format-version: 1.0 date: 17:11:2005 17:22 saved-by: yamamotosatoko auto-generated-by: DAG-Edit 1.419 rev 3 default-namespace: genome_sequence remark: autogenerated-by: DAG-Edit version 1.417 remark: saved-by: yamagake remark: date: Tue Oct 12 14:23:09 JST 2004 remark: version: $Revision: 1.28 $ [Term] id: IGS:0000000 name: Sequence_Ontology xref_analog: SO:000000 [Term] id: IGS:0000001 name: CRE synonym: "cAMP responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000002 name: CRE synonym: "circadian clock responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000003 name: GC-rich_region def: "A conserved GC-rich region located upstream of the start point of eukaryotic transcription units which may occur in multiple copies or in either orientation; consensus=GGGCGG." [SO:0000173] synonym: "GC box" [] synonym: "GC_rich_region" [] xref_analog: SO:0000173 is_a: IGS:0000087 ! RNApol_II_promoter [Term] id: IGS:0000004 name: TATA_box def: "A conserved AT-rich septamer found about 25-bp before the start point of many eukaryotic RNA polymerase II transcript units; may be involved in positioning the enzyme for correct initiation; consensus=TATA(A|T)A(A|T)." [SO:0000174] synonym: "TATA box" [] xref_analog: SO:0000174 is_a: IGS:0000087 ! RNApol_II_promoter [Term] id: IGS:0000005 name: gene def: "A locatable region of genomic sequence\, corresponding to a unit of inheritance\, which is associated with regulatory regions\, transcribed regions and/or other functional sequence regions" [SO:0000704] xref_analog: SO:0000704 is_a: IGS:0000017 ! region [Term] id: IGS:0000006 name: Ets synonym: "ETS motif" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000007 name: SRE synonym: "serum responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000008 name: ZRE synonym: "UAS" [] synonym: "zinc-responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000009 name: CarG Box is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000010 name: NFkB binding motif synonym: "NFkB" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000011 name: AP-1 synonym: "12- O-tetradecanoylphorbol-13-acetate-responsive element" [] synonym: "Phorbolester-responsive element" [] synonym: "TPA-responsive element" [] synonym: "TRE" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000012 name: Box A is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000013 name: UBR is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000014 name: TRE def: "#seq-motif\:TGAGTCA #comment\:seq-info\:palindrome name-info\:signal substance responsive element " [XX:0] synonym: "12-0-tetradecanoyl-phorbol-13-acetate-responsive element" [] synonym: "TPA-responsive element" [] is_obsolete: true [Term] id: IGS:0000015 name: PPRE synonym: "PPAR-responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000016 name: GRE synonym: "glucocorticoid-receptor responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000017 name: region def: "Continous sequence." [SO:0000001] synonym: "sequence" [] xref_analog: SO:0000001 is_a: IGS:0000000 ! Sequence_Ontology [Term] id: IGS:0000018 name: GAS synonym: "gamma actived site" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000019 name: SIE synonym: "APRE" [] synonym: "acute phase response element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000020 name: ERE synonym: "estrogen responsive elemennt" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000021 name: ISRE synonym: "the IFN-stimulated response element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000022 name: E box is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000023 name: ZRE synonym: "Z responsive element" [] synonym: "Zta responsive element" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000028 name: responsive element def: "Response elements are the recognition sites of certain transcription factors" [http://www.web-books.com/MoBio/Free/Ch4C6.htm] synonym: "RE" [] synonym: "response element" [] is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000029 name: promoter def: "The region on a DNA molecule involved in RNA polymerase binding to initiate transcription." [SO:0000167] xref_analog: SO:0000167 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000036 name: regulatory_region def: "A DNA sequence that controls the expression of a gene." [SO:0005836] xref_analog: SO:0005836 relationship: part_of IGS:0000005 ! gene [Term] id: IGS:0000037 name: transcript def: "An RNA synthesized on a DNA or RNA template by an RNA polymerase." [SO:0000673] xref_analog: SO:0000673 relationship: part_of IGS:0000005 ! gene [Term] id: IGS:0000038 name: primary_transcript def: "The primary (initial\, unprocessed) transcript; includes five_prime_clip (SO\:0000555)\, five_prime_untranslated_region (SO\:0000204)\, open reading frames (SO\:0000236)\, introns (SO\:0000188) and three_prime_ untranslated_region (three_prime_UTR)\, and three_prime_clip (SO\:0000557)." [SO:0000185] synonym: "precursor RNA" [] xref_analog: SO:0000185 is_a: IGS:0000037 ! transcript [Term] id: IGS:0000040 name: mRNA def: "Messenger RNA is the intermediate molecule between DNA and protein. It includes UTR and coding sequences. It does not contain introns." [SO:0000234] synonym: "messenger_RNA" [] xref_analog: SO:0000234 is_a: IGS:0000042 ! processed_transcript [Term] id: IGS:0000041 name: CDS def: "A contiguous sequence which begins with\, and includes\, a start codon and ends with\, and includes\, a stop codon." [SO:0000316] synonym: "coding sequence" [] xref_analog: SO:0000316 relationship: part_of IGS:0000040 ! mRNA [Term] id: IGS:0000042 name: processed_transcript def: "A transcript which has undergone processing to remove parts such as introns and transcribed_spacer_regions." [SO:0000233] xref_analog: SO:0000233 is_a: IGS:0000037 ! transcript [Term] id: IGS:0000044 name: enhancer def: "A cis-acting sequence that increases the utilization of (some) eukaryotic promoters\, and can function in either orientation and in any location (upstream or downstream) relative to the promoter." [SO:0000165] xref_analog: SO:0000165 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000045 name: silencer def: "Combination of short DNA sequence elements which suppress the transcription of an adjacent gene or genes." [SO:0000625] xref_analog: SO:0000625 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000046 name: attenuator def: "A sequence segment located between the promoter and a structural gene that causes partial termination of transcription." [SO:0000140] xref_analog: SO:0000140 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000047 name: terminator def: "The sequence of DNA located either at the end of the transcript that causes RNA polymerase to terminate transcription." [SO:0000141] xref_analog: SO:0000141 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000048 name: ncRNA def: "An mRNA sequence that does not encode for a protein rather the RNA molecule is the gene product." [SO:0000655] synonym: "noncoding RNA" [] xref_analog: SO:0000655 is_a: IGS:0000042 ! processed_transcript [Term] id: IGS:0000049 name: tRNA def: "Transfer RNA (tRNA) molecules are approximately 80 nucleotides in length. Their secondary structure includes four short double-helical elements and three loops (D\, anti-codon\, and T loops). Further hydrogen bonds mediate the characteristic L-shaped molecular structure. tRNAs have two regions of fundamental functional importance\: the anti-codon\, which is responsible for specific mRNA codon recognition\, and the 3' end\, to which the tRNA's corresponding amino acid is attached (by aminoacyl-tRNA synthetases). tRNAs cope with the degeneracy of the genetic code in two manners\: having more than one tRNA (with a specific anti-codon) for a particular amino acid; and 'wobble' base-pairing\, i.e. permitting non-standard base-pairing at the 3rd anti-codon position." [SO:0000253] synonym: "transfer RNA" [] xref_analog: SO:0000253 is_a: IGS:0000048 ! ncRNA [Term] id: IGS:0000050 name: rRNA def: "RNA that comprises part of a ribosome\, and that can provide both structural scaffolding and catalytic activity." [SO:0000252] synonym: "ribosomal RNA" [] xref_analog: SO:0000252 is_a: IGS:0000048 ! ncRNA [Term] id: IGS:0000051 name: snoRNA def: "Small nucleolar RNAs (snoRNAs) are involved in the processing and modification of rRNA in the nucleolus. There are two main classes of snoRNAs\: the box C/D class\, and the box H/ACA class. U3 snoRNA is a member of the box C/D class. Indeed\, the box C/D element is a subset of the six short sequence elements found in all U3 snoRNAs\, namely boxes A\, A'\, B\, C\, C'\, and D. The U3 snoRNA secondary structure is characterised by a small 5' domain (with boxes A and A')\, and a larger 3' domain (with boxes B\, C\, C'\, and D)\, the two domains being linked by a single-stranded hinge. Boxes B and C form the B/C motif\, which appears to be exclusive to U3 snoRNAs\, and boxes C' and D form the C'/D motif. The latter is functionally similar to the C/D motifs found in other snoRNAs. The 5' domain and the hinge region act as a pre-rRNA-binding domain. The 3' domain has conserved protein-binding sites. Both the box B/C and box C'/D motifs are sufficient for nuclear retention of U3 snoRNA. The box C'/D motif is also necessary for nucleolar localization\, stability and hypermethylation of U3 snoRNA. Both box B/C and C'/D motifs are involved in specific protein interactions and are necessary for the rRNA processing functions of U3 snoRNA." [SO:0000275] synonym: "small_nucleolar_RNA" [] xref_analog: SO:0000275 is_a: IGS:0000048 ! ncRNA [Term] id: IGS:0000052 name: scRNA def: "Any one of several small cytoplasmic RNA moleculespresent in the cytoplasm and sometimes nucleus of a eukaryote." [SO:0000013] xref_analog: SO:0000013 is_a: IGS:0000048 ! ncRNA [Term] id: IGS:0000056 name: TF_binding_site def: "A region of a molecule that binds to a transcription factor." [SO:0000235] synonym: "Transcription Factor binding site" [] xref_analog: SO:0000235 is_a: IGS:0000036 ! regulatory_region [Term] id: IGS:0000057 name: waiting list is_a: IGS:0000000 ! Sequence_Ontology [Term] id: IGS:0000060 name: codon def: "A set of (usually) three nucleotide bases in a DNA or RNA sequence\, which together signify a unique amino acid or the termination of translation." [SO:0000360] xref_analog: SO:0000360 relationship: part_of IGS:0000040 ! mRNA [Term] id: IGS:0000061 name: polyA_sequence def: "Sequence of about 100 nucleotides of A added to the 3' end of most eukaryotic mRNAs." [SO:0000610] synonym: "3' poly(A) tail" [] synonym: "RNA 3' poly(A) tail" [] synonym: "poly-A tail" [] xref_analog: SO:0000610 relationship: part_of IGS:0000086 ! three_prime_UTR [Term] id: IGS:0000062 name: nc_primary_transcript def: "A primary transcript that is never translated into a protein." [SO:0000483] synonym: "non coding primary transcript" [] synonym: "precursor nc RNA" [] synonym: "precursor noncoding RNA" [] xref_analog: SO:0000483 is_a: IGS:0000038 ! primary_transcript [Term] id: IGS:0000070 name: exon def: "A region of the genome that codes for portion of spliced messenger RNA (SO\:0000234); may contain 5'-untranslated region (SO\:0000204)\, all open reading frames (SO\:0000236) and 3'-untranslated region (SO\:0000205)." [SO:0000147] xref_analog: MeSH:D005091 xref_analog: SO:0000147 relationship: part_of IGS:0000037 ! transcript [Term] id: IGS:0000077 name: coding region DNA synonym: "coding DNA" [] relationship: part_of IGS:0000005 ! gene [Term] id: IGS:0000081 name: E2F is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000082 name: HSE synonym: "heat shock promoter elements" [] is_a: IGS:0000028 ! responsive element [Term] id: IGS:0000083 name: intron def: "A segment of DNA that is transcribed\, but removed from within the transcript by splicing together the sequences (exons) on either side of it." [SO:0000188] xref_analog: SO:0000188 relationship: part_of IGS:0000038 ! primary_transcript [Term] id: IGS:0000084 name: UTR def: "Messenger RNA sequences that are untranslated and lie five prime and three prime to sequences which are translated." [SO:0000203] xref_analog: SO:0000203 relationship: part_of IGS:0000040 ! mRNA [Term] id: IGS:0000085 name: five_prime_UTR def: "A region at the 5' end of a mature transcript (preceding the initiation codon) that is not translated into a protein." [SO:0000204] synonym: "5'UTR" [] xref_analog: SO:0000204 is_a: IGS:0000084 ! UTR [Term] id: IGS:0000086 name: three_prime_UTR def: "A region at the 3' end of a mature transcript (following the stop codon) that is not translated into a protein." [SO:0000205] synonym: "3'UTR" [] xref_analog: SO:0000205 is_a: IGS:0000084 ! UTR [Term] id: IGS:0000087 name: RNApol_II_promoter def: "A DNA sequence in eukaryotic DNA to which RNA polymerase II binds\, to begin transcription." [SO:0000170] xref_analog: SO:0000170 is_a: IGS:0000029 ! promoter [Term] id: IGS:0200005 name: snRNA def: "Small non-coding RNA in the nucleoplasm. A small nuclear RNA molecule involved in pre-mRNA splicing and processing" [SO:0000274] synonym: "small nuclear RNA" [] xref_analog: SO:0000274 is_a: IGS:0000048 ! ncRNA [Term] id: IGS:0200013 name: cap def: "A structure consisting of a 7-methylguanosine in 5'-5' triphosphate linkage with the first nucleotide of an mRNA. It is added post-transcriptionally\, and is not encoded in the DNA." [SO:0000581] synonym: "5'RNA cap" [] synonym: "RNA Caps" [] xref_analog: MeSH:D012315 xref_analog: SO:0000581 relationship: part_of IGS:0000042 ! processed_transcript relationship: part_of IGS:0000085 ! five_prime_UTR [Typedef] id: part_of name: part of