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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacaactttgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

Basic information

species Oryza sativa
transcript LOC_Os03g11570.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM5G868757_T02 (Zea mays), 3'ss of exon 1
gtacaactttgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
          |  || |  || |  |  |     | |||| |    || ||||| |||      ||| | |    |  |    ||||| ||  || ||| | || ||||| |||||||| |||||||||||||| || ||||| ||||||||||| |||||||| ||||||| ||||||||||||||||||||||
----------gtaacct--ttgtggaatctttttctaatgccacctccattttctttt------tctga-catgttacttgccttcat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCGGACTAAGCTTTCAATCAGTGACGTGGAATGTCTTCTTATGAAGAGCCTCTCG

upper sequence: LOC_Os03g11570.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G083076_T03 (Zea mays), 3'ss of exon 5
gtacaactt-tgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
|||  | || ||  |  | |||||||           ||||||    || ||||| |||     |  |   |    | ||  | || || ||  || ||| | || ||||| |||||||| |||||||||||||| || ||||  ||||||||||| |||||||||||||| ||||| ||||||||||||||||||
gtaacatttgtggaatcttcttttct-----------aatgtcacctccattttctttt-----tctttgacatgttatttgtctttat-tttcagTCGGCCATCTGAAGATAGAACTATTCCATTAAGTGTTATTGCTGAGCAGACTAAGCTTTCAATCAGTGATGTGGAGTATCTCCTTATGAAGAGCCTCTCG
















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|86892494|gb|CI311963.1|CI311963
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTTATCCCATTAAGTGTTATAGCCGAGCGCA
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAAC-TATCCCATTAAGTGTTATAGCCGAGCGCA
EST: gi|88828563|gb|CI073433.1|CI073433
EST:     GGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: GGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|86479673|gb|CI122306.1|CI122306
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|86888615|gb|CI305683.1|CI305683
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|88841830|gb|CI081086.1|CI081086
EST:     GCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTNATAGCCGAGCGCAC
genomic: GCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|29673014|gb|CB669289.1|CB669289
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|86503584|gb|CI146217.1|CI146217
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|88490342|gb|CI427614.1|CI427614
EST:     AACTGGTAGAGAAGATCNACATTCTATGTTTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|396941592|gb|HO188249.1|HO188249
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAAAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|40492914|gb|BX900508.1|BX900508
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAAAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|88674097|gb|CI728210.1|CI728210
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|89166556|gb|CI103842.1|CI103842
EST:     TGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: TGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|88675197|gb|CI729310.1|CI729310
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|88672110|gb|CI726226.1|CI726226
EST:     AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: AAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
EST: gi|94362995|gb|CI053156.1|CI053156
EST:     ACATTCTATGTCTGATGGAGATAATCTTTAG                         CCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC
genomic: ACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCAC

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), 74 (downstream exon)
Score: 44

TCCACAATGCTGCTCTCAGTGCTCAGCCAGCTTTGGTGCAGAATGAACGGAAACTGCTAGAGAAGATCAACATTCTATGTCTGATGGAGATAATCTTTAGgtacaacttt ... catgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG
                              ccctgtgttctttttc  CT-rich tract
                                     ttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacaactttgctacttgcttttctatgccaccacaaatgtcttgccccttttcctttattccttctaagccctgtgttctttttcatgttgtagCCGGGCGTCAGAAGACAGAACTATCCCATTAAGTGTTATAGCCGAGCGCACTAAGCTTTCTATCAGTGATGTGGAATATCTTCTTATGAAGAGCCTCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA