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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataacaacaccctcctgttgttgttttcttttttttttttgcggggacaccttcctgttgttgttagtattgcatacatcaaaacatttatctcatgcttgttcggtggcctcaataatcctcctgtacag

Basic information

species Oryza sativa
transcript LOC_Os05g24550.4
intron # 4
splice site 5'
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|29688861|gb|CB685136.1|CB685136
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|27578059|gb|CB000754.1|CB000754
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|29680417|gb|CB676692.1|CB676692
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|29686789|gb|CB683064.1|CB683064
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|33798896|gb|CF325305.1|CF325305
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|58693640|gb|CK082327.1|CK082327
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|33806214|gb|CF328987.1|CF328987
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|88400733|gb|CI596154.1|CI596154
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACAC-GCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|58593972|gb|CF992280.1|CF992280
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGT
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGT
EST: gi|29640250|gb|CB645259.1|CB645259
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|66923450|gb|CX110298.1|CX110298
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|88351318|gb|CI627334.1|CI627334
EST:     CCAATGGTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACAT
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACAT
EST: gi|29656220|gb|CB652495.1|CB652495
EST:     CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTGAAGCCAACACCGCATAGTGTG
EST: gi|58593525|gb|CF991833.1|CF991833
EST:     CCAATGCTGGCTGGACGGATGCACGGAATCCATACTTTGCAAACTATACT                         ACTGCGCAATTCAAACATATCCTTGGAGTG
genomic: CCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataaca ... tcctgtacagACTGCGCAATTCAAACATATCCTTGGAGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACGACATCATAAAGGCAATCAACAAGCATCCCAATGCTGGCTGGACGGCTGCACGGAATCCATACTTTGCAAACTATACTgtaaataacaacaccctcctgttgttgttttcttttttttttttgcggggacaccttcctgttgttgttagtattgcatacatcaaaacatttatctcatgcttgttcggtggcctcaataatcctcctgtacag

- - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - GCTGGA