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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagttaatgtcagagacttacgaatatattgaacagcagcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg...

Basic information

species Oryza sativa
transcript LOC_Os02g40830.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g40830.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G064695_T01 (Zea mays), 5'ss of exon 3
AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagt---taatgtcagagacttacgaatatattgaacagca---gcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg
||||||||||| ||||||||||| ||  ||||||| |||||||| |||||||| |||||||| |||||||||||||| ||||||||||||    | ||| ||| | ||   | || |   |       ||||  |||    | |    |||||    |  |   | |       |      |  | ||| ||||  |  ||     
AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGACTGCAAGGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgtattatatagcaagtacttgaattcattatgtatcgctggcttgctgtgacttgacgaaggaaaacaaactataatagtt-cttcctagaat-----

upper sequence: LOC_Os02g40830.3 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G094614_T01 (Zea mays), 5'ss of exon 3
AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagt---taatgtcagagacttacgaatatattgaacagca---gcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg
||||||||||| ||||||||||| ||  ||||||| |||||||| ||| ||||  ||||||| |||||||||||||| ||||||||||||    | ||| ||| | ||   | || |   |       ||||  |||    |      |||||    |  |   | |       |      |    ||| ||||  |  ||     
AGTCAAATCCTTGCTGGTGGCCGAGGGCTGGGAACTTTCAAAAGCGGATTGCAAAGTGGTGTCCATATTGTTAAGGCTGAGGAAGCTGAATTGATTGCAAgtaagtgtgtattatatagcaagtacttgaattcattatgtattgctggcttgctgtgacttgacgaaggaaaacaaactataacagtt-cttcctagaat-----

upper sequence: LOC_Os02g40830.3 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagttaatgtcagagacttacgaatatattgaacagcagcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg-
|| ||||| || || ||||| || || |||||||||||||||||||| ||  ||||||| ||||| ||||||||| | ||  | | |||    || || ||||  |   | |||     |  |   | | ||         |  ||      | | |||     | || |||  |||  | |   ||   ||| ||| || 
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagctttgtttcctttgaatctcttttatcatg-taaaggt

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|163928461|gb|EG715441.1|EG715441
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|66913068|gb|CX099916.1|CX099916
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88426486|gb|CI576728.1|CI576728
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAA
EST: gi|58681651|gb|CK070338.1|CK070338
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88361440|gb|CI605221.1|CI605221
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|55434355|gb|CV730299.1|CV730299
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|58668786|gb|CK057472.1|CK057472
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         GAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88363539|gb|CI618100.1|CI618100
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         G
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcag-
EST: gi|88363539|gb|CI618100.1|CI618100
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         G
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcag-
EST: gi|29662328|gb|CB658603.1|CB658603
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|58588874|gb|CF987182.1|CF987182
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|4714828|gb|AU055945.1|AU055945
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88301023|gb|CI592203.1|CI592203
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTT
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTT
EST: gi|29662110|gb|CB658385.1|CB658385
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|38478366|gb|CF962499.1|CF962499
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAAGAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|58684186|gb|CK072873.1|CK072873
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|58588447|gb|CF986755.1|CF986755
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|33688588|gb|CF316827.1|CF316827
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGG
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGG-
EST: gi|58594936|gb|CF993244.1|CF993244
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88391665|gb|CI600854.1|CI600854
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCC
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCC
EST: gi|88730444|gb|CI754057.1|CI754057
EST:     GGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|4880970|gb|AU065269.1|AU065269
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGNCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: -CAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|58592643|gb|CF990951.1|CF990951
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|33794775|gb|CF323267.1|CF323267
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88370572|gb|CI590150.1|CI590150
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTG
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTG
EST: gi|88315087|gb|CI610146.1|CI610146
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACA
EST: gi|27577186|gb|CA999880.1|CA999880
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGA
EST: gi|88356838|gb|CI619324.1|CI619324
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATT-TGGTAACAAAAGAAAGTGGTCCA
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCA
EST: gi|88397989|gb|CI585492.1|CI585492
EST:     GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAG                         CAAAAATGCTTGGCCAGATTCTG
genomic: GCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTG

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: 70 (upstream exon), 69 (downstream exon)
Score: 84

AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagtta ... tcctctgcagCAAAAATGCTTGGCCAGATTCTGGTAACAAAACAAACTGGTCCACAGGGGAAGATTGTGAGCAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTCAAATCCTGGCTGGTGGCCGTGGATTGGGAACATTCAAAAGTGGACTGCAGGGTGGTGTTCATATTGTTAAGGCAGAGGAAGCTGAAAGCCTCGCAGgtacgagttaatgtcagagacttacgaatatattgaacagcagcttgacaagtttctcccagtatgtgcttcagttgtttgttgcttcagatgataatgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA