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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATGAGATAGTTCGCAACCTTAGGAAGGTCAAACACCCAGCCTTTGACTCCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccacaacctcttctcttgagttatcttcttcccttcagtcattatacagggtatccagtgtctggcatgtgaacaaacttcattctcatgtcaatgtgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g49770.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g49770.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G122223_T01 (Zea mays), 5'ss of exon 3
---GGATGAGATAGTTCGCAACCTTAGGAAGGTCAAACACCCAGCCTTTGACTCCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccacaacctct-tctcttgagttatcttctt------cccttcagtcattatacagggtatccagtg-tctggcatgtgaacaaacttcattctcatgtcaatgtgttgcag
    || |||||   |||||||||| |||||||||| |||||| ||||    ||||     ||||   |||||||||||||||  |||||||| ||||| ||||||||||   || ||  | |||| |   ||  |         ||  |   |  |  |||   ||   | ||| |   |  |   ||| |   | |||   |   |  |  |||||||
TGACGACGAGATTACTCGCAACCTTCGGAAGGTCAAGCACCCATCCTTCAGTTCCTTA---CGGTTCGCAACAGAAATGGAAAGAAAATGCAGCATTTGCCAAgtatgcccatacttccatttctttaaacatgattccatggaacctctttatgttagtaccctgtggactgtggttcagtcttaaaactagtctaatttata---ctgtacgttgcag
















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|300215681|gb|HO088307.1|HO088307
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGTCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|88519249|gb|CI446903.1|CI446903
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAANCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|29637298|gb|CB642307.1|CB642307
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|86885857|gb|CI295880.1|CI295880
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|88983372|gb|CI028608.1|CI028608
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|163920093|gb|EG709863.1|EG709863
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|88460629|gb|CI534501.1|CI534501
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGANATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|38480914|gb|CF965003.1|CF965003
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGTCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|33801112|gb|CF326429.1|CF326429
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|702896|gb|D49187.1|D49187
EST:     CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|86885038|gb|CI315609.1|CI315609
EST:     CCTCGTTCC-GTATTCAACAGAAATGGAAAAGAAATACAGTATTTTTCAA                         GAAGAGTTTGAAGCCAATTAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
genomic: CCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCTGGATTGCGGCCACAGC
EST: gi|15849993|gb|BI798269.1|BI798269
EST:     CTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCCAA                         GAAGAGTTTGAAGCCAATGAAGAGATGGGGAGGCCTGGATTGCGGTCACA
genomic: CTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGT-CAAgtatgccaca ... tgtgttgcagGAAGAGTTTGAAGCCAATGAAGAGATGGGGAGG-CTGGATTGCGGCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATGAGATAGTTCGCAACCTTAGGAAGGTCAAACACCCAGCCTTTGACTCCTCGTTCCGGTATTCAACAGAAATGGAAAAGAAATGCAGTATTTGTCAAgtatgccacaacctcttctcttgagttatcttcttcccttcagtcattatacagggtatccagtgtctggcatgtgaacaaacttcattctcatgtcaatgtgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA