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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttgttgcttgtacaagccttcaatctcttcactcttactgtccatttacgcaaaatgaccttagtaaatacttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATCCTTCAAATTTCAAGGTCAATGGCATATACCCAGTTCGGAAGTTATGGGG

Basic information

species Oryza sativa
transcript LOC_Os01g13570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g13570.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G114550_T01 (Zea mays), 3'ss of exon 2
gtatgttgttgcttgtacaagccttcaatctctt-cactcttactgtccatttacgcaaaatgaccttagtaaatacttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATCCTTCAAATTTCAAGGTCAATGGCATATACCCAGTTCGGAAGTTATGGGG
         |  |     ||  |||| |    |  | |  | | |     |||| | ||| ||||| |  || || ||||| | ||||||||||||||||| ||||||| ||| ||||||||| |||| ||||||| ||| |||||||  | |||||||||||||||||  || ||||||| |||||
--------gtaatgaagtaaatcttctaggagtagctcgttcatttcggttttaggaaaattgaccatgttacatgcttggggacagCGGATGCTAAGAAGCAATATCCGGAGCTGTACACCAAATGGAGGGAGGACCCTGCAAATTTTCATGTCAATGGCATATACCCGATTAGGAAGTTGTGGGG
















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|29688716|gb|CB684991.1|CB684991
EST:     TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATG                         CGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
genomic: TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATGgtatgttgtt ... ttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
EST: gi|88214195|gb|CI214044.1|CI214044
EST:     CTTCTTAGAGGGCATGACCAATG                         CGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
genomic: CTTCTTAGAGGGCATGACCAATGgtatgttgtt ... ttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
EST: gi|29688715|gb|CB684990.1|CB684990
EST:     TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATG                         CGGATGCTAAGAAGGAATATCCAGAGTTGTACCCCAGATGGCGGGAGGATC
genomic: TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATGgtatgttgtt ... ttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
EST: gi|29663287|gb|CB659562.1|CB659562
EST:     TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATG                         CGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
genomic: TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATGgtatgttgtt ... ttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
EST: gi|29663288|gb|CB659563.1|CB659563
EST:     TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATG                         CGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC
genomic: TGATTCTTTAAAAGAGGCTCATCTATTCTTCTTAGAGGGCATGACCAATGgtatgttgtt ... ttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcactcttactgtccatttacgcaaaatgaccttagtaaatacttggaggcagCGGATGCTAAGAAGGAATATCCAGAGTTGTACACCAGATGGCGGGAGGATCCTTCAAATTTCAAGGTCAATGGCATATACCCAGTTCGGAAGTTATGGGG
     ctcttac  putative branch site (score: 3)
                                  ttagtaaata  TA-rich tract