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Gene transcriptions/Boxes/Ys

< Gene transcriptions/Boxes

The "Y-box [is] an inverted CCAAT box, in the promoter region of many genes; this domain is highly conserved in evolution [1, 3, 4]."[1]

Human genes

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Gene ID: 4904 is YBX1 Y-box binding protein 1. "This gene encodes a highly conserved cold shock domain protein that has broad nucleic acid binding properties. The encoded protein functions as both a DNA and RNA binding protein and has been implicated in numerous cellular processes including regulation of transcription and translation, pre-mRNA splicing, DNA reparation and mRNA packaging. This protein is also a component of messenger ribonucleoprotein (mRNP) complexes and may have a role in microRNA processing. This protein can be secreted through non-classical pathways and functions as an extracellular mitogen. Aberrant expression of the gene is associated with cancer proliferation in numerous tissues. This gene may be a prognostic marker for poor outcome and drug resistance in certain cancers. Alternate splicing results in multiple transcript variants. Pseudogenes of this gene are found on multiple chromosomes."[2]

  1. NP_004550.2 nuclease-sensitive element-binding protein 1.
  2. NR_132737.1 RNA Sequence (variant 2), non-coding RNA.

Gene ID: 8531 is YBX3 Y-box binding protein 3.

  1. NP_003642.3 Y-box-binding protein 3 isoform a.
  2. NP_001138898.1 Y-box-binding protein 3 isoform b.
  3. XP_016875611.1 Y-box-binding protein 3 isoform X1.
  4. XP_016875612.1 Y-box-binding protein 3 isoform X2.
  5. XP_011519173.1 Y-box-binding protein 3 isoform X3.
  6. XR_001748906.2 RNA Sequence, transcript variant X3, misc RNA.

Gene ID: 51087 is YBX2 Y-box binding protein 2. "This gene encodes a nucleic acid binding protein which is highly expressed in germ cells. The encoded protein binds to a Y-box element in the promoters of certain genes but also binds to mRNA transcribed from these genes. Pseudogenes for this gene are located on chromosome 10 and 15."[3]

  1. NP_057066.2 Y-box-binding protein 2.
  2. XP_016880202.1 Y-box-binding protein 2 isoform X1.

Consensus sequences

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On the template strand, the CAAT box consensus sequence is 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5'. An inverted CAAT box has the consensus sequence 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5'.

Sampling of A1BG promoters

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For the Basic programs (starting with SuccessablesYbox.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:

  1. negative strand in the negative direction (from ZSCAN22 to A1BG) is SuccessablesYbox--.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  2. negative strand in the positive direction (from ZNF497 to A1BG) is SuccessablesYbox-+.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  3. positive strand in the negative direction is SuccessablesYbox+-.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  4. positive strand in the positive direction is SuccessablesYbox++.bas, looking for 3'-(A/G)CTAACC(A/G)(A/G)(C/T)-5', 0,
  5. complement, negative strand, negative direction is SuccessablesYboxc--.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  6. complement, negative strand, positive direction is SuccessablesYboxc-+.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  7. complement, positive strand, negative direction is SuccessablesYboxc+-.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  8. complement, positive strand, positive direction is SuccessablesYboxc++.bas, looking for 3'-(C/T)GATTGG(C/T)(C/T)(A/G)-5', 0,
  9. inverse complement, negative strand, negative direction is SuccessablesYboxci--.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  10. inverse complement, negative strand, positive direction is SuccessablesYboxci-+.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  11. inverse complement, positive strand, negative direction is SuccessablesYboxci+-.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  12. inverse complement, positive strand, positive direction is SuccessablesYboxci++.bas, looking for 3'-(A/G)(C/T)(C/T)GGTTAG(C/T)-5', 0,
  13. inverse, negative strand, negative direction, is SuccessablesYboxi--.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  14. inverse, negative strand, positive direction, is SuccessablesYboxi-+.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  15. inverse, positive strand, negative direction, is SuccessablesYboxi+-.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0,
  16. inverse, positive strand, positive direction, is SuccessablesYboxi++.bas, looking for 3'-(C/T)(A/G)(A/G)CCAATC(A/G)-5', 0.

See also

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References

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  1. ↑ Koji Koike, Takeshi Uchiumi, Takefumi Ohga, Satoshi Toh, Morimasa Wada, Kimitoshi Kohno, and Michihiko Kuwano (17 November 1997). "Nuclear translocation of the Y-box binding protein by ultraviolet irradiation". FEBS Letters 417 (3): 390-4. doi:10.1016/S0014-5793(97)01296-9. http://onlinelibrary.wiley.com/doi/10.1016/S0014-5793(97)01296-9/full. Retrieved 2017-04-05. 
  2. ↑ RefSeq (September 2015). YBX1 Y-box binding protein 1 ( Homo sapiens (human) ). Bethesda, MD, USA: National Center for Biotechnology Information, U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/gene/4904. Retrieved 19 November 2018. 
  3. ↑ RefSeq (February 2012). YBX2 Y-box binding protein 2 ( Homo sapiens (human) ). Bethesda, MD, USA: National Center for Biotechnology Information, U.S. National Library of Medicine. https://www.ncbi.nlm.nih.gov/gene/51087. Retrieved 19 November 2018. 
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