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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgagtttcacttgtgttctctcttatgcgctcctctgcttaccttacccctgtgctctcctctgcttaccttacctctgtgctcagcttgtagctcatgatacctccttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTTCGCAAAGAAATCTGAACCTCCCTCTGAACCTCCAAGTAACAAGAAAATG

Basic information

species Oryza sativa
transcript LOC_Os07g32400.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g32400.1 (Oryza sativa), 3'ss of exon 18
lower sequence: GRMZM2G027756_T01 (Zea mays), 3'ss of exon 18
gtctgagtttcacttgtgttctctcttatgcgctcctctgcttaccttacccctgtgc-tctcctctgcttaccttacctctgtgctcagcttgtagctcatgatacctccttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTTCGCAAAGAAATCTGAACCTCCCTCTGAACCTCCAAGTAACAAGAAAATG
              || |  |     ||||| |||     |||||  ||      | |  ||  |    ||| || |||||          |  | |||||   ||||| |      ||||||| ||||| |||||  ||||| ||||||| ||||||||||  ||| ||||| | ||| || |||||||||||||||||    || |  |||||||  | 
-------------gtgcgaccatcactatgctctcacgatcttacgatagagagattcaccttgtgcagttatctcacctca---------tgatggctcacattaccttccc----gcagCTCAAAGGATTCCTCATTGCAAGGTCTTCAGGAGACGGCGATGTCAATTTTCACTAAGGAACCTGAACCTCCCTCTGAAAAAGCAGGCGACAAGAAGTTA
















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|88273108|gb|CI388564.1|CI388564
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|86844981|gb|CI340969.1|CI340969
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|87020794|gb|CI269511.1|CI269511
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|33678909|gb|CF307148.1|CF307148
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGTTAGGGAG                         CTCGAAGGAGTCCTCGCTGC
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGC
EST: gi|87032664|gb|CI270299.1|CI270299
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|88228909|gb|CI226760.1|CI226760
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|88997813|gb|CI390351.1|CI390351
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|29661925|gb|CB658200.1|CB658200
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|86820988|gb|CI357680.1|CI357680
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|87038070|gb|CI190694.1|CI190694
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|86528838|gb|CI169044.1|CI169044
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|88236841|gb|CI234692.1|CI234692
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
EST: gi|88290287|gb|CI550509.1|CI550509
EST:     CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAG                         CTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT
genomic: CCTGGATCTTGTGAGGTGCTGATTGGCAGAATGCTCCATCGGCTAGGGAGgtctgagttt ... ttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcttaccttacctctgtgctcagcttgtagctcatgatacctccttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTTCGCAAAGAAATCTGAACCTCCCTCTGAACCTCCAAGTAACAAGAAAATG
                                        cctccttgttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgagtttcacttgtgttctctcttatgcgctcctctgcttaccttacccctgtgctctcctctgcttaccttacctctgtgctcagcttgtagctcatgatacctccttgtttgcagCTCGAAGGAGTCCTCGCTGCAAAGTCTTCAAGAGACGGCGACATCAGTTTTCGCAAAGAAATCTGAACCTCCCTCTGAACCTCCAAGTAACAAGAAAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA