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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttacttctcacttctcataaccttgcatgctcttaataagttatgaatcatgtgtatgattcccttattaatctctctttccttgctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG

Basic information

species Oryza sativa
transcript LOC_Os12g04990.3
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 12
-gtttacttctcacttctcata-accttgcatgctcttaataagttatg-aatcatgtgtatgattcccttattaatctctctttccttgctgcacc-agCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG
  ||  ||  ||   ||| |   || | |||   ||| |||     ||  || |     | |  | |  | ||  || | | ||    | |||  || |||||||||||||||||||||| |||||||||   ||||| ||||| || |||||| | || |||||||||||||||||||| ||||||
gtttctctcttctgctctgacccacgtagcaaattctaaatgttcaatccaagcgaaactcttgtgctgtgat-gatttatattggtcttctgtgcccagCTAAGAGGTTTTGAATTTGCTAAAGCTGTTCGGCTTGTCGCTGAGCCATTCACAGTGGACAATGGTCTCCTCACCCCAACATTCAAG

upper sequence: LOC_Os12g04990.1 (Oryza sativa), 3'ss of exon 21
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 21
-----------------------------gtttacttctcacttctcataaccttgcatgctc--ttaataagttatgaatcatgt-gtatgattcccttattaatctctctttccttgctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG
                                 | || |  ||   || ||   |  |  |    |     ||||    |   ||  ||    |||   |||| || | | | | | |    |  ||| | |||||||||||||||||||||||||| ||  | ||   |||||| || ||  | || |||| ||| || || ||||| ||||||
gtaatctatctcatctctcataagaaaagaaacatttttgtctgaacaaaaatgttaaaaccagatcttctagtttcacaatgtgcagttcttttcttctatttattt-tatgtacatttcactgcagTTGAGAGGTTTTGAATTTGCCAAAGCTGTGACTTTGGTGCTTGAACCATTTACCATGGACAATGATCTGCTTACTCCAACATTCAAG
















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|29630787|gb|CB635796.1|CB635796
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|86534809|gb|CI175015.1|CI175015
EST:     TCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: TCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|29625658|gb|CB630669.1|CB630669
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|89185151|gb|CI050885.1|CI050885
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|29622085|gb|CB627096.1|CB627096
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|29626658|gb|CB631669.1|CB631669
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|313081138|gb|HO213724.1|HO213724
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|25806439|gb|CA762400.1|CA762400
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|88273599|gb|CI394005.1|CI394005
EST:     GACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: GACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|89184059|gb|CI046624.1|CI046624
EST:     AGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCCAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: AGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|88907984|gb|CI090580.1|CI090580
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|86477377|gb|CI120010.1|CI120010
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|29665115|gb|CB661390.1|CB661390
EST:     CAAGATCTGCTGTCCTGGGTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|29674288|gb|CB670563.1|CB670563
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|86851191|gb|CI312592.1|CI312592
EST:     CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAG                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CAAGATCTGCTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
EST: gi|86841829|gb|CI337476.1|CI337476
EST:     CTGTCCTGGCTGAGATGGACTCTATT-GAAACGAATCACAC                         CTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC
genomic: CTGTCCTGGCTGAGATGGACTCTATTGGAAAGGAAGCACAGgtttacttct ... gctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttatgaatcatgtgtatgattcccttattaatctctctttccttgctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG
                          tattaat  putative branch site (score: 2)
                    ttcccttattaatctc  CT-rich tract
                         ttattaatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttacttctcacttctcataaccttgcatgctcttaataagttatgaatcatgtgtatgattcccttattaatctctctttccttgctgcaccagCTAAGAGGTTTTGAATTTGCCAAAGCTGTTACCCTTGTTGCTGAACCTTTCACATTAGAAAATGGTCTCCTCACCCCAACTTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC