Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag

Basic information

species Oryza sativa
transcript LOC_Os09g32526.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G115757_T02 (Zea mays), 5'ss of exon 4
GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag
|||||||||||||||||||| | ||||||||| |||||||||||||||||||| || |||||||| ||||||||||| ||||||||||||||| ||  |||| | |       ||  |||     |   ||  || |  |||  ||     | | |||  ||| || ||||    | |                     
GGAAAACTTACTGATGGAACGGTTTTTGATTCAAGCTATGAAAGAGGTGACCCGATTGAATTTGAATTGGGCACTGGACAAGTGATCAAAGgtgat--taattggc-------atgtctactctttgtgttggttgtgttatgtttctctgtctgaat--tcctttatctactctatag--------------------

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA16G10750.1 (Glycine max), 5'ss of exon 4
GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag-
|||||||| ||||||||||| | ||| |||||||||| |||||||  | | ||||| ||||||||| | || ||||| ||||||||||||||||    |  ||  |  || |||   || | |  ||||| |  | ||  | ||  ||    | |  ||||   ||   ||| ||   |     | | |   |   ||  
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgta----tgttgtgcataaacaacttctggtt--tcatt-acctataaaagtgactag--ctgctgtgcttgtttacttatttattgaaaatgaaagtaagtagataaa

upper sequence: LOC_Os09g32526.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GLYMA03G21680.1 (Glycine max), 5'ss of exon 4
GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag
|||||||| ||||||||||| | ||| |||||||||| |||||||  | | ||||| ||||||||| | || ||||| |||||||||||||||| |  |     |    | |   ||   | || |  | |  ||| | ||    | ||| |  | | ||| |  ||  | | |    |||| |  |            
GGAAAACTCACTGATGGAACTGTTTTCGATTCTAGCTTTGAAAGAAATAATCCAATTGAATTTGAGCTTGGTACTGGTCAAGTGATCAAAGgta-tgttgtgcataaacaacttcagtctgttaattttctggtttcattacctataaaagtgacta-gctgctgtgcttgtttgcttatttaatgaaaatga------

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|88694794|gb|CI738832.1|CI738832
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88376918|gb|CI639243.1|CI639243
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88733695|gb|CI756872.1|CI756872
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGA
EST: gi|163925746|gb|EG714582.1|EG714582
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|55432912|gb|CV729479.1|CV729479
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88515169|gb|CI442823.1|CI442823
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88827078|gb|CI777643.1|CI777643
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|5004128|gb|AU069277.1|AU069277
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|33687579|gb|CF315818.1|CF315818
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|66928292|gb|CX115140.1|CX115140
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|218484090|gb|FG956007.1|FG956007
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|163927898|gb|EG713510.1|EG713510
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|58678099|gb|CK066786.1|CK066786
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88375448|gb|CI681220.1|CI681220
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGC-ATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88739216|gb|CI762724.1|CI762724
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|58676104|gb|CK064791.1|CK064791
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTAGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|86509969|gb|CI152602.1|CI152602
EST:     TTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: TTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|86903638|gb|CI300492.1|CI300492
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGNCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|38480031|gb|CF964120.1|CF964120
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|33686364|gb|CF314603.1|CF314603
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88347332|gb|CI632617.1|CI632617
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|89168554|gb|CI038908.1|CI038908
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88574137|gb|CI665906.1|CI665906
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|218491364|gb|FG953091.1|FG953091
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|163920086|gb|EG709856.1|EG709856
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|2799478|gb|AA752467.1|AA752467
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|88576196|gb|CI670341.1|CI670341
EST:     AAGAGGTGACCCAATCGAATTTGAGTCGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCAT-CTTGGGCATGTGCGTNGGCGAGAAGAGGAAGCTG
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCT-GGGCATGTGCGTTGGCGAGAAGAGGAAGCTG
EST: gi|88332240|gb|CI643657.1|CI643657
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTNGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
EST: gi|10794952|gb|AU108918.1|AU108918
EST:     AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAG                         GGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA
genomic: AAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaa ... ccatttgtagGGTGGGATCAGGGCATTCTGGGCATGTGCGTTGGCGAGAAGAGGAAGCTGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAAAACTTACTGATGGAACAGATTTTGATTCTAGCTATGAAAGAGGTGACCCAATCGAATTTGAGTTGGGCACTGGCCAAGTGATCAAAGgtaatagtaatggtcccaatcaatagctagctactcatttaattttagtattgtttaaaatttcaatgctccattgtctatctaaaaatttcaatactccatttgtag

- - - - - - - - - - - - - - - - - - - -  AAGAGG