJ10496 3p21.31
Hs.501293 BSG 2801 25 text pic Basigin (OK blood group) 19p13.3
Hs.436093 BAT2 836 25 text pic HLA-B associated transcript 2 6p21.3
Hs.198161 PLA2G4B 232 25 text pic Phospholipase A2, group IVB (cytosolic) 15q11.2-q21.3
Hs.474751 MYH9 1680 25 text pic Myosin, heavy polypeptide 9, non-muscle 22q13.1
Hs.186350 RPL4 6628 26 text pic Ribosomal protein L4 15q22
Hs.79322 QARS 1374 26 text pic Glutaminyl-tRNA synthetase 3p21.3-p21.1
Hs.525205 NDRG2 871 26 text pic NDRG family member 2 14q11.2
Hs.440900 BAT3 882 26 text pic HLA-B associated transcript 3 6p21.3
Hs.178551 RPL8 4042 27 text pic Ribosomal protein L8 8q24.3
Hs.515524 NUCB1 1002 27 text pic Nucleobindin 1 19q13.2-q13.4
Hs.513490 ALDOA 5686 27 text pic Aldolase A, fructose-bisphosphate 16q22-q24
Hs.499839 RPL7A 5372 27 text pic Ribosomal protein L7a 9q34
Hs.504062 PHLDB1 477 27 text pic Pleckstrin homology-like domain, family B, member 1 11q23.3
Hs.78601 UROD 768 28 text pic Uroporphyrinogen decarboxylase 1p34
Hs.529892 SQSTM1 3356 28 text pic Sequestosome 1 5q35
Hs.421907 GLTSCR2 1919 28 text pic Glioma tumor suppressor candidate region gene 2 19q13.3
Hs.439777 CPT1B 490 28 text pic Carnitine palmitoyltransferase 1B (muscle) 22q13.33
Hs.166011 CTNND1 976 28 text pic Catenin (cadherin-associated protein), delta 1 11q11
Hs.533566 H19 1800 29 text pic H19, imprinted maternally expressed untranslated mRNA 11p15.5
Hs.8022 TU3A 1034 29 text pic TU3A protein 3p21.1
Hs.514220 GRN 2405 30 text pic Granulin 17q21.32
Hs.502769 SLC3A2 1464 30 text pic Solute carrier family 3 (activators of dibasic and neutral amino acid transport), member 2 11q13
Hs.446852 EIF3S6IP 3419 30 text pic Eukaryotic translation initiation factor 3, subunit 6 interacting protein 22q
Hs.533977 TXNIP 2345 30 text pic Thioredoxin interacting protein 1q21.1
Hs.515070 EEF2 1726 30 text pic Eukaryotic translation elongation factor 2 19pter-q12
Hs.155218 HNRPUL1 1101 30 text pic Heterogeneous nuclear ribonucleoprotein U-like 1 19q13.2
Hs.502328 CD44 1729 30 text pic CD44 antigen (homing function and Indian blood group system) 11p13
Hs.75069 SHMT2 1397 31 text pic Serine hydroxymethyltransferase 2 (mitochondrial) 12q12-q14
Hs.53985 GP2 348 31 text pic Glycoprotein 2 (zymogen granule membrane) 9q21.11-q21.2
Hs.270291 ACTN4 1323 31 text pic Actinin, alpha 4 19q13
Hs.443625 COL3A1 2539 31 text pic Collagen, type III, alpha 1 (Ehlers-Danlos syndrome type IV, autosomal dominant) 2q31
Hs.517949 MAP4 1089 31 text pic Microtubule-associated protein 4 3p21
Hs.442798 RNF10 821 32 text pic Ring finger protein 10 12q24.31
Hs.508848 HNRPC 2900 32 text pic Heterogeneous nuclear ribonucleoprotein C (C1/C2) 14q11.2
Hs.464336 P4HB 2643 33 text pic Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), beta polypeptide (protein disulfide isomerase; thyroid hormone binding protein p55) 17q25
Hs.252418 ELN 293 33 text pic Elastin (supravalvular aortic stenosis, Williams-Beuren syndrome) 7q11.23
Hs.367767 PRSS2 2213 34 text pic Protease, serine, 2 (trypsin 2) 7q34
Hs.35052 TEGT 3428 34 text pic Testis enhanced gene transcript (BAX inhibitor 1) 12q12-q13
Hs.525600 HSPCA 5462 34 text pic Heat shock 90kDa protein 1, alpha 14q32.33
Hs.369849 MDM2 136 35 text pic Mdm2, transformed 3T3 cell double minute 2, p53 binding protein (mouse) 12q14.3-q15
Hs.523004 PSAP 4444 35 text pic Prosaposin (variant Gaucher disease and variant metachromatic leukodystrophy) 10q21-q22
Hs.355867 MARS 1081 35 text pic Methionine-tRNA synthetase 12q13.2
Hs.498569 RPS2 10888 36 text pic Ribosomal protein S2 16p13.3
Hs.418167 ALB 8935 36 text pic Albumin 4q11-q13
Hs.437178 ACADVL 1221 36 text pic Acyl-Coenzyme A dehydrogenase, very long chain 17p13-p11
Hs.172928 COL1A1 3360 36 text pic Collagen, type I, alpha 1 17q21.3-q22.1
Hs.436657 CLU 4494 37 text pic Clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) 8p21-p12
Hs.449621 IGKC 2569 37 text pic Immunoglobulin kappa constant 2p12
Hs.195464 FLNA 2042 37 text pic Filamin A, alpha (actin binding protein 280) Xq28
Hs.203717 FN1 6041 37 text pic Fibronectin 1 2q34
Hs.180414 HSPA8 6287 38 text pic Heat shock 70kDa protein 8 11q24.1
Hs.517145 ENO1 9748 39 text pic Enolase 1, (alpha) 1p36.3-p36.2
Hs.79110 NCL 1487 39 text pic Nucleolin 2q12-qter
Hs.513711 HP 1064 41 text pic Haptoglobin 16q22.1
Hs.198281 PKM2 7413 44 text pic Pyruvate kinase, muscle 15q22
Hs.471851 HDLBP 3043 45 text pic High density lipoprotein binding protein (vigilin) 2q37
Hs.436568 CD74 7050 47 text pic CD74 antigen (invariant polypeptide of major histocompatibility complex, class II antigen-associated) 5q32
Hs.509736 HSPCB 6289 47 text pic Heat shock 90kDa protein 1, beta 6p12
Hs.517033 TGM2 1555 49 text pic Transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase) 20q12
Hs.533059 OK/SW-cl.56 7063 56 text pic Beta 5-tubulin 6p21.33
Hs.514227 GFAP 1764 59 text pic Glial fibrillary acidic protein 17q21
Hs.514581 ACTG1 15961 60 text pic Actin, gamma 1 17q25
Hs.439552 EEF1A1 30924 61 text pic Eukaryotic translation elongation factor 1 alpha 1 6q14.1
Hs.501262 MBP 2326 64 text pic Myelin basic protein 18q23
Hs.134602 TTN 1281 64 text pic Titin 2q31
Hs.524390 K-ALPHA-1 10731 84 text pic Tubulin, alpha, ubiquitous 12q13.12


Last updated on 2003-11-01 by Fu, Gloria Chiung-Ling