Potential Regulatory Sequences in Co-Regulated Genes of Normal and Alzheimer's Hemisections
| Gene pair[i] | Homology blocksb | |||
| RAB2 and ABCA4(+) | ||||
| RAB2 | cct[ccaaatattccaga]c(17/17) | [cttgtttctgaa]dtcatttagtaa (23/23) | tttgcaa[gttttaaaat]eact (20/20) | |
| (8 exons) | 1188bp 5′ upstrm ATG | 3060bp 3′ dstrm exon 1 (intron 1) | 7268bp 3′ dstrm exon 1 (intron 1) | |
| Fly RAB2 | aatattgcag (10/11) | |||
| (6 exons)/90% | 12892bp 5′ upstrm ATG | |||
| ABCA4 | cct[ccaaatattccaga]c(17/17) | [cttgtttctgaa]dtaattcagtaa (21/23) | tttgcaa[gttttaaaac]eact (19/20) | |
| (50 exons) | 6865bp 5′ upstrm ATG | 17313bp 5′ upstrm ATG | 12300bp 5′ upstrm ATG | |
| Fly ABCA4 | tttgcaagcttt (11/12) | |||
| (8 exons)/30% | 9642bp 5′ upstrm ATG | |||
| BAP1 and ABCA4 (+) | ||||
| BAP1 (17 exons) | ggcagtgaggg[tttgactgg]f (20/20) (1415bp 5′ upstrm ATG [4087bp 5′ upstrm ATG of HSPC226]) | |||
| ABCA4 (50 exons) | ggcagtcaggg[tttgactgg]f (19/20) (353bp 5′ upstrm ATG [255bp 3′ dstrm start promoter, BCA4]) | |||
| Fly ABCA4 (8 exons)/30% | gcagtcaagttttga (13/15) (7664bp 3′ dstrm stop codon) | |||
| BAP1 and RNPS1 (+) | ||||
| BAP1 (17 exons) | c[tc(catccctgcc]gccaa)h (17/17) (257bp 3′ dstrm exon 11) (intron 11) | |||
| RNPS1 (7 exons) | c[tc(catccctgcc]gccaa)h (17/17) (9153bp 5′ upstrm ATG[in intron 21, ABCA3]) | |||
| MSX2 and BAP1(−) | ||||
| MSX2 (14 exons) | actatgg[g(ccaggtgc)ic]jttgc (21/21) (6150bp 3′ dstrm stop codon [in intron 4, ZNF151]) | |||
| BAP1 (17 exons) | actatgg[g(ccaggtgc)ic]j atgc (20/21) (3574bp 3′ dstrm stop codon [in intron 14, FLJ13704fis]) | |||
| RNPS1 and U5-100K (−) | ||||
| RNPS1 | tggag[gcaggga(cagaggg]katgct)lgt | ggaaggatggtgtctcctg | gac[agcagggagcca]mgggg | |
| (7 exons) | (26/26) 13335bp 5′ upstrm ATG | (19/19) 6684bp 5′ upstrm | (19/19) 8844bp 3′ dstrm stop | |
| [in intron 27, ABCA3] | ATG | codon [in intron 9, E4F1] | ||
| Fly RNPS1 | gaggcaggaatagag (13/15) | |||
| (2 exons)/33% | 10266bp 3′ dstrm stop codon | |||
| [814bp 3′ dstrm stop codon, RPA1] | ||||
| U5-100K | tggag[acagaga(cagaggg]katggt)lgt | ggaaggatggtatctcctg | gac[atcagggagcca]mgggg | |
| (17 exons) | (23/26) 2626bp upstrm ATG | (18/19) | (18/19) 1030bp 3′ dstrm stop | |
| 675bp 5′ upstrm ATG | codon [in intron 1 CAL Bet3] | |||
| aggatcatatctcc | cagggagtcagg (11/12) | |||
| Fly U5-100K (8 exons) 41% | (12/14) 17652bp 5′ upstrm ATG | 656bp 3′ dstrm stop codon | ||
| LRP6 and U5-100K (+) | ||||
| LRP6 (26 exons) | gggt[(ggaagggaataa]nt)ogga (20/20) (4972bp 3′ dstrm stop codon) | |||
| U5-100K (17 exons) | gggt[(ggaagggaataa]nt)ogga (20/20) (10261bp 3′ dstrm stop codon [in intron 1, CAL Bet3]) | |||
| Fly U5-100K (8 exons)/41% | aagggtataatgg (12/13) (12661bp 5′ upstrm ATG) | |||
| TAF2F and LRP6 (−) | ||||
| TAF2F (1 exon) | ct[atatgtt(cacttc]p qtttaaatg)rtgc (26/26) (9542bp 5′ upstrm ATG) | |||
| LRP6 (26 exons) | ct[atatgtt[tacata]p qtttaaatg)rtgc (23/26) (5612bp 3′ dstrm stop codon) | |||
| Fly LRP6 (6 exons)/32% | t[atatggctaaata]p qtttaaa (17/20) (5236bp 5′ upstrm ATG[836bp 3′ dstrm stop codon H3-like protein]) | |||
| TBXAS1 and ECHS1 (+) | ||||
| TBXAS1 | acac[cccagctgcc]s(19/19) | cac[cccagctgcc]scagcac(19/19) | ||
| (13 exons) | 1318bp 3′ dstrm stop codon | 1337bp 3′ dstrm stop codon | ||
| ECHS1 | acac[ccctgctgcc]scagca (18/19) | cac[ccctgctgcc]scagcac (18/19) | ||
| (7 exons) | 5989bp 3′ dstrm stop codon | 6051bp 3′ dstrm stop codon | ||
| [in intron 16, GCP2] | [in intron 16, GCP2] | |||
| Fly ECHS1 | cac[gcctgctgcc]scag (15/16) | cac[gcctgctgcc]scag (15/16) | ||
| (3 exons)/77.6% | 1609bp 3′ dstrm stop codon | 1609bp 3′ dstrm stop codon | ||
[i] (+) Correlated pair; (−) anti-correlated pair; % aa (amino acid) homology to human gene shown. bNucleotide matches shown in parentheses, mismatches in bold. Potential binding sites (core in capitals): cOCT-1 ccaaatATTCcagan,dHFH8 nctTGTTtctgaa, eTFIID gtTTTAAAAt,fAP1 ttTGACtggnn, gIK2 tccaTCCCtgcc (anti-sense strand), hSp1 catcccTGCCccaa (anti-sense strand),iUSF ccAGGTGc (anti-sense strand), jMYOD gccaGGTGcc (anti-sense strand), kGKLF acagagacagAGGG, lIK2 cagaGGGAtggt, mIK2 atcaGGGAgcca, nIK2 ggaaGGGAataa,oIK1 ggaaGG GAataat, pHFH3 ataTGTTtacata,qHFH8 ataTGTTtacata, rXFD1 tacataTTTAaatg (anti-sense strand), sAP4 ccctGCTGcc (anti-sense strand).