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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattttttcagaagaaaaaagaaaaggaaagacttatcgtgagccatgacactagtgtactgcttaccacag

Basic information

species Oryza sativa
transcript LOC_Os11g06760.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G146472_T02 (Zea mays), 5'ss of exon 5
AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattttttcagaagaaaaaagaaaaggaaagacttatcgtgagccatgacactagtgtactgcttaccacag
|||||| | || |||||||||||||  ||  ||||||||||  |||| ||||| ||||| |||||||||||||||||||||||||||||||||| |      | ||       | |       | || |             ||||||    | | ||   |||||
AGAAGGGTTGGAGGTCTTCATCAGAACACTGCTACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagga------cggatattcttatattccttcaaacatg----agattgaaacactaacacatttctgtacacag

upper sequence: LOC_Os11g06760.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G050982_T01 (Zea mays), 5'ss of exon 4
AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattttttcagaagaaaaaagaaaaggaaagacttatcgtgagccatgacactagtgtactgcttaccacag
|||||| | || |||||||||||||  |   | ||||||||  |||| ||||| ||||| |||||||||||||||||||||||||||||||||| || || | | |       | | |     ||| | |            || |||    ||| | |  |||||
AGAAGGGTTGGAGGTCTTCATCAGAACAGTGCCACTGAATCTGTTGATATCACAGACACATGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaaggatattcttatattccttcaaacagaaggagattga-----------aacgctaacacacttccttacacag
















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|88571169|gb|CI662542.1|CI662542
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCG
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCG
EST: gi|218484821|gb|FG946766.1|FG946766
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|56157893|gb|C27653.2|C27653
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTTCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|25799906|gb|CA755867.1|CA755867
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|88305212|gb|CI652932.1|CI652932
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATC
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATC
EST: gi|66916064|gb|CX102912.1|CX102912
EST:     GGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: GGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|13818900|gb|AB060279.1|AB060279
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCTGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|88309325|gb|CI655333.1|CI655333
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCAT
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCAT
EST: gi|29677609|gb|CB673884.1|CB673884
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|86897912|gb|CI289086.1|CI289086
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCG                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
EST: gi|38474027|gb|CF958159.1|CF958159
EST:     TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCC                         CCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA
genomic: TCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattt ... cttaccacagCCTAGAGACCACCCGGCATGTATCAATGATCGCCATAACATTATCCAAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAGGATCGGTGGTCTTCATCAGATTACATCTACTGAATCAATTGACATCACGGACACTTGGGAACCTTTGGAAGAAGGCCTTCTCCCgtaagtattttttcagaagaaaaaagaaaaggaaagacttatcgtgagccatgacactagtgtactgcttaccacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG