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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaggcaaggaattgtatacgatgcatggtgttactaagtttacatcaagcaccacatgcgataagtttctctctcttttcttttccttggttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGCTCTTCAATTGGGGCTTATATTGCAATCCATGTGCTCAAAGCAAAACCAC

Basic information

species Oryza sativa
transcript LOC_Os04g59550.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G127591_T03 (Zea mays), 3'ss of exon 2
gaaggcaaggaattgtatacgatgcatggtgttactaagtttaca--tcaagcaccacatgcgataagtttctctctcttttcttttccttggttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGCTCTTCAATTGGGGCTTATATTGCAATCCATGTGCTCAAAGCAAAACCAC
|| |  |   | |  | | | || |||  | |   |    | |    |||||  ||     |  |   | |   |   |    |  ||  |  |   || |||| ||||||||||| || ||||| || ||||| || ||||||||||| |||||||| ||||| ||||| |||||||||||||| ||||| || ||||| |
gaggttacctactcatctcccat-catcttatgggtggtgtcaagactcaagagccgtgcccttttgatataa-taagtaagttgctctctcttctctgcagAAACTGGATTTCAAGTTCCCTCTCACCGTGTCCTGCGTCCACTTCATCTGCTCTTCCATTGGAGCTTACATTGCAATCCATGTCCTCAAGGCGAAACCCC

upper sequence: LOC_Os04g59550.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv18s0001g02970.t01 (Vitis vinifera), 3'ss of exon 1
gaaggcaaggaattgtatacgatgcatggtgttactaagtttacatcaa-gcaccac-atgcgataagtttctctctcttttcttttccttggttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGCTCTTCAATTGGGGCTTATATTGCAATCCATGTGCTCAAAGCAAAACCAC
      |||||||||| |        |  | |   | | | | ||| |  |||     |||   | | |||||     | |    |   ||   | ||| |||| ||||||||||||||||||||| | ||||| ||| | ||||||||||||||| | ||||| || ||| | | |||| | || || ||    || ||||
tggaaaaaggaattgtttggtccctttcatttgtttcattgttcatgactgcatggttatgatctgaatttctgggaatctgaagtaattt--cttgtgcagAAACTGGATTTCAAATTTCCTCTGTCAGTGTCATGTATTCACTTCATATGCTCTGCTATTGGAGCCTATCTAGTAATCAAGGTACTGAAGCTTAAGCCAC
















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|33801646|gb|CF326695.1|CF326695
EST:     ATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: ATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|29660579|gb|CB656854.1|CB656854
EST:     GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|33674856|gb|CF303095.1|CF303095
EST:     GTCACCGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: GTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|218483001|gb|FG956129.1|FG956129
EST:     GGT-GGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|58679490|gb|CK068177.1|CK068177
EST:     CGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: CGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|58675642|gb|CK064329.1|CK064329
EST:     GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
EST: gi|58687093|gb|CK075780.1|CK075780
EST:     GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAG                         AAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC
genomic: GGTGGGGCTTCAACGTCACCGTCATCATCATCAACAAGTGGATCTTCCAGgtccagattt ... gttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaagcaccacatgcgataagtttctctctcttttcttttccttggttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGCTCTTCAATTGGGGCTTATATTGCAATCCATGTGCTCAAAGCAAAACCAC
                     tttctctctcttttct  CT-rich tract
                               ttttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaggcaaggaattgtatacgatgcatggtgttactaagtttacatcaagcaccacatgcgataagtttctctctcttttcttttccttggttggtgtagAAGCTGGATTTCAAATTTCCTCTGACGGTGTCTTGTGTCCACTTCATATGCTCTTCAATTGGGGCTTATATTGCAATCCATGTGCTCAAAGCAAAACCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA