CARE gene transcriptions
"Some other cis-acting elements, such as pyrimidine boxes (GGTTTT) and TAT boxes (TATCCAT), are usually present in the vicinity of the GARE sequence of genes regulated by GA in cereal aleurone cells (Gubler and Jacobsen 1992; Cercos et al. 1999; Tsuji et al. 2006). For example, GARE and a novel CARE (CAACTC regulatory elements) elements are present in the promoter of rice RAmy1A (Ueguchi-Tanaka et al. 2000; Sutoh and Yamauchi 2003). Cis-element analyses have shown that the OsGAMYB protein activates RAmy1A expression through interaction with GARE in the promoter (Washio 2003). In addition, GARE and CARE are also present in a cysteine proteinase gene REP-1, which is expressed in rice aleurone and is induced by GAs and repressed by ABA. These two elements have been identified as necessary and sufficient for conferring GA inducibility of the REP-1 promoter. Mutations of CARE in the promoters of RAmy1A and REP-1 result in loss of GA inducibility and GAMYB transactivation, suggesting that CARE is a regulatory element for the GA-inducible expression of hydrolase genes in germinating seeds (Sutoh and Yamauchi 2003)."
"ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP38,39 that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).39 In the region from -625 to -618 bp relative to the SESN2 translation start codon (from -228 to -221 bp relative to the transcription start site) we found a candidate sequence for the ATF4 binding site TTTTCATCA."

# CARE (Fan) sampling of A1BG promoters
For the Basic programs (starting with SuccessablesCARE.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 (+), including extending the number of nts from 958 to 4445, the programs are, are looking for, and found:
- Negative strand, negative direction: 1, CAACTC at 86.
- Negative strand, positive direction: 1, CAACTC at 3292.
- Positive strand, negative direction: 0.
- Positive strand, positive direction: 0.
- inverse complement, negative strand, negative direction: 1, GAGTTG at 1406.
- inverse complement, negative strand, positive direction: 0.
- inverse complement, positive strand, negative direction: 4, GAGTTG at 4096, GAGTTG at 3115, GAGTTG at 2704, GAGTTG at 2592.
- inverse complement, positive strand, positive direction: 2, GAGTTG at 3290, GAGTTG at 1621.

## CARE (Fan) UTR promoters
- Positive strand, negative direction: GAGTTG at 4096, GAGTTG at 3115.

## CARE (Fan) Proximal promoters
- Positive strand, negative direction: GAGTTG at 2704.

## CARE (Fan) distal promoters
- Negative strand, negative direction: GAGTTG at 1406, CAACTC at 86.
- Positive strand, negative direction: GAGTTG at 2592.
- Negative strand, positive direction: CAACTC at 3292.
- Positive strand, positive direction: GAGTTG at 3290, GAGTTG at 1621.

# CARE (Fan) random dataset samplings
- CAREr0: 0.
- CAREr1: 0.
- CAREr2: 2, CAACTC at 3285, CAACTC at 1310.
- CAREr3: 0.
- CAREr4: 0.
- CAREr5: 0.
- CAREr6: 0.
- CAREr7: 2, CAACTC at 3148, CAACTC at 69.
- CAREr8: 4, CAACTC at 3816, CAACTC at 2042, CAACTC at 1912, CAACTC at 1907.
- CAREr9: 1, CAACTC at 1315.
- CAREr0ci: 1, GAGTTG at 3165.
- CAREr1ci: 0.
- CAREr2ci: 3, GAGTTG at 1396, GAGTTG at 1035, GAGTTG at 299.
- CAREr3ci: 1, GAGTTG at 2263.
- CAREr4ci: 0.
- CAREr5ci: 0.
- CAREr6ci: 1, GAGTTG at 430.
- CAREr7ci: 2, GAGTTG at 2937, GAGTTG at 2872.
- CAREr8ci: 1, GAGTTG at 3150.
- CAREr9ci: 2, GAGTTG at 2739, GAGTTG at 538.

## CARE (Fan) random UTRs
- CAREr2: CAACTC at 3285.
- CAREr8: CAACTC at 3816.
- CAREr0ci: GAGTTG at 3165.
- CAREr8ci: GAGTTG at 3150.

## CARE (Fan) random distal promoters
- CAREr2: CAACTC at 1310.
- CAREr8: CAACTC at 2042, CAACTC at 1912, CAACTC at 1907.
- CAREr2ci: GAGTTG at 1396, GAGTTG at 1035, GAGTTG at 299.
- CAREr6ci: GAGTTG at 430.
- CAREr7: CAACTC at 3148, CAACTC at 69.
- CAREr9: CAACTC at 1315.
- CAREr3ci: GAGTTG at 2263.
- CAREr7ci: GAGTTG at 2937, GAGTTG at 2872.
- CAREr9ci: GAGTTG at 2739, GAGTTG at 538.

# CARE analysis and results
CAREs occur in the negative transcription direction in the UTR with an occurrence of 1.0, not in the core promoters on either side, in the proximal promoters in the negative direction for an occurrence of 0.5, and the distal promoters: negative direction occurrence of 1.5 and the positive direction occurrence of 1.5.
The random datasets had an occurrence in the UTR of 0.4, none in the core promoters, none in the proximal promoters, and an occurrence of 0.8 in the arbitrary negative direction and 0.8 in the positive direction.
The lack of closeness between the real and random datasets suggests that the real CAREs are likely active or activable.
"GARE and a novel CARE (CAACTC regulatory elements) elements are present in the promoter of rice RAmy1A (Ueguchi-Tanaka et al. 2000; Sutoh and Yamauchi 2003)."
Comparison:
The occurrences of real CAREs are greater than the randoms. This suggests that the real responsive element consensus sequences are likely active or activable.

# CARE (Garaeva) samplings
Copying a responsive elements consensus sequence AAAAAAAA and putting the sequence in "F" finds none between ZNF497 and A1BG or none between ZSCAN22 and A1BG as can be found by the computer programs.
For the Basic programs testing consensus sequence (A/G/T)TT(A/G/T)CATCA (starting with SuccessablesCAREG.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: 0.
- Positive strand, negative direction: 1, ATTTCATCA at 2888.
- Negative strand, positive direction: 0.
- Positive strand, positive direction: 0.
- inverse complement, negative strand, negative direction: 0.
- inverse complement, positive strand, negative direction: 0.
- inverse complement, negative strand, positive direction: 1, TGATGAAAC at 2147.
- inverse complement, positive strand, positive direction: 0.

## CARE (Garaeva) UTRs
- Positive strand, negative direction: ATTTCATCA at 2888.

## CARE (Garaeva) positive direction distal promoters
- Negative strand, positive direction: TGATGAAAC at 2147.

# CARE (Garaeva) random dataset samplings
- CAREGr0: 0.
- CAREGr1: 0.
- CAREGr2: 0.
- CAREGr3: 0.
- CAREGr4: 0.
- CAREGr5: 0.
- CAREGr6: 0.
- CAREGr7: 0.
- CAREGr8: 0.
- CAREGr9: 1, GTTTCATCA at 1242.
- CAREGr0ci: 1, TGATGAAAC at 1932.
- CAREGr1ci: 0.
- CAREGr2ci: 0.
- CAREGr3ci: 0.
- CAREGr4ci: 0.
- CAREGr5ci: 1, TGATGTAAA at 3714.
- CAREGr6ci: 0.
- CAREGr7ci: 0.
- CAREGr8ci: 0.
- CAREGr9ci: 0.

## CARE (Garaeva)r alternate UTRs
- CAREGr5ci: TGATGTAAA at 3714.

## CARE (Garaeva)r arbitrary negative direction distal promoters
- CAREGr0ci: TGATGAAAC at 1932.

## CARE (Garaeva)r alternate negative direction distal promoters
- CAREGr9: GTTTCATCA at 1242.

## CARE (Garaeva)r arbitrary positive direction distal promoters
- CAREGr9: GTTTCATCA at 1242.
- CAREGr5ci: TGATGTAAA at 3714.

## CARE (Garaeva)r alternate positive direction distal promoters
- CAREGr0ci: TGATGAAAC at 1932.

# CARE (Garaeva) analysis and results
"ATF4 regulates transcription of its target genes through the formation of homodimers or heterooligomers with the transcription factors Jun, AP-1 and C/EBP38,39 that bind to CARE (C/EBP-ATF) responsive elements having the consensus sequence XTTXCATCA (where X = G, A or T).39"
Comparison:
The occurrences of real CARE (Garaeva) are greater than the randoms. This suggests that the real CARE (Garaeva) are likely active or activable.

# Acknowledgements
The content on this page was first contributed by: Henry A. Hoff.
Initial content for this page in some instances came from Wikiversity.