Bioinformatics tool gene transcriptions

Associate Editor(s)-in-Chief:  Henry A. Hoff

Def. a "field of science in which biology, computer science, and information technology merge into a single discipline to analyse biological information using computers and statistical techniques"[1] is called bioinformatics.

"To understand the gene function and regulation patterns of CsSODs, sequences of 1000 bp upstream regions from the translation start site of each CsSOD were identified from [Cucumber Genome Initiative (CuGI, http://cucumber.genomics.org.cn/)] CuGI and were subsequently determined using PlantCARE. The results showed that 59 types of cis-acting regulatory elements were found in the promoter region of CsSODs and all CsSOD promoters contained typical TATA and CAAT boxes, which are essential elements of the promoters [...]."[2]

## Contents

* 1 Human genes
* 2 Human promoter occurrences
* 3 Acknowledgements
* 4 See also
* 5 References
* 6 External links

## Human genes

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Main article: Human genes

"Briefly, the mRNA sequences were obtained from the NCBI Reference Sequence Database (RefSeq) for human SIRT2 gene. The reference mRNA sequences was submitted to BLAST for comparison with the human genomic DNA sequence in the human genome database."[3]

## Human promoter occurrences

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Main article: Promoter occurrence gene transcriptions

"After noting the orientation of the alignment, the appropriate 5-Kb genomic DNA sequence upstream from the transcription start point corresponding to the promoter region of the gene was isolated and analyzed using a web-based bioinformatics tool TESS at http://www.cbil.upenn.edu/cgi-bin/tess/tess. Because TESS results are model-based, the potential CArG sequence was verified by both using LALIGN (http://www.ch.embnet.org/software/LALIGN_form.html) and visual confirmation."[3]

## Acknowledgements

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

## See also

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* A1BG gene transcription core promoters
* A1BG gene transcriptions
* A1BG regulatory elements and regions
* A1BG response element negative results
* A1BG response element positive results
* Complex locus A1BG and ZNF497

## References

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1. ↑ 201.129.67.142 (6 May 2005). "bioinformatics". San Francisco, California: Wikimedia Foundation, Inc. Retrieved 23 February 2021.
2. ↑ Yong Zhou, Lifang Hu, Hao Wu, Lunwei Jiang, and Shiqiang Liu (20 July 2017). "Genome-Wide Identification and Transcriptional Expression Analysis of Cucumber Superoxide Dismutase (SOD) Family in Response to Various Abiotic Stresses". International Journal of Genomics. 2017: 7243973. doi:10.1155/2017/7243973. Retrieved 26 February 2021.CS1 maint: Multiple names: authors list (link)
3. ↑ 3.0 3.1 Xiaomin Zhang, Gohar Azhar, Jeanne Y. Wei (21 December 2017). "SIRT2 gene has a classic SRE element, is a downstream target of serum response factor and is likely activated during serum stimulation". PLOS One. 12 (12): e0190011. doi:10.1371/journal.pone.0190011. Retrieved 23 February 2021.CS1 maint: Multiple names: authors list (link)

## External links

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* GenomeNet KEGG database
* Home - Gene - NCBI
* NCBI All Databases Search
* NCBI Site Search
* PubChem Public Chemical Database

* v
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Gene project

Articles|

* Complex locus A1BG and ZNF497
* Grainyhead-like Genes in Regulating Development and Genetic Defects
* Lysenin
* Lysine: biosynthesis, catabolism and roles
* RIG-I like receptors
* ShK toxin: history, structure and therapeutic applications for autoimmune diseases

Categories|

* Biochemistry
* Biology
* Genetics
* Medicine

Laboratories|

* AGC box gene transcription laboratory
* ATA box gene transcription laboratory
* C and D boxes gene transcription laboratory
* CArG box gene transcription laboratory
* CGCG box gene transcription laboratory
* CRE box gene transcription laboratory
* E2 box gene transcription laboratory
* Enhancer box gene transcription laboratory
* Factor II B recognition element gene transcription laboratory
* GA responsive complex gene transcription laboratory
* GC box gene transcription laboratory
* H box gene transcription laboratory
* HNF6 gene transcription laboratory
* HY box gene transcription laboratory
* Initiator element gene transcription laboratory
* Metal responsive element gene transcription laboratory
* STAT5 gene transcription laboratory
* TATA box gene transcription laboratory

Lessons|

* A1BG gene transcription programming
* Amino Acids
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Lists|

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Projects|

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Transcription resources|

* A1BG gene transcription core promoters
* A1BG gene transcriptions
* A1BG regulatory elements and regions
* A1BG response element gene transcriptions
* A1BG response element negative results
* A1BG response element positive results
* ABA-response element gene transcriptions
* Abf1 regulatory factor gene transcriptions
* A box gene transcriptions
* Abscisic acid-responsive elements
* ACGT-containing element gene transcriptions
* Activating protein gene transcriptions
* Activating transcription factor gene transcriptions
* Adenylate–uridylate rich element gene transcriptions
* Adr1p gene transcriptions
* Aft1p gene transcriptions
* AGC box gene transcriptions
* AGCE gene transcriptions
* Alpha-amylase conserved element gene transcriptions
* Amino acid response element gene transcriptions
* AARE-like
* Androgen response element gene transcriptions
* Angiotensinogen core promoter element gene transcriptions
* Antioxidant-electrophile responsive element gene transcriptions
* AP-2 (Roesler) elements
* ATA box gene transcriptions
* Auxin response factor gene transcriptions
* B box gene transcriptions
* Bioinformatics tool gene transcriptions
* Box gene transcriptions
* B recognition element upstream
* Bridge gene transcriptions
* CAAT box gene transcriptions
* CACA elements
* CadC binding domain gene transcriptions
* Calcineurin-responsive transcription factor gene transcriptions
* Calcium-response element gene transcriptions
* cAMP response element gene transcriptions
* C and D boxes gene transcriptions
* Carbohydrate response element gene transcriptions
* Carbon source-responsive element gene transcriptions
* Carcinoembryonic antigen gene family
* CARE gene transcriptions
* CArG box gene transcriptions
* CAT box gene transcriptions
* CAT-box-like elements
* Cat8p gene transcriptions
* Cbf1 regulatory factor gene transcriptions
* C box gene transcriptions
* CCCTC-binding factor gene transcriptions
* C-EBP box gene transcriptions
* Cell-cycle box gene transcriptions
* Cell cycle regulation gene transcriptions
* CENP-B box gene transcriptions
* CGCG box gene transcriptions
* Circadian control element gene transcriptions
* "Class C" (Leal) samplings
* Cold-responsive element gene transcriptions
* Complement copy gene transcriptions
* Complement-inverse copy gene transcriptions
* Consensus sequence gene transcriptions
* Constitutive decay elements
* Copper response element gene transcriptions
* Core promoter gene transcriptions
* Coupling element gene transcriptions
* CRE box gene transcriptions
* Cytokinin response regulator gene transcriptions
* Cytoplasmic polyadenylation element gene transcriptions
* DAF-16-associated element gene transcriptions
* DAF-16 binding element gene transcriptions
* D box gene transcriptions
* Defense and stress-responsive element gene transcriptions
* Degenerate nucleotide gene transcriptions
* Dispersed promoter gene transcriptions
* Distal promoter gene transcriptions
* DNA melting gene transcriptions
* DNA damage response element gene transcriptions
* DNA replication-related element gene transcriptions
* Downstream core element gene transcriptions
* Downstream promoter element gene transcriptions
* Downstream TFIIB recognition element gene transcriptions
* DREB box gene transcriptions
* E2 box gene transcriptions
* EIF4E basal element gene transcriptions
* EIN3 binding site gene transcriptions
* Enhancer activity copy gene transcriptions
* E box gene transcriptions
* Element gene transcriptions
* Endoplasmic reticulum stress response element gene transcriptions
* Endosperm expression gene transcriptions
* Enhancer box gene transcriptions
* Estrogen response element gene transcriptions
* Ethylene responsive element gene transcriptions
* Families of TATA box genes
* F box gene transcriptions
* Focused promoter gene transcriptions
* Forkhead box gene transcriptions
* Fur box gene transcriptions
* GAAC element gene transcriptions
* Gal4p gene transcriptions
* Γ-interferon activated sequence gene transcriptions
* GARE gene transcriptions
* GA responsive complex gene transcriptions
* GATA gene transcriptions
* G box gene transcriptions
* GC box gene transcriptions
* GCC box gene transcriptions
* Gcn4p gene transcriptions
* Gcr1p gene transcriptions
* Gene expressions
* General factor II D gene transcriptions
* General regulatory factors
* General transcription factor II A gene transcriptions
* General transcription factor II B gene transcriptions
* General transcription factor II D gene transcriptions
* General transcription factor II F gene transcriptions
* General transcription factor II H gene transcriptions
* General transcription factor gene transcriptions
* Gene transcriptions
* GGC triplet gene transcriptions
* Gibberellin responsive element gene transcriptions
* GLM box gene transcriptions
* Glucocorticoid response element gene transcriptions
* Grainy head gene transcriptions
* Grainy head transcription factor gene transcriptions
* Growth hormone response element gene transcriptions
* GT boxes
* Hac1p gene transcriptions
* Hair color gene expressions
* H and ACA box gene transcriptions
* H box gene transcriptions
* Heat-responsive element gene transcriptions
* Heat shock elements
* Hex sequence gene transcriptions
* HMG box gene transcriptions
* HNF gene transcriptions
* Homeobox gene transcriptions
* Hsf1p gene transcriptions
* HY box gene transcriptions
* Hybrid C, A boxes
* Hybrid C, G boxes
* Hybrid C, T boxes
* Hypoxia-inducible factor gene transcriptions
* Hypoxia response elements
* I box gene transcriptions
* Immunoglobulin like domain containing family
* Initiator element gene transcriptions
* Initiator-like element gene transcriptions
* Inositol/choline-responsive elements
* Interaction gene transcriptions
* Interferon regulatory factors
* Inverse copy gene transcriptions
* Jasmonic acid-responsive element gene transcriptions
* K-boxes
* Kozak sequence gene transcriptions
* Kruppel-associated box gene transcriptions
* Krüppel-like factor gene transcriptions
* L box gene transcriptions
* Leu3 gene transcriptions
* M35 box gene transcriptions
* MADS box gene transcriptions
* Maf recognition element gene transcriptions
* M box gene transcriptions
* M-CAT boxes
* Mcm1 regulatory factor gene transcriptions
* Met3 gene transcriptions
* Met31p box gene transcriptions
* Metal responsive element gene transcriptions
* Middle sporulation element gene transcriptions
* Mig1p gene transcriptions
* Model samplings
* Motif ten element gene transcriptions
* Msn2,4p gene transcriptions
* Musashi binding element gene transcriptions
* MYB recognition element gene transcriptions
* Myelocytomatosis transcription factor gene transcriptions
* Myocyte enhancer factor gene transcriptions
* N-boxes
* Nanos/Pumilio response element
* Ndt80p gene transcriptions
* Nuclear factor 1
* Nuclear factor 𝜿B
* Nuclear factor gene transcriptions
* Nuclear factor of activated T cell gene transcriptions (NFAT)
* Nuclear factor Y gene transcriptions
* Nutrient-sensing response element gene transcriptions
* Oaf1p gene transcriptions
* ORE1 binding site gene transcriptions
* p53 response element gene transcriptions
* P63 DNA-binding site gene transcriptions
* P box gene transcriptions
* Pdr1,3p gene transcriptions
* Peroxisome proliferator hormone response element gene transcriptions
* Phosphate starvation-response transcription factor gene transcriptions
* Pollen1 element gene transcriptions
* Polycomb response element gene transcriptions
* Preinitiation complex
* Preinitiation complex gene transcriptions
* Pribnow box gene transcriptions
* Prolamin box gene transcriptions
* Promoter gene transcriptions
* Proximal promoter gene transcriptions
* Promoter occurrence gene transcriptions
* Pyrimidine box gene transcriptions
* Q element gene transcriptions
* Rap1 regulatory factor gene transcriptions
* Reb1 general regulatory factor gene transcriptions
* Retinoblastoma control element gene transcriptions
* Retinoic acid response element gene transcriptions
* Rgt1p gene transcriptions
* Rlm1p gene transcriptions
* RNA polymerase II gene transcriptions
* RNA polymerase II holoenzyme complex
* Root specific element gene transcriptions
* ROR-response element gene transcriptions
* Rox1p gene transcriptions
* Rpn4p gene transcriptions
* R response element gene transcriptions
* SARE gene transcriptions
* Seed-specific element gene transcriptions
* Serum response element gene transcriptions
* Servenius sequence gene transcriptions
* Shoot specific element gene transcriptions
* Shue boxes
* Sip4p gene transcriptions
* Smp1p gene transcriptions
* Sp1 (Berberich) elements
* Sp1 gene transcriptions
* Spaceflight gene expressions
* Specificity protein gene transcriptions
* STAT gene transcriptions
* Ste12p gene transcriptions
* Sterol response element gene transcriptions
* Sucrose box gene transcriptions
* Synaptic Activity-Responsive Elements
* TACTAAC box gene transcriptions
* TAGteam gene transcriptions
* Tapetum box gene transcriptions
* TATA binding protein associated factor gene transcriptions
* TATA binding protein gene transcriptions
* TATA box actin/cytoskeleton/contractile family
* TATA box albumin family
* TATA box aldolase family
* TATA box alkaline phosphatase family
* TATA box annexin family
* TATA box cytochrome superfamily
* TATA box gene transcriptions
* TATA box heat shock family
* TATA box histone family
* TATA box human genes
* TATA box keratin family
* TATA box lipase family
* TATA box peptidase family
* TATA box platelet-derived growth factor family
* TATA box selenium-binding family
* TATA box serine protease family
* TATA box serpin superfamily
* TATA box transforming growth factor superfamily
* TATA box trefoil family
* TATA box tumor necrosis factor superfamily
* TATA box zinc metalloenzyme family
* TAT box gene transcriptions
* TATC box gene transcriptions
* Tbf1 regulatory factor gene transcriptions
* T box gene transcriptions
* TCCACCATA element gene transcriptions
* TC element gene transcriptions
* TCT gene transcriptions
* TEA consensus sequence gene transcriptions
* Tec1p gene transcriptions
* Telomeric repeat DNA-binding factor gene transcriptions
* Tetradecanoylphorbol-13-acetate response element gene transcriptions
* TGF-β control elements (TCEs)
* TGF-β inhibitory elements (TIEs)
* Thyroid hormone response element gene transcriptions
* Transcriptional regulation
* Transcription bubble gene transcriptions
* Transcription factor gene transcriptions
* Transcription factor 3 gene transcriptions
* Transcription factory gene transcriptions
* Transcription start site gene transcriptions
* Translational control sequence gene transcriptions
* Tryptophan residue
* U box gene transcriptions
* Unfolded protein response element gene transcriptions
* Upstream repressor site 1
* Upstream response element gene transcriptions
* Upstream stimulatory factor gene transcriptions
* UTR promoter gene transcriptions
* V and P box gene transcriptions
* V box gene transcriptions
* Vhr1p gene transcriptions
* Vitamin D response element gene transcriptions
* W box gene transcriptions
* X box gene transcriptions
* Xbp1p gene transcriptions
* X core promoter element gene transcriptions
* Xenobiotic response element gene transcriptions
* Xenobiotic responsive element gene transcriptions
* Yap1p,2p gene transcriptions
* Y box gene transcriptions
* YY1 gene transcriptions
* Zap1p gene transcriptions
* Z box gene transcriptions
* Zinc responsive element gene transcriptions

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