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'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acaccctttctcagacactaaaccaagtgcttcttagggctggattttaaccccaatgatttggtactgacattttctggaaatgcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG

Basic information

species Oryza sativa
transcript LOC_Os01g43540.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G149704_T02 (Zea mays), 3'ss of exon 4
acaccctttctcagacactaaaccaagtgcttcttagggctggattttaaccccaatgatttggtactgacattttctggaaat----------gcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG
            ||     ||   || |||||||        ||  ||||   |||  ||  | | ||  | ||||    || |            |  | ||| |||||||| |||| |||||||||||| |||||||| ||  | ||||| | ||| ||||||||||||||||| | ||| ||  ||||||||||||| || |||
----------caaggaggaaagaaaaatgcttctctcttactgaaattaatgtcaagcatgagttgctagctttttgctaaagttttctcctaaataatttgtgatgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTCCTCACAATATATGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGATCAGATG

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G105019_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------------------------------acaccctttctcag-aca------ctaaaccaagtgcttcttagggctggattttaaccccaatgatttggtactgacattttctggaaatgcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG
                                                                         ||| |||| ||| |||       | |   |   || | ||     |      | ||      | |||  | || |  ||||||   ||  ||  | ||| |||||||| |||| |||||||||||| |||||||| ||| ||||||| ||||| ||||||||||||||||| | ||| ||  |||||||||||||||| |||
gtaactcctgtaaattcctagaactctttgaaccacctagcttggattgaatgctgtgtaatcaaaccactttaccttttcccagtacagatttgtttactgataagcatattctaattcaggcatgacttgctagtttttttgctaaatttttctcttaa-acaatttgtgctgcagGCATGACTACTACAACAGTGCCACAGAAGTGGTACTGACAATATTTGCTAAGGGTGTTCCTGCTGATAGTGTAGTCATTGATTTTGGTGAACAGATG

upper sequence: LOC_Os01g43540.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv16s0050g01510.t01 (Vitis vinifera), 3'ss of exon 4
--------------------------------------------------------------------------------acaccctttctcagacactaaaccaagtgcttcttagggctg-gattttaac--cccaatgatttggt--actgacattttctgga------aatgcacctggtgt-tgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG
                                                                                  |  |||  |   |   |           |   || |  ||  |||| |      || | ||   ||  | |  || ||||  ||      |||| |     | | |||||||| || |  ||| | |   |   |||||| ||  | || || |||||||| || || || | ||| |||||||||||||| |||||||||||||| 
gtatggttacacttgcttgtctgtgccatttgtttggtacatagacaagagagtaacattattttgtatatatatactttctagtcttctttcaaggttgcctaggagattgtatatgtttgcaatttcagtgattcattaatactgtccattagcagtttcatgatcattaaatgtataacatatgtgcagGCATGAATATTACCAGAAACCACAAGAAGTGGTTGTCACCATATTTGCAAAAGGCGTACCAGATGAAAATGTTGTTGTTGACTTTGGTGAACAAATA

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|87008059|gb|CI297037.1|CI297037
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29661448|gb|CB657723.1|CB657723
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|58662717|gb|CK051403.1|CK051403
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|58593415|gb|CF991723.1|CF991723
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29660562|gb|CB656837.1|CB656837
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29625917|gb|CB630928.1|CB630928
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|33797195|gb|CF324461.1|CF324461
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|27578357|gb|CB001052.1|CB001052
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29660561|gb|CB656836.1|CB656836
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|163920381|gb|EG714468.1|EG714468
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|33686913|gb|CF315152.1|CF315152
EST:     GCGAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|58594119|gb|CF992427.1|CF992427
EST:     CAAACATGGATNATACACCACCAATGGTAGAAGTGAAGCGCGAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: CAAACATGGATAATACACCACCAATGGTAGAAGTGAAGC-CAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|218487981|gb|FG959844.1|FG959844
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29659289|gb|CB655564.1|CB655564
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29669129|gb|CB665404.1|CB665404
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|29658976|gb|CB655251.1|CB655251
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
EST: gi|33678214|gb|CF306453.1|CF306453
EST:     GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAG                         GCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA
genomic: GCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAA

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: 74 (upstream exon), 75 (downstream exon)
Score: 87

GAGCAGCTGCCCCCTCTGTTGCTTCTTTTGTTGAGGAAAAGGATGATGCTGCAAACATGGATAATACACCACCAATGGTAGAAGTGAAGCCAAAATACAGgtaaccagtt ... ggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaccccaatgatttggtactgacattttctggaaatgcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG
                   tactgac  putative branch site (score: 87)
         aatgattt  TA-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acaccctttctcagacactaaaccaagtgcttcttagggctggattttaaccccaatgatttggtactgacattttctggaaatgcacctggtgttgcagGCACGACTTCTACAACAGTGCTACAGAAGTTGTATTGACAATTTTTGCAAAGGGTGTTCCTGCTGAGAATGTTGTTGTTGATTTTGGTGAACAAATG

- - - - - - - - - -aaaccaa
- - - - - - - - - - - - - -tgcttct
- - - - - - - - - - - - - - - - - - - gctggat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggtactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgcac