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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatatcaaattagctgtaatattgcatttccatctcatgtaacatcctgtaaattattgactaatttaattggcatgatgcttttccatttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAGATTGACGTAGATGGAGGGAAAAGCAGAGTG

Basic information

species Oryza sativa
transcript LOC_Os01g51700.1
intron # 4
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|88240343|gb|CI239505.1|CI239505
EST:     ATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
EST: gi|58693252|gb|CK081939.1|CK081939
EST:     ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
EST: gi|58598437|gb|CK008965.1|CK008965
EST:     ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTC
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTC
EST: gi|163925455|gb|EG711568.1|EG711568
EST:     ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
EST: gi|87035544|gb|CI190166.1|CI190166
EST:     ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCNAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
EST: gi|27576487|gb|CA999181.1|CA999181
EST:     ACAGGTCATTTGACACTCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
EST: gi|87035485|gb|CI190107.1|CI190107
EST:     ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAA                         GCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG
genomic: ACAGGTCATTTGACACGCTCAACACATGGCATGATGAGTTCCTCAACCAAgtaagttatt ... ttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctgtaaattattgactaatttaattggcatgatgcttttccatttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAGATTGACGTAGATGGAGGGAAAAGCAGAGTG
                                  tgcttttccatttcct  CT-rich tract
     taaattattgactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatatcaaattagctgtaatattgcatttccatctcatgtaacatcctgtaaattattgactaatttaattggcatgatgcttttccatttccttttagGCTAGCCCATCAGATCCCAAAACTTTTCCATTCATCTTACTTGGGAACAAGATTGACGTAGATGGAGGGAAAAGCAGAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG