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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtggctccttcctcgatcgatccttcccccgtcttgttgttcggatagatgtcaccgatccgttgttccatcgtgttcttgatgctgaggtttttgttggtatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGACGATGAGCCTCATCGCGCGGCAGGCGTTCGAGATCGACGAGTACGTCAGG

Basic information

species Oryza sativa
transcript LOC_Os01g62370.1
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|38471950|gb|CF956081.1|CF956081
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88355657|gb|CI628941.1|CI628941
EST:     AGATCCGCTCCGCGCGGCTCGCGCTCACCGCATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AGATCCGCTCCGCGCGGCTCGCGCTCACCG-ATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88352145|gb|CI613796.1|CI613796
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGC
EST: gi|29672128|gb|CB668403.1|CB668403
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|218487431|gb|FG961345.1|FG961345
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88356447|gb|CI652884.1|CI652884
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGG
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGG
EST: gi|58673234|gb|CK061920.1|CK061920
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|86887605|gb|CI294239.1|CI294239
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88573653|gb|CI665422.1|CI665422
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAA
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAA
EST: gi|88400016|gb|CI588320.1|CI588320
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88731779|gb|CI753499.1|CI753499
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|88316220|gb|CI620498.1|CI620498
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGGGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|117233785|gb|CT847729.1|CT847729
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
EST: gi|58678107|gb|CK066794.1|CK066794
EST:     AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCT                         GATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC
genomic: AAGATCCGCTCCGCGCGGCTCGCGCTCACCGATGTTACCCCGACGCAGCTgtgagtggct ... tatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgatccgttgttccatcgtgttcttgatgctgaggtttttgttggtatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGACGATGAGCCTCATCGCGCGGCAGGCGTTCGAGATCGACGAGTACGTCAGG
                     tcttgat  putative branch site (score: 4)
                                   tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtggctccttcctcgatcgatccttcccccgtcttgttgttcggatagatgtcaccgatccgttgttccatcgtgttcttgatgctgaggtttttgttggtatggtccagGATGACGGAGGAGGCGACGAGCGGGGACGCATCGCCGCCGAACGTGAAGACGATGAGCCTCATCGCGCGGCAGGCGTTCGAGATCGACGAGTACGTCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGCCGCCG