Y box gene transcriptions

Gene ID: 4904 is YBX1 Y-box binding protein 1 aka CCAAT-binding transcription factor I subunit A, DNA-binding protein B, Y-box transcription factor, enhancer factor I subunit A, major histocompatibility complex, class II, Y box-binding protein I, nuclease-sensitive element-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]
2. NR_132737.1 RNA Sequence (variant 2), non-coding RNA.^[2]

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.

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

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.

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

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