Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtag

Basic information

species Oryza sativa
transcript LOC_Os04g51630.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G094051_T06 (Zea mays), 5'ss of exon 3
GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttga--ctgtag
|||||||| |||||||| |||||||||||||| ||  |||||||||||||||||||||| ||||| | |||| |||| ||||||||||| ||||| |||| ||      || | |||    ||  |  || | || ||  ||  ||          ||||||| | |||||  | || ||  ||||||||  ||  ||
GAGAAGGAACTGGTGCAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAAGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagt-----ctcaggttcatatgccagtattttacagaggatgaat----------ttgtatgcttatgctg-ttttccatttctgttgaaactacag

upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM5G868433_T02 (Zea mays), 5'ss of exon 3
GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtag
|||||||| ||||| || |||||||||||||| ||  |||||||||||||||||||||| ||||||| |||| |||| |||||| |||| |||||||||| ||   | | |    || |     ||| ||||    || | |  ||||| ||     | | |  |   | | |   ||||                
GAGAAGGAACTGGTACAGCTTAAGCGTGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTATTTGTGATCCGCATCCGTGGgtgagtcgcaagt--gcttatgccagtattatgtagaggaatttgtatgattatgcttgtttttaattccgttgaaactacag---------------

upper sequence: LOC_Os04g51630.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G344279_T01 (Zea mays), 5'ss of exon 3
GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttga--ctgtag
|||||||| |||||||| |||||||| ||||| ||  |||||||||||||||||||||| ||||||| |||| |||| ||||||||||| ||||| |||| ||      || | |||    | |   | | | |     || ||| |||||     ||||| | | |||||  | || ||  ||||||||  || |||
GAGAAGGAACTGGTGCAGCTTAAGCGCGAGGCCCGTTTGAAGGGTGGTTTCTATGTCAGTCCTGAGGCAAAGCTGCTCTTTGTGGTCCGCATCCGGGGgtgagt-----ctcaggttca--tatgccagtatta-----tacagaggatgaat---ttgtaggcttatgctgtt-ttccatttctgttgaaactatag

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|38470057|gb|CF954188.1|CF954188
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|23380534|gb|BU666979.1|BU666979
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|38483035|gb|CF966837.1|CF966837
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|33683621|gb|CF311860.1|CF311860
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58686835|gb|CK075522.1|CK075522
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|88310572|gb|CI659362.1|CI659362
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGAACAGGAAGATTTTGCACCTCTTGCGTCT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|218489137|gb|FG964941.1|FG964941
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|29615310|gb|CB620322.1|CB620322
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|29618049|gb|CB623061.1|CB623061
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58599035|gb|CK009563.1|CK009563
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|7378457|gb|AU088728.1|AU088728
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|29687687|gb|CB683962.1|CB683962
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58596632|gb|CK007160.1|CK007160
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|29687177|gb|CB683452.1|CB683452
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58687026|gb|CK075713.1|CK075713
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|5004133|gb|AU069282.1|AU069282
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|218499248|gb|FG947277.1|FG947277
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|5003988|gb|AU069137.1|AU069137
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|218489781|gb|FG969217.1|FG969217
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|29618047|gb|CB623059.1|CB623059
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|218490697|gb|FG945225.1|FG945225
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|38475830|gb|CF959963.1|CF959963
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58589167|gb|CF987475.1|CF987475
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTGCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGAGCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58693620|gb|CK082307.1|CK082307
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|33679130|gb|CF307369.1|CF307369
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|218485188|gb|FG948603.1|FG948603
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCAAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
EST: gi|58600013|gb|CK010541.1|CK010541
EST:     TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGG                         TATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT
genomic: TTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 58 (downstream exon)
Score: 111

GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaacc ... ttgactgtagTATCAATGCCATGCACCCGAAGACCAGGAAGATTTTGCAGCTCTTGCGTTTGAGGCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAGAAGGAGCTGGTGCAACTTAAGCGTGAGGCTCGGATGAAGGGTGGTTTCTATGTCAGCCCTGAGGAAAAGTTGCTGTTTGTGGTCCGTATCCGTGGgtaaggaaccacttaagttgtattgttataatgtcactgactatagatgatgatctggttgtatgttgatgctaatgttacaaatctgttgactgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT