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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacttgataccataaattgttctgaattgtgtttgaggcacctgattatgtatggaggttctcatcatacttttgtttcctgaaaaaaaactgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGGATTGCCGCATTATGGGCTTCTATAAATCTTGTAGAG

Basic information

species Oryza sativa
transcript LOC_Os01g55570.2
intron # 2
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|55409935|gb|CV722311.1|CV722311
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88573876|gb|CI665645.1|CI665645
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|86903736|gb|CI300590.1|CI300590
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88346141|gb|CI634014.1|CI634014
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88342540|gb|CI637116.1|CI637116
EST:     ACAGTTCAAAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAAACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88574306|gb|CI666075.1|CI666075
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88368616|gb|CI648094.1|CI648094
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|14714366|gb|AU198287.1|AU198287
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88296188|gb|CI667578.1|CI667578
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|88348094|gb|CI637555.1|CI637555
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG
EST: gi|33672558|gb|CF300797.1|CF300797
EST:     ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCG                         TTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGG-
genomic: ACAGTTCAGAACCGTCATCCGGGAGCGTTGTGAAGTATGTCCAGAGTTCGgtgagttttt ... actgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatgtatggaggttctcatcatacttttgtttcctgaaaaaaaactgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGGATTGCCGCATTATGGGCTTCTATAAATCTTGTAGAG
 acctgat  putative branch site (score: 4)
                                      aaaaaaaactgaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacttgataccataaattgttctgaattgtgtttgaggcacctgattatgtatggaggttctcatcatacttttgtttcctgaaaaaaaactgaaacagTTCAGCAGTCCTGAAGACCTCTTTGCTCTAGCTGGTATAGGATTTGCAGGGATTGCCGCATTATGGGCTTCTATAAATCTTGTAGAG

- - - - -accataa
- - - - - - - - - tgttctg
- - - - - - - - - - - - - - - tgtttga
- - - - - - - - - - - - - - - - - - - gcacctg
- - - - - - - - - - - - - - - - - - - - - - - - atgtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa