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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggcccgttaattctgttgcaggagatctcgatacctaaggtgctaattctctatctcaatgatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATGTACGCACAACTGCGTGAAGCAGAATCAACAAAGTCCAAGTTGTAATTAC

Basic information

species Oryza sativa
transcript LOC_Os11g04980.2
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 13
--------------------------gtaggcccgttaattctgttgcaggagatctcgatacctaaggtgctaattctctatctcaatgatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATGTACGCACAACTGCGTGAAGCAGAATCAACAAAGTCCAAGTTGTAATTAC
                          | |        |  |    ||| |     ||     |||   |  |    || || |||||||  |  ||||| ||||||| | |||||| ||| ||||||||||||| |||||  |||||||||||||  | ||||| || |||||  || | | ||| |||||||||| | 
gtaggccccccactggcgactctagaggaaatttacaagctgaaatgctgagtggct-atggccttttgcaccccctccct-tctcaatacttgtgcagGTCAAAAGGCAGCAAGCAAAGACATACTTTGCAAAGGAAATTTCAGATATGTACGCGGAGCTGCGGGAGGCAGAGGCACCCAGGTCGAAGTTGTAATGAT

upper sequence: LOC_Os11g04980.2 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 22
--------------------gtaggcccgttaattctgttgcaggagatctcgatacctaaggtgcta----attctctatctcaatgatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATGTACGCACAACTGCGTGAAGCAGAA---TCAACAAAGTCCAAGTTGTAATTAC
                       |      |||  |    ||||      |  |     | | |  ||    ||| |||   |  ||| | || |||||||| ||||| ||||| ||||||||||||||||| | |||  |  | ||||| ||  | ||   |  | | ||    ||  |  ||  |||||||| |    
gcaagtgttcaatttaaaaatctgagaaaataaaaccagagcagacacaataaaatggcaggctcttactgcattatcttctttcatgttcttccagATCAAGAGACCTCAAGCAAAGGCATACTTTGCAAATGCAATATCTAACATGTATGCTGAGCTCTCTACATCCGATCCCTCCCCTCAGAGCAAGTTGTGAA---
















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|33800033|gb|CF325882.1|CF325882
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86893388|gb|CI313463.1|CI313463
EST:     ACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAATCTAAGGCATAC-TTGCAAAAGAAATCGCAGATATG
genomic: ACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29671404|gb|CB667679.1|CB667679
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGCCCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|87009403|gb|CI313876.1|CI313876
EST:     TGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86841792|gb|CI337449.1|CI337449
EST:     AAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: AAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86876180|gb|CI325637.1|CI325637
EST:     AAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: AAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29618419|gb|CB623431.1|CB623431
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86872257|gb|CI323707.1|CI323707
EST:     TAGAAAAT-GTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGGTAAGGCATACTTTGCAAAAGAAATCCCAGATATG
genomic: TAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29679208|gb|CB675483.1|CB675483
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29679210|gb|CB675485.1|CB675485
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29665943|gb|CB662218.1|CB662218
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGTTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88966653|gb|CI365876.1|CI365876
EST:     TAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGTCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|25806438|gb|CA762399.1|CA762399
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|88959624|gb|CI002234.1|CI002234
EST:     GCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: GCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86884655|gb|CI313034.1|CI313034
EST:     CCTTTCACACTAGAAAAT-GTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAGATCGCAGATATG
genomic: CCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29665942|gb|CB662217.1|CB662217
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGTTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|86887216|gb|CI326031.1|CI326031
EST:     TCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29674249|gb|CB670524.1|CB670524
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29670549|gb|CB666824.1|CB666824
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
EST: gi|29622335|gb|CB627346.1|CB627346
EST:     TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAG                         ATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG
genomic: TTGCTGAGCCTTTCACACTAGAAAATGGTCTCCTCACCCCAACATTCAAGgtaggcccgt ... gatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcaggagatctcgatacctaaggtgctaattctctatctcaatgatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATGTACGCACAACTGCGTGAAGCAGAATCAACAAAGTCCAAGTTGTAATTAC
                         tgctaat  putative branch site (score: 2)
                            taattct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggcccgttaattctgttgcaggagatctcgatacctaaggtgctaattctctatctcaatgatgttgcagATCAAAAGACCGCAAGCTAAGGCATACTTTGCAAAAGAAATCGCAGATATGTACGCACAACTGCGTGAAGCAGAATCAACAAAGTCCAAGTTGTAATTAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC