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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcactaacgatgatatccttccttgcttgctagtactagttgatacttgtatcgaacagcagttaactcagcgtcaggcaacttatgttctttcaactgtttctgtcttgcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os03g02590.4
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g02590.4 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G029824_T03 (Zea mays), 3'ss of exon 1
gtcactaacgatgatatccttccttgcttgctagtacta-gttgatacttgtatcgaacagcagttaactcagcgtcaggcaacttatgttctttcaactgtttctgtcttgcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG
                ||  |||    |     || ||  |||  |       ||| ||       | |||| |      |    ||   |    |   || |   |  |   || | |||||||||||||||||||||| |||||||||||| || || || |||||||| || || || ||  ||||||| || 
---------------gtcagtccagattcagatgtgctgtgttcttctccccgtcgtac------cagctcaactgttctcggtgtagaataac-cgcttgatgtcgcatgtaatgtccagTGGGTCAATGATCTGCATGCTCTTATCAGCCCGCCGGCCAAAGGGACTCCGCTCACCCTCGTTCTGCTTGGCAAA
















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|218487592|gb|FG945521.1|FG945521
EST:     ATGTTGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|33662420|gb|CF293387.1|CF293387
EST:     ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|313084054|gb|HO213837.1|HO213837
EST:     ATGTTGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|84117673|gb|CD151440.1|CD151440
EST:     ATGTTGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|86829554|gb|CI286745.1|CI286745
EST:     ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|25798400|gb|CA754361.1|CA754361
EST:     ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
genomic: ATGTCGACAGGTCCACCACCCTTGCTCGCAAAGTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT
EST: gi|58585983|gb|CF984291.1|CF984291
EST:     GTTTTCCGGCTTCTCAAG                         TGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCGGAGGGGACTCCT
genomic: GTTTTCCGGCTTCTCAAGgtcactaacg ... gcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactcagcgtcaggcaacttatgttctttcaactgtttctgtcttgcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG
 agttaac  putative branch site (score: 3)
               aacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcactaacgatgatatccttccttgcttgctagtactagttgatacttgtatcgaacagcagttaactcagcgtcaggcaacttatgttctttcaactgtttctgtcttgcatttgcagTGGGTCAATGATCTGCATGGTCTTATCAGCCCTCCTGCTAAGGGGACTCCTCTTACACTGGTCTTGCTTGGGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC