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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcatttcagaacttgttgtgagtttccattttttttgttcgcaaggttaatatgcttttccttgtgcag

Basic information

species Oryza sativa
transcript LOC_Os03g06620.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06620.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G165998_T03 (Zea mays), 5'ss of exon 3
AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgca------------tttcagaacttgttgtgagtttccattttttttgttcgcaaggttaatatgcttttccttgtgcag-------------------------------
|  |||||||||||||||||||||| ||||||||||| ||||||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||||             |||  | |||||||||    || |  |   ||   | ||||||| ||||    ||      | |||                               
AACTAGGAATATTAAGCTGGCGCCTAAATGCTGATGATTGGGAGAATGATGAGAACCTCAAGAAAATTCGTGAAGCCAGGGGTTACTCTTACATGgtttgctaataagtttatttttgggcacttgttgttttgttactctaccttgagtagcaaggtcaatacctattcaaagattcagactagtatgataagcatttttccttatgtag
















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|33664076|gb|CF295043.1|CF295043
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCANAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88410806|gb|CI578612.1|CI578612
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAAATATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88432267|gb|CI565300.1|CI565300
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88392897|gb|CI614779.1|CI614779
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|58594368|gb|CF992676.1|CF992676
EST:     GAACCTCAAGAAAATCCGTGAGGCCA-GGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: GAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|700773|gb|D47064.1|D47064
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|58591300|gb|CF989608.1|CF989608
EST:     ATGATGAGAACCTCGAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88300984|gb|CI592164.1|CI592164
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|313084041|gb|HO213824.1|HO213824
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|218497580|gb|FG955135.1|FG955135
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCCAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88573345|gb|CI664916.1|CI664916
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|58657720|gb|CK046400.1|CK046400
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|33662546|gb|CF293513.1|CF293513
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|117246064|gb|CT862529.1|CT862529
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|66916156|gb|CX103004.1|CX103004
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88738682|gb|CI762190.1|CI762190
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88423723|gb|CI617075.1|CI617075
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88341716|gb|CI641468.1|CI641468
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88311755|gb|CI574972.1|CI574972
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88728915|gb|CI752425.1|CI752425
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88354257|gb|CI637823.1|CI637823
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88398782|gb|CI601118.1|CI601118
EST:     ATGATGAGAACCTCAACAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88354747|gb|CI614025.1|CI614025
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88337236|gb|CI629526.1|CI629526
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCC
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCC
EST: gi|88719684|gb|CI743194.1|CI743194
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88447697|gb|CI579773.1|CI579773
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|33659100|gb|CF281713.1|CF281713
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88570475|gb|CI661848.1|CI661848
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88371298|gb|CI600146.1|CI600146
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88693640|gb|CI737215.1|CI737215
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTA
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTA
EST: gi|218494503|gb|FG957959.1|FG957959
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCANGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|58587763|gb|CF986071.1|CF986071
EST:     TGATGAGAACCTCAAGAAAATCCGTGAGGCCANGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: TGATGAGAACCTCAAGAAAATCCGTGAGGCCA-GGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88445319|gb|CI587213.1|CI587213
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88575234|gb|CI669379.1|CI669379
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88669169|gb|CI720126.1|CI720126
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGGCAGGGGATACTCTTACATG                         GATATCTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
EST: gi|88730508|gb|CI754121.1|CI754121
EST:     ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATG                         GATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG
genomic: ATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTG

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: 68 (upstream exon), 74 (downstream exon)
Score: 94

AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcattt ... ccttgtgcagGATATTTGTGATGTGTGTCCAGAAAAGCTGCCAAACTATGAGGCTAAGCTGAAAAATTTCTTTGAAGAACACTTGCATACTGATGAAGAGATACGCTATT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTAGGAATATTAAGCTGGCGCCTGAATGCTGATGACTGGGAGAATGATGAGAACCTCAAGAAAATCCGTGAGGCCAGGGGATACTCTTACATGgtttgcatttcagaacttgttgtgagtttccattttttttgttcgcaaggttaatatgcttttccttgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA