Potential Regulatory Sequences in Coregulated Genes
| Gene pair | Homology Blocks | ||
| SIAT9 | t[ttgatatgt] cacttgattgggaaaf(26/26) | ccttt[gccaatacaatgca]gcaaatgctt (29/29) | |
| (6 exons) | (689 bp 3′ downstream exon 2) | (4358 bp 3′ downstream stop codon) | |
| HIVEP2+ | t[ttgatatat] caattgattaggaaac(23/26) | cctct[gccaatcacatgca] gcaaatgctt(25/29) | |
| (6 exons) | (8331 bp 5′ upstream start codon) | (7558 bp 3′ downstream stop codon) | |
| HIVEP2 | ttttta{(t[ttcatctga) c] a} a(19/19) | gataattttacttggtattt[ctttttcttga] (31/31) | |
| (6 exons) | (16087 bp 5′ upstream start codon) | (823 bp 3′ downstream exon 3) | |
| SEPP1+ | tttttc({t[ttcatctga) c] a} a(18/19) | gattatttcattttgttttt[ctttttcttga] (26/31) | |
| (5 exons) | (16520 bp 5′ upstream start codon) | (3784 bp 3′ downstream stop codon) | |
| HIVEP2 | [agaaaatctcttccttttaa] atttct(26/26) | [atgaa] agctctcagtatattggc(23/23) | [tttttttttttt] gcttgtaaaa(22/22) |
| (6 exons) | (7281 bp 5′ upstream start codon) | (802 bp 5′ upstream start codon) | (17498 bp 3′ downstream stop codon) |
| NEFL mm+ | [agaaaatcttttcctattaa] aattct(23/26) | [atgaa] ggctctcagtgtattggc(21/23) | [tttttttttttt] tcttctaaaa(20/22) |
| (4 exons) | (19520 bp 5′ upstream start codon) | (1611 bp 3′ downstream stop codon) | (9527 bp 5′ upstream start codon) |
| HIVEP2 | aa[aaagaatgaatctgttttaa] (22/22) | ||
| (6 exons) | (17972 bp 3′ downstream stop codon) | ||
| SCYD1+ | aa[aaaaaacgaatctgttttaa] (20/22) | ||
| (3 exons) | (1816 bp 3′ downstream exon 1) | ||
| SEPP1 | gaatctgcaaa[gcctttcct] (20/20) | [cttctgtttactctca] ctct(20/20) | |
| (5 exons) | (15110 bp 5′ upstream start codon) | (14403 bp 5′ upstream start codon) | |
| SCYD1+ | gaaactgtaaa[gcctttcct] (18/20) | [cttcttgttactctca] ctct(18/20) | |
| (3 exons) | (9285 bp 3′ downstream stop codon) | (19725 bp 3′ downstream stop codon) | |
| SCYD1 | atgcata[aatatttacatata] t(22/22) | aaattttcttctgcttagct (20/20) | |
| (3 exons) | (5003 bp 3′ downstream 3′ exon 1) | (5235 bp 3′ downstream exon 1) | |
| NEFL+ | atgcata[tatattcacatata] t(20/22) | aaatttttttctgcttagct (19/20) | |
| (4 exons) | (13633 bp 3′ downstream stop codon) | (6321 bp 5′ upstream start codon) | |
| CUGBP2 | at[ggaaaatgcaaagg] agaaaacag(25/25) | gcccccct[aggagaggcaggtg] ctgc(26/26) | |
| (13 exons) | (65490 bp 3′ downstream exon 1) | (89115 bp 3′ downstream exon 1) | |
| MBP+ | at[ggaaaaagcaaagg] agaaatcag(23/25) | gcccacca[aggagaggcagggg] ctgc(23/26) | |
| (7 exons) | (33 bp 3′ downstream exon 1) | (17744 bp 5′ upstream) | |
| MBP | atgcaaa[tacataaaat] aa(19/19) | tcagtaacatttat[tttaacaactt] (25/25) | |
| (7 exons) | (10021 bp 5′ upstream start codon) | (6019 bp 3′ downstream stop codon) | |
| CBLN1+ | atgtaaa[tacataaaat] aa(18/19) | tcattaaaatttat[tttaaaaactt] (22/25) | |
| (3 exons) | (12012 bp 5′ upstream start codon) | (9085 bp 5′ upstream start codon) | |
| MBP | catgtttgcagtggagt (17/17) | tttcttt[cttgctttctgg] (19/19) | |
| (7 exons) | (1122 bp 5′ upstream exon 6) | (3434 bp 3′ downstream end of exon 6) | |
| NEFL− | catgtttgcagtggagt (17/17) | tttcttt[ctagctttctgg] (18/19) | |
| (4 exons) | (1045 bp 3′ downstream codon) | (623 bp 5′ upstream start codon) | |
| NEFL | t[gttgt{tgttgtt] u gtttt} g(19/19) | gatac[tttcaaagcatctgg] (20/20) | |
| (4 exons) | (17091 bp 5′ upstream start codon) | (5611 bp 5′ upstream start codon) | |
| CBLN1− | t[gttgt{tgttgtt] u gttt} g(19/19) | gattc[tttcaaagcatctgg] (19/20) | |
| (3 exons) | (461 bp 3′ downstream stop codon) | (18945 bp 5′ upstream start codon) | |
| NEFL | a{(a[aaaaaaaaaaaa] ) a} aaagcacttca(26/26) | aa[t(aaataaataaat) aa ] bb,cc gtcc(19/19) | |
| (4 exons) | (9536 bp 5′ upstream start codon) | (4175 bp 3′ downstream stop codon) | |
| PNUTL2 nn | a{(a[aaaaaaaaaaaa] ) a} agagagcttca(23/26) | aa[t(aaataaataaat) aa ] bb,cc ttcc(18/19) | |
| (13 exons) | (15553 bp 5′ upstream start codon) | (2140 bp 3′ downstream exon 5) | |
| NEFL | atctttgttagtt[tttttttttttt] t(26/26) | gaggttttggtagcattct (1919) | |
| (4 exons) | (9120 bp 5′ upstream start codon) | (412 bp 3′ downstream exon 3) | |
| USP9X− | atctttgttagga[tttttttttttt] t(24/26) | gaggatttggtagcattct (18/19) | |
| (44 exons) | (963 bp 3′ downstream exon 22) | (1737 bp 5′ upstream start codon) | |
| NEFL | aaacaaaa[aaaagaaaaaaat] dd tatttt(27/27) | ||
| (4 exons) | (745 bp 3′ downstream exon 1) | ||
| INA+ | aaagaaag[aaaagaaaaaaat] dd tagttt(24/27) | ||
| (3 exons) | (12338 bp 5′ upstream start codon) | ||
| CBLN1 | tagactacactccaaaattt[ggacattc] ee(28/28) | ttttggtga[aagttaagatattt] ff c(25/25) | g[gc(c{ctcatctgca} gg g) hh g] ii c(17/17) |
| (3 exons) | (10346 bp 5′ upstream start codon) | (4822 bp 5′ upstream start codon) | (6168 bp 3′ downstream stop codon) |
| USP9X+ | tagactacacttcaaaagta[ggatattc] ee(24/28) | tttttggtgt[aatttaagaaattt] ff c(22/25) | g[gc(c{ctcatctgca} gg g) hh g] ii c(17/17) |
| (44 exons) | (3010 bp 3′ downstream exon 34) | (4799 bp 3′ downstream stop codon) | (18415 bp 3′ downstream stop codon) |
| [ctttgttttt] jj gttttttttgg(22/22) | |||
| (8167 bp 3′ downstream stop codon) | |||
| [ctttgttttt] jj gctttttattgg(20/22) | |||
| (13160 bp 3′ downstream stop codon) | |||
| USP9X | ttttttg(tttttt[t{ttttt) kk } ll(23/23) | ||
| (44 exons) | (1572 bp 3′ downstream exon 11) | ||
| PNUTL2+ | tttgttt(tttttt[t{ttttt) cctg] kk } ll(21/23) | ||
| (13 exons) | (625 bp 5′ upstream start codon) | ||
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↵(+) correlated pair, (−) anti-correlated pair.
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Nucleotide matches shown in parentheses, mismatches in bold. Potential binding sites (core in capitals).
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↵LMO2COM ttGATAtat.
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↵OCT1 gccaatcacATGCa.
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↵ GATA2 & GATA3 tcaGATGaaa(anti-sense strand).
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↵MYOD ttCATCgac.
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↵LMO2COMtgtCAGAtgaaa (anti-sense strand).
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↵NFAT ntcaaGAAAaag (anti-sense strand).
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↵GFI1 nnnnagaaAATCttttcctattaa.
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↵TCF11 TTCAtnnnnnnnn (anti-sense strand).
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↵HFH2 tttTTTTttttt.
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↵GFI1 aaagaatgAATCtgttttaannnn.
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↵NFAT nnnagGAAAggc (anti-sense strand).
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↵FREAC2 tgagagTAAAcagaag (anti-sense strand).
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↵ICT1 tatattcacATATa.
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↵GKLF ggaaaaagcaAAGG.
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↵GKLF aggagaggcaGGGG.
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↵TATA taCATAAAAt.
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↵SRY tttaACAActtn.
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↵TH1E47 cttgctttCTGGnnnn.uSRYaacaACAAcaac anti-sense strand).
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↵HFH2 tgtTGTTgtttt.
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↵BARBIE tttcAAAGcatctgg.
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↵HFH2 tttTTTTttttt (anti-sense strand).
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↵HFH3 tttTTTTtttttt (anti-sense strand).
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↵HNF3B tttttTTTTtttttt (anti-sense strand).
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aaHFH2 attTATTtattt (anti-sense strand).
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bb,ccHFH8 & HFH3 attTATTtattta (anti-sense strand).
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ddHFH-3 attTTTTtctttt (anti-sense strand).
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eeGATA gGATATtcnnn.
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ffCEBPB aatttaaGAAAttt.
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ggMYOD ctCATCtgca.
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hhLMO2COM ctgCAGAtgagg (anti-sense strand).
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iiE47 cctGCAGatgagggc (anti-sense strand).
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jjSRY aaaaACAAagnn (anti-sense strand).
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kkNFAT nncagGAAAaaa (anti-sense strand).
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llCETS1P54 ncAGGAaaaa (anti-sense strand).
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mmhuman NEFL = mouse Nfl.
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nnhuman PNUTL2 = mouse Sept4.
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↵No known transcription factor binding site.
