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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcctgcatgtttctgagctcatcgatcacttgatatgtagtagtagcattgtgctgtggttcactgctcacatgattcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTGCCATCGGTAGCCGAGATGCTAGGAAGAACTCCGGCTCAGGTTGCTCTGC

Basic information

species Oryza sativa
transcript LOC_Os01g62880.1
intron # 5
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|86424033|gb|CI062794.1|CI062794
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAG-GGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|86497899|gb|CI140532.1|CI140532
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|58688119|gb|CK076806.1|CK076806
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|88486762|gb|CI424033.1|CI424033
EST:     CAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: CAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|86495195|gb|CI137828.1|CI137828
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|9865213|gb|AU100963.1|AU100963
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|88250236|gb|CI348466.1|CI348466
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|86862765|gb|CI331649.1|CI331649
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|88441514|gb|CI554738.1|CI554738
EST:     GGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: GGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|86595317|gb|CI262555.1|CI262555
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|88269472|gb|CI380770.1|CI380770
EST:     AAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|88257105|gb|CI359493.1|CI359493
EST:     GCGAAGCTCAGAGCGTTCTCCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: GCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|33689716|gb|CF317955.1|CF317955
EST:     AAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
EST: gi|87025584|gb|CI254630.1|CI254630
EST:     AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCT                         GCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG
genomic: AGCAGGCGAAGCTCAGAGCGTTCTGCCACACCAGTGGCGTTCATCTCTCTgtaagtcctg ... attcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgatatgtagtagtagcattgtgctgtggttcactgctcacatgattcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTGCCATCGGTAGCCGAGATGCTAGGAAGAACTCCGGCTCAGGTTGCTCTGC
                                   tgctcac  putative branch site (score: 2)
 ttcttgc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcctgcatgtttctgagctcatcgatcacttgatatgtagtagtagcattgtgctgtggttcactgctcacatgattcttgcagGCGTATGCTCCATTGGGCAGGATGAAGGGCATCGCCGTTGATTCGGTGTTGCCATCGGTAGCCGAGATGCTAGGAAGAACTCCGGCTCAGGTTGCTCTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC