CCCTC-binding factor gene transcriptions

# Consensus sequences
"Experiments using chromatin immunoprecipitation exonuclease (ChIP-exo) uncovered a broad CTCF-binding motif that contains a 1215 bp consensus sequence, 5-NCA-NNA-G(G/A)N-GGC-(G/A)(C/G)(T/C)-3 (Nakahashi et al., 2013, Rhee and Pugh, 2011) ."

# Hashimoto samplings
Copying the consensus of the CTCF: 5'-CACCAGG-3' and putting the sequence in "F" finds no locations between ZSCAN22 and A1BG and CTCF: 5'-CACCAGGAGG-3' finds no locations between ZNF497 and A1BG as can be found by the computer programs.
For the Basic programs SuccessablesCFbox.bas written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- negative strand, negative direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
- negative strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
- positive strand, negative direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
- positive strand, positive direction, looking for 5'-NCA-NNA-G(A/G)N-GGC-(A/G)(C/G)(C/T)-3', 0.
- complement, negative strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
- complement, negative strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
- complement, positive strand, negative direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
- complement, positive strand, positive direction, looking for 5'-NGT-NNT-C(C/T)N-CCG-(C/T)(C/G)(A/G)-3', 0.
- inverse complement, negative strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
- inverse complement, negative strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
- inverse complement, positive strand, negative direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
- inverse complement, positive strand, positive direction, looking for 5'-(A/G)(C/G)(C/T)-GCC-N(C/T)C-TNN-TGN-3', 0.
- inverse, negative strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
- inverse, negative strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
- inverse, positive strand, negative direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.
- inverse, positive strand, positive direction, looking for 5'-(C/T)(C/G)(A/G)-CGG-N(A/G)G-ANN-ACN-3', 0.

# CTCF (Lobanenkov) samplings
CCCTC-Binding factor or CTCF was initially discovered as a negative regulator of the chicken c-myc gene. This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor.
For the Basic programs testing consensus sequence CCCTC (starting with SuccessablesCTCF.bas) written to compare nucleotide sequences with the sequences on either the template strand (-), or coding strand (+), of the DNA, in the negative direction (-), or the positive direction (+), the programs are, are looking for, and found:
- Negative strand, negative direction: 22, CCCTC at 4560, CCCTC at 4549, CCCTC at 4497, CCCTC at 4303, CCCTC at 4271, CCCTC at 4153, CCCTC at 4002, CCCTC at 3989, CCCTC at 3888, CCCTC at 3752, CCCTC at 3714, CCCTC at 3080, CCCTC at 2701, CCCTC at 2221, CCCTC at 2104, CCCTC at 1962, CCCTC at 1930, CCCTC at 1795, CCCTC at 1018, CCCTC at 686, CCCTC at 550, CCCTC at 413.
- Positive strand, negative direction: 1, CCCTC at 2626.
- Negative strand, positive direction: 7, CCCTC at 4294, CCCTC at 3502, CCCTC at 3355, CCCTC at 3206, CCCTC at 1772, CCCTC at 95, CCCTC at 87.
- Positive strand, positive direction: 16, CCCTC at 4432, CCCTC at 4044, CCCTC at 3978, CCCTC at 3673, CCCTC at 3657, CCCTC at 3453, CCCTC at 3184, CCCTC at 2288, CCCTC at 1896, CCCTC at 1782, CCCTC at 1683, CCCTC at 661, CCCTC at 493, CCCTC at 382, CCCTC at 368, CCCTC at 313.
- inverse complement, negative strand, negative direction: 3, GAGGG at 4258, GAGGG at 1507, GAGGG at 388.
- inverse complement, positive strand, negative direction: 5, GAGGG at 4558, GAGGG at 3652, GAGGG at 2699, GAGGG at 1673, GAGGG at 88.
- inverse complement, negative strand, positive direction: 16, GAGGG at 4434, GAGGG at 3980, GAGGG at 3906, GAGGG at 3879, GAGGG at 3653, GAGGG at 3479, GAGGG at 3182, GAGGG at 2796, GAGGG at 2655, GAGGG at 2290, GAGGG at 1898, GAGGG at 311, GAGGG at 258, GAGGG at 245, GAGGG at 181, GAGGG at 18.
- inverse complement, positive strand, positive direction: 9, GAGGG at 4296, GAGGG at 3554, GAGGG at 3332, GAGGG at 3198, GAGGG at 3077, GAGGG at 2531, GAGGG at 2395, GAGGG at 2382, GAGGG at 465.

## CTCF (4560-2846) UTRs
- Negative strand, negative direction: CCCTC at 4560, CCCTC at 4549, CCCTC at 4497, CCCTC at 4303, CCCTC at 4271, CCCTC at 4153, CCCTC at 4002, CCCTC at 3989, CCCTC at 3888, CCCTC at 3752, CCCTC at 3714, CCCTC at 3080.
- Negative strand, negative direction: GAGGG at 4258.
- Positive strand, negative direction: GAGGG at 4558, GAGGG at 3652.

## CTCF positive direction (4445-4265) core promoters
- Negative strand, positive direction: CCCTC at 4294.
- Negative strand, positive direction: GAGGG at 4434.
- Positive strand, positive direction: CCCTC at 4432.
- Positive strand, positive direction: GAGGG at 4296.

## CTCF negative direction (2811-2596) proximal promoters
- Negative strand, negative direction: CCCTC at 2701.
- Positive strand, negative direction: CCCTC at 2626.
- Positive strand, negative direction: GAGGG at 2699.

## CTCF positive direction (4265-4050) proximal promoters
- Negative strand, positive direction: CCCTC at 4294.

## CTCF negative direction (2596-1) distal promoters
- Negative strand, negative direction: CCCTC at 2221, CCCTC at 2104, CCCTC at 1962, CCCTC at 1930, CCCTC at 1795, CCCTC at 1018, CCCTC at 686, CCCTC at 550, CCCTC at 413.
- Negative strand, negative direction: GAGGG at 1507, GAGGG at 388.
- Positive strand, negative direction: GAGGG at 1673, GAGGG at 88.

## CTCF positive direction (4050-1) distal promoters
- Negative strand, positive direction: CCCTC at 3502, CCCTC at 3355, CCCTC at 3206, CCCTC at 1772, CCCTC at 95, CCCTC at 87.
- Negative strand, positive direction: GAGGG at 4434, GAGGG at 3980, GAGGG at 3906, GAGGG at 3879, GAGGG at 3653, GAGGG at 3479, GAGGG at 3182, GAGGG at 2796, GAGGG at 2655, GAGGG at 2290, GAGGG at 1898, GAGGG at 311, GAGGG at 258, GAGGG at 245, GAGGG at 181, GAGGG at 18.
- Positive strand, positive direction: CCCTC at 4044, CCCTC at 3978, CCCTC at 3673, CCCTC at 3657, CCCTC at 3453, CCCTC at 3184, CCCTC at 2288, CCCTC at 1896, CCCTC at 1782, CCCTC at 1683, CCCTC at 661, CCCTC at 493, CCCTC at 382, CCCTC at 368, CCCTC at 313.
- Positive strand, positive direction: GAGGG at 3554, GAGGG at 3332, GAGGG at 3198, GAGGG at 3077, GAGGG at 2531, GAGGG at 2395, GAGGG at 2382, GAGGG at 465.

# CTCF (Lobanenkov) random dataset samplings
- CTCFr0: 5, CCCTC at 2873, CCCTC at 2302, CCCTC at 1863, CCCTC at 587, CCCTC at 26.
- CTCFr1: 8, CCCTC at 2735, CCCTC at 2580, CCCTC at 2300, CCCTC at 1369, CCCTC at 859, CCCTC at 424, CCCTC at 217, CCCTC at 127.
- CTCFr2: 8, CCCTC at 4478, CCCTC at 3917, CCCTC at 3842, CCCTC at 3643, CCCTC at 956, CCCTC at 894, CCCTC at 692, CCCTC at 670.
- CTCFr3: 5, CCCTC at 3829, CCCTC at 3519, CCCTC at 2497, CCCTC at 1521, CCCTC at 1429.
- CTCFr4: 8, CCCTC at 4306, CCCTC at 2619, CCCTC at 2356, CCCTC at 1908, CCCTC at 1525, CCCTC at 1521, CCCTC at 1177, CCCTC at 1058.
- CTCFr5: 7, CCCTC at 4416, CCCTC at 4356, CCCTC at 3244, CCCTC at 2134, CCCTC at 1860, CCCTC at 1853, CCCTC at 1405.
- CTCFr6: 10, CCCTC at 4408, CCCTC at 3983, CCCTC at 3805, CCCTC at 3560, CCCTC at 2969, CCCTC at 2361, CCCTC at 2272, CCCTC at 2095, CCCTC at 1736, CCCTC at 886.
- CTCFr7: 7, CCCTC at 3262, CCCTC at 3246, CCCTC at 2909, CCCTC at 2643, CCCTC at 1747, CCCTC at 978, CCCTC at 543.
- CTCFr8: 3, CCCTC at 4032, CCCTC at 3783, CCCTC at 3756.
- CTCFr9: 14, CCCTC at 3586, CCCTC at 3516, CCCTC at 3402, CCCTC at 3023, CCCTC at 2828, CCCTC at 2746, CCCTC at 2574, CCCTC at 2157, CCCTC at 1787, CCCTC at 1778, CCCTC at 1343, CCCTC at 856, CCCTC at 191, CCCTC at 101.
- CTCFr0ci: 6, GAGGG at 4403, GAGGG at 2464, GAGGG at 1396, GAGGG at 1072, GAGGG at 920, GAGGG at 733.
- CTCFr1ci: 5, GAGGG at 3317, GAGGG at 3133, GAGGG at 1179, GAGGG at 1149, GAGGG at 838.
- CTCFr2ci: 5, GAGGG at 4295, GAGGG at 2839, GAGGG at 2396, GAGGG at 1179, GAGGG at 170.
- CTCFr3ci: 7, GAGGG at 2864, GAGGG at 2319, GAGGG at 1920, GAGGG at 1628, GAGGG at 1623, GAGGG at 1368, GAGGG at 962.
- CTCFr4ci: 2, GAGGG at 2309, GAGGG at 1017.
- CTCFr5ci: 8, GAGGG at 3901, GAGGG at 3839, GAGGG at 3301, GAGGG at 2752, GAGGG at 2381, GAGGG at 2252, GAGGG at 1392, GAGGG at 517.
- CTCFr6ci: 7, GAGGG at 4103, GAGGG at 3830, GAGGG at 2832, GAGGG at 2694, GAGGG at 1507, GAGGG at 1159, GAGGG at 109.
- CTCFr7ci: 6, GAGGG at 4318, GAGGG at 1782, GAGGG at 1728, GAGGG at 1243, GAGGG at 1189, GAGGG at 631.
- CTCFr8ci: 7, GAGGG at 4205, GAGGG at 3551, GAGGG at 3273, GAGGG at 2864, GAGGG at 2632, GAGGG at 2018, GAGGG at 686.
- CTCFr9ci: 4, GAGGG at 1578, GAGGG at 1332, GAGGG at 789, GAGGG at 227.

## CTCFr arbitrary (evens) (4560-2846) UTRs
- CTCFr0: CCCTC at 2873.
- CTCFr2: CCCTC at 4478, CCCTC at 3917, CCCTC at 3842, CCCTC at 3643.
- CTCFr4: CCCTC at 4306.
- CTCFr6: CCCTC at 4408, CCCTC at 3983, CCCTC at 3805, CCCTC at 3560, CCCTC at 2969.
- CTCFr8: CCCTC at 4032, CCCTC at 3783, CCCTC at 3756.
- CTCFr0ci: GAGGG at 4403.
- CTCFr2ci: GAGGG at 4295.
- CTCFr6ci: GAGGG at 4103, GAGGG at 3830.
- CTCFr8ci: GAGGG at 4205, GAGGG at 3551, GAGGG at 3273, GAGGG at 2864.

## CTCFr alternate (odds) (4560-2846) UTRs
- CTCFr3: CCCTC at 3829, CCCTC at 3519.
- CTCFr5: CCCTC at 4416, CCCTC at 4356, CCCTC at 3244.
- CTCFr7: CCCTC at 3262, CCCTC at 3246, CCCTC at 2909.
- CTCFr9: CCCTC at 3586, CCCTC at 3516, CCCTC at 3402, CCCTC at 3023.
- CTCFr1ci: GAGGG at 3317, GAGGG at 3133.
- CTCFr3ci: GAGGG at 2864.
- CTCFr5ci: GAGGG at 3901, GAGGG at 3839, GAGGG at 3301.
- CTCFr7ci: GAGGG at 4318.

## CTCFr arbitrary negative direction (evens) (2846-2811) core promoters
- CTCFr2ci: GAGGG at 2839.
- CTCFr6ci: GAGGG at 2832.

## CTCFr alternate negative direction (odds) (2846-2811) core promoters
- CTCFr9: CCCTC at 2828.

## CTCFr arbitrary positive direction (odds) (4445-4265) core promoters
- CTCFr5: CCCTC at 4416, CCCTC at 4356.
- CTCFr7ci: GAGGG at 4318.

## CTCFr alternate positive direction (evens) (4445-4265) core promoters
- CTCFr4: CCCTC at 4306.
- CTCFr6: CCCTC at 4408.
- CTCFr0ci: GAGGG at 4403.
- CTCFr2ci: GAGGG at 4295.

## CTCFr arbitrary negative direction (evens) (2811-2596) proximal promoters
- CTCFr6ci: GAGGG at 2694.
- CTCFr8ci: GAGGG at 2632.

## CTCFr alternate negative direction (odds) (2811-2596) proximal promoters
- CTCFr1: CCCTC at 2735.
- CTCFr7: CCCTC at 2643.
- CTCFr9: CCCTC at 2746.
- CTCFr5ci: GAGGG at 2752.

## CTCFr alternate positive direction (evens) (4265-4050) proximal promoters
- CTCFr6ci: GAGGG at 4103.
- CTCFr8ci: GAGGG at 4205.

## CTCFr arbitrary negative direction (evens) (2596-1) distal promoters
- CTCFr0: CCCTC at 2302, CCCTC at 1863, CCCTC at 587, CCCTC at 26.
- CTCFr2: CCCTC at 956, CCCTC at 894, CCCTC at 692, CCCTC at 670.
- CTCFr4: CCCTC at 2356, CCCTC at 1908, CCCTC at 1525, CCCTC at 1521, CCCTC at 1177, CCCTC at 1058.
- CTCFr6: CCCTC at 2361, CCCTC at 2272, CCCTC at 2095, CCCTC at 1736, CCCTC at 886.
- CTCFr0ci: GAGGG at 2464, GAGGG at 1396, GAGGG at 1072, GAGGG at 920, GAGGG at 733.
- CTCFr4ci: GAGGG at 2309, GAGGG at 1017.
- CTCFr6ci: GAGGG at 1507, GAGGG at 1159, GAGGG at 109.
- CTCFr8ci: GAGGG at 2018, GAGGG at 686.

## CTCFr alternate negative direction (odds) (2596-1) distal promoters
- CTCFr1: CCCTC at 2580, CCCTC at 2300, CCCTC at 1369, CCCTC at 859, CCCTC at 424, CCCTC at 217, CCCTC at 127.
- CTCFr3: CCCTC at 2497, CCCTC at 1521, CCCTC at 1429.
- CTCFr5: CCCTC at 2134, CCCTC at 1860, CCCTC at 1853, CCCTC at 1405.
- CTCFr7: CCCTC at 1747, CCCTC at 978, CCCTC at 543.
- CTCFr9: CCCTC at 2574, CCCTC at 2157, CCCTC at 1787, CCCTC at 1778, CCCTC at 1343, CCCTC at 856, CCCTC at 191, CCCTC at 101.
- CTCFr1ci: GAGGG at 1179, GAGGG at 1149, GAGGG at 838.
- CTCFr3ci: GAGGG at 2319, GAGGG at 1920, GAGGG at 1628, GAGGG at 1623, GAGGG at 1368, GAGGG at 962.
- CTCFr5ci: GAGGG at 2381, GAGGG at 2252, GAGGG at 1392, GAGGG at 517.
- CTCFr7ci: GAGGG at 1782, GAGGG at 1728, GAGGG at 1243, GAGGG at 1189, GAGGG at 631.
- CTCFr9ci: GAGGG at 1578, GAGGG at 1332, GAGGG at 789, GAGGG at 227.

## CTCFr arbitrary positive direction (odds) (4050-1) distal promoters
- CTCFr1: CCCTC at 2735, CCCTC at 2580, CCCTC at 2300, CCCTC at 1369, CCCTC at 859, CCCTC at 424, CCCTC at 217, CCCTC at 127.
- CTCFr3: CCCTC at 3829, CCCTC at 3519, CCCTC at 2497, CCCTC at 1521, CCCTC at 1429.
- CTCFr5: CCCTC at 3244, CCCTC at 2134, CCCTC at 1860, CCCTC at 1853, CCCTC at 1405.
- CTCFr7: CCCTC at 3262, CCCTC at 3246, CCCTC at 2909, CCCTC at 2643, CCCTC at 1747, CCCTC at 978, CCCTC at 543.
- CTCFr9: CCCTC at 3586, CCCTC at 3516, CCCTC at 3402, CCCTC at 3023, CCCTC at 2828, CCCTC at 2746, CCCTC at 2574, CCCTC at 2157, CCCTC at 1787, CCCTC at 1778, CCCTC at 1343, CCCTC at 856, CCCTC at 191, CCCTC at 101.
- CTCFr1ci: GAGGG at 3317, GAGGG at 3133, GAGGG at 1179, GAGGG at 1149, GAGGG at 838.
- CTCFr3ci: GAGGG at 2864, GAGGG at 2319, GAGGG at 1920, GAGGG at 1628, GAGGG at 1623, GAGGG at 1368, GAGGG at 962.
- CTCFr5ci: GAGGG at 3901, GAGGG at 3839, GAGGG at 3301, GAGGG at 2752, GAGGG at 2381, GAGGG at 2252, GAGGG at 1392, GAGGG at 517.
- CTCFr7ci: GAGGG at 1782, GAGGG at 1728, GAGGG at 1243, GAGGG at 1189, GAGGG at 631.
- CTCFr9ci: GAGGG at 1578, GAGGG at 1332, GAGGG at 789, GAGGG at 227.

## CTCFr alternate positive direction (evens) (4050-1) distal promoters
- CTCFr0: CCCTC at 2873, CCCTC at 2302, CCCTC at 1863, CCCTC at 587, CCCTC at 26.
- CTCFr2: CCCTC at 3917, CCCTC at 3842, CCCTC at 3643, CCCTC at 956, CCCTC at 894, CCCTC at 692, CCCTC at 670.
- CTCFr4: CCCTC at 2619, CCCTC at 2356, CCCTC at 1908, CCCTC at 1525, CCCTC at 1521, CCCTC at 1177, CCCTC at 1058.
- CTCFr6: CCCTC at 3983, CCCTC at 3805, CCCTC at 3560, CCCTC at 2969, CCCTC at 2361, CCCTC at 2272, CCCTC at 2095, CCCTC at 1736, CCCTC at 886.
- CTCFr8: CCCTC at 4032, CCCTC at 3783, CCCTC at 3756.
- CTCFr0ci: GAGGG at 2464, GAGGG at 1396, GAGGG at 1072, GAGGG at 920, GAGGG at 733.
- CTCFr2ci: GAGGG at 2839, GAGGG at 2396, GAGGG at 1179, GAGGG at 170.
- CTCFr4ci: GAGGG at 2309, GAGGG at 1017.
- CTCFr6ci: GAGGG at 3830, GAGGG at 2832, GAGGG at 2694, GAGGG at 1507, GAGGG at 1159, GAGGG at 109.
- CTCFr8ci: GAGGG at 3551, GAGGG at 3273, GAGGG at 2864, GAGGG at 2632, GAGGG at 2018, GAGGG at 686.

# CTCF analysis and results
This protein was found to be binding to three regularly spaced repeats of the core sequence CCCTC and thus was named CCCTC binding factor.
Comparison:
The occurrences of real CTCF UTRs, cores, proximals and distals are greater than or outside the randoms. This suggests that the real CTCFs are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.