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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggcggcgctgcccttcccccttgttcttcttccttgcatctgcttccctcccgttttgcttctaattgtatttctctttcgtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC

Basic information

species Oryza sativa
transcript LOC_Os07g12650.2
intron # 1
splice site 3'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|66914528|gb|CX101376.1|CX101376
EST:     GCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: GCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|6727454|gb|AU082119.1|AU082119
EST:     CGCCGCCGCCGNTTTCCCAAG                         ATCCCTCCNGTCGTCGTCGCCTGTCGGGCCCNTCGGGTCTTTCCTAGCGCA
genomic: CGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCG-CTGTC-GGCCCCTCGGGTCTTT-CTAGCGCA
EST: gi|88722319|gb|CI745829.1|CI745829
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|13806613|gb|AU181586.1|AU181586
EST:     CTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88358899|gb|CI619403.1|CI619403
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|396941191|gb|HO188400.1|HO188400
EST:     CGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCCAAG                         ATCCCTCCCGTCGTCGTCGCAGTCGGCTCCTCGGGTCTTTCGAGTGCAGG
genomic: CGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCT-CCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGG
EST: gi|88357562|gb|CI623616.1|CI623616
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88332492|gb|CI651652.1|CI651652
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|10423675|gb|AU108196.1|AU108196
EST:     CCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|88339791|gb|CI649048.1|CI649048
EST:     TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: TCGCGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|218485304|gb|FG956287.1|FG956287
EST:     CCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
EST: gi|427734|gb|D23869.1|D23869
EST:     CGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAG                         ATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA
genomic: CGAAAACCCTAACCCTCCTCCTCCTCCGCCGCCGCCGCTCTCCCAAGgtggcggcgc ... gtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatctgcttccctcccgttttgcttctaattgtatttctctttcgtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC
                        ttctaat  putative branch site (score: 2)
                              ttgtatttctctttcg  CT-rich tract
                        ttctaattgtattt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtggcggcgctgcccttcccccttgttcttcttccttgcatctgcttccctcccgttttgcttctaattgtatttctctttcgtttccgcagATCCCTCCCGTCGTCGTCGCTGTCGGCCCCTCGGGTCTTTCTAGCGCAGGAGACATGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA