Table 2.
Potential Regulatory Sequences in Coregulated Genes
| Gene paira | Homology Blocks | ||
|---|---|---|---|
| SIAT9 | t[ttgatatgt]ccacttgattgggaaaf (26/26) | ccttt[gccaatacaatgca]d gcaaatgctt (29/29) | |
| (6 exons) | (689 bp 3′ downstream exon 2) | (4358 bp 3′ downstream stop codon) | |
| HIVEP2+ | t[ttgatatat]ccaattgattaggaaac (23/26) | cctct[gccaatcacatgca]dgcaaatgctt (25/29) | |
| (6 exons) | (8331 bp 5′ upstream start codon) | (7558 bp 3′ downstream stop codon) | |
| HIVEP2 | ttttta{(t[ttcatctga)ec]fa}ga (19/19) | gataattttacttggtattt[ctttttcttga]h (31/31) | |
| (6 exons) | (16087 bp 5′ upstream start codon) | (823 bp 3′ downstream exon 3) | |
| SEPP1+ | tttttc({t[ttcatctga)ec]fa}ga (18/19) | gattatttcattttgttttt[ctttttcttga]h (26/31) | |
| (5 exons) | (16520 bp 5′ upstream start codon) | (3784 bp 3′ downstream stop codon) | |
| HIVEP2 | [agaaaatctcttccttttaa]latttct (26/26) | [atgaa]lagctctcagtatattggc (23/23) | [tttttttttttt]kgcttgtaaaa (22/22) |
| (6 exons) | (7281 bp 5′ upstream start codon) | (802 bp 5′ upstream start codon) | (17498 bp 3′ downstream stop codon) |
| NEFLmm+ | [agaaaatcttttcctattaa]iaattct (23/26) | [atgaa]jggctctcagtgtattggc (21/23) | [tttttttttttt]ktcttctaaaa (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]l (22/22) | ||
| (6 exons) | (17972 bp 3′ downstream stop codon) | ||
| SCYD1+ | aa[aaaaaacgaatctgttttaa]l (20/22) | ||
| (3 exons) | (1816 bp 3′ downstream exon 1) | ||
| SEPP1 | gaatctgcaaa[gcctttcct]m (20/20) | [cttctgtttactctca]nctct (20/20) | |
| (5 exons) | (15110 bp 5′ upstream start codon) | (14403 bp 5′ upstream start codon) | |
| SCYD1+ | gaaactgtaaa[gcctttcct]m (18/20) | [cttcttgttactctca]nctct (18/20) | |
| (3 exons) | (9285 bp 3′ downstream stop codon) | (19725 bp 3′ downstream stop codon) | |
| SCYD1 | atgcata[aatatttacatata]ot (22/22) | aaattttcttctgcttagct* (20/20) | |
| (3 exons) | (5003 bp 3′ downstream 3′ exon 1) | (5235 bp 3′ downstream exon 1) | |
| NEFL+ | atgcata[tatattcacatata]ot (20/22) | aaatttttttctgcttagct* (19/20) | |
| (4 exons) | (13633 bp 3′ downstream stop codon) | (6321 bp 5′ upstream start codon) | |
| CUGBP2 | at[ggaaaatgcaaagg]pagaaaacag (25/25) | gcccccct[aggagaggcaggtg]qctgc (26/26) | |
| (13 exons) | (65490 bp 3′ downstream exon 1) | (89115 bp 3′ downstream exon 1) | |
| MBP+ | at[ggaaaaagcaaagg]gagaaatcag (23/25) | gcccacca[aggagaggcagggg]qctgc (23/26) | |
| (7 exons) | (33 bp 3′ downstream exon 1) | (17744 bp 5′ upstream) | |
| MBP | atgcaaa[tacataaaat]raa (19/19) | tcagtaacatttat[tttaacaactt]s (25/25) | |
| (7 exons) | (10021 bp 5′ upstream start codon) | (6019 bp 3′ downstream stop codon) | |
| CBLN1+ | atgtaaa[tacataaaat]raa (18/19) | tcattaaaatttat[tttaaaaactt]s (22/25) | |
| (3 exons) | (12012 bp 5′ upstream start codon) | (9085 bp 5′ upstream start codon) | |
| MBP | catgtttgcagtggagt* (17/17) | tttcttt[cttgctttctgg]t (19/19) | |
| (7 exons) | (1122 bp 5′ upstream exon 6) | (3434 bp 3′ downstream end of exon 6) | |
| NEFL− | catgtttgcagtggagt* (17/17) | tttcttt[ctagctttctgg]t (18/19) | |
| (4 exons) | (1045 bp 3′ downstream codon) | (623 bp 5′ upstream start codon) | |
| NEFL | t[gttgt{tgttgtt]ugtttt}vg (19/19) | gatac[tttcaaagcatctgg]w (20/20) | |
| (4 exons) | (17091 bp 5′ upstream start codon) | (5611 bp 5′ upstream start codon) | |
| CBLN1− | t[gttgt{tgttgtt]ugttt}vg (19/19) | gattc[tttcaaagcatctgg]w (19/20) | |
| (3 exons) | (461 bp 3′ downstream stop codon) | (18945 bp 5′ upstream start codon) | |
| NEFL | a{(a[aaaaaaaaaaaa]x)ya}zaaagcacttca (26/26) | aa[t(aaataaataaat)aa]bb,ccgtcc (19/19) | |
| (4 exons) | (9536 bp 5′ upstream start codon) | (4175 bp 3′ downstream stop codon) | |
| PNUTL2nn | a{(a[aaaaaaaaaaaa]x)ya}zagagagcttca (23/26) | aa[t(aaataaataaat)aa]bb,ccttcc (18/19) | |
| (13 exons) | (15553 bp 5′ upstream start codon) | (2140 bp 3′ downstream exon 5) | |
| NEFL | atctttgttagtt[tttttttttttt]kt (26/26) | gaggttttggtagcattct* (1919) | |
| (4 exons) | (9120 bp 5′ upstream start codon) | (412 bp 3′ downstream exon 3) | |
| USP9X− | atctttgttagga[tttttttttttt]kt (24/26) | gaggatttggtagcattct* (18/19) | |
| (44 exons) | (963 bp 3′ downstream exon 22) | (1737 bp 5′ upstream start codon) | |
| NEFL | aaacaaaa[aaaagaaaaaaat]ddtatttt (27/27) | ||
| (4 exons) | (745 bp 3′ downstream exon 1) | ||
| INA+ | aaagaaag[aaaagaaaaaaat]ddtagttt (24/27) | ||
| (3 exons) | (12338 bp 5′ upstream start codon) | ||
| CBLN1 | tagactacactccaaaattt[ggacattc]ee (28/28) | ttttggtga[aagttaagatattt]ffc (25/25) | g[gc(c{ctcatctgca}ggg)hhg]iic (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]ffc (22/25) | g[gc(c{ctcatctgca}ggg)hhg]iic (17/17) |
| (44 exons) | (3010 bp 3′ downstream exon 34) | (4799 bp 3′ downstream stop codon) | (18415 bp 3′ downstream stop codon) |
| [ctttgttttt]jjgttttttttgg (22/22) | |||
| (8167 bp 3′ downstream stop codon) | |||
| [ctttgttttt]jjgctttttattgg (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)kcctg]kk}ll (21/23) | ||
| (13 exons) | (625 bp 5′ upstream start codon) | ||
(+) correlated pair, (−) anti-correlated pair.
Nucleotide matches shown in parentheses, mismatches in bold. Potential binding sites (core in capitals).
LMO2COM ttGATAtat.
OCT1 gccaatcacATGCa.
GATA2 & GATA3 tcaGATGaaa (anti-sense strand).
MYOD ttCATCgac.
LMO2COMtgtCAGAtgaaa (anti-sense strand).
NFAT ntcaaGAAAaag (anti-sense strand).
GFI1 nnnnagaaAATCttttcctattaa.
TCF11 TTCAtnnnnnnnn (anti-sense strand).
HFH2 tttTTTTttttt.
GFI1 aaagaatgAATCtgttttaannnn.
NFAT nnnagGAAAggc (anti-sense strand).
FREAC2 tgagagTAAAcagaag (anti-sense strand).
ICT1 tatattcacATATa.
GKLF ggaaaaagcaAAGG.
GKLF aggagaggcaGGGG.
TATA taCATAAAAt.
SRY tttaACAActtn.
TH1E47 cttgctttCTGGnnnn.uSRY aacaACAAcaac anti-sense strand).
HFH2 tgtTGTTgtttt.
BARBIE tttcAAAGcatctgg.
HFH2 tttTTTTttttt (anti-sense strand).
HFH3 tttTTTTtttttt (anti-sense strand).
HNF3B tttttTTTTtttttt (anti-sense strand).
aaHFH2 attTATTtattt (anti-sense strand).
bb,ccHFH8 & HFH3 attTATTtattta (anti-sense strand).
ddHFH-3 attTTTTtctttt (anti-sense strand).
eeGATA gGATATtcnnn.
ffCEBPB aatttaaGAAAttt.
ggMYOD ctCATCtgca.
hhLMO2COM ctgCAGAtgagg (anti-sense strand).
iiE47 cctGCAGatgagggc (anti-sense strand).
jjSRY aaaaACAAagnn (anti-sense strand).
kkNFAT nncagGAAAaaa (anti-sense strand).
llCETS1P54 ncAGGAaaaa (anti-sense strand).
mmhuman NEFL = mouse Nfl.
nnhuman PNUTL2 = mouse Sept4.
No known transcription factor binding site.