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'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatgtagttgttcaaacgttcgatgtgatagggtgtaaaatttttgtgtgggaaccaaacagggccttatttaatttggctgtgcgttattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA

Basic information

species Oryza sativa
transcript LOC_Os02g01010.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G134889_T01 (Zea mays), 3'ss of exon 10
ttatgtagttgttcaaacgttcgatgtga-tagggtgtaaaatttttgtgtgggaaccaaacagggccttat----ttaatttggctgtgcgt-tattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA
      ||    |     |   | | | | | | |     ||  |||| |  ||   |        |  | |    ||  ||||  | ||| | ||   | | ||||| |||||||||||||| || || ||||| ||  |||||||||| |||||||| || |||||||||||||||||  ||||||| | ||| |||  | |  
------agccaatttgtggccaggtattagttgagcaggcaacgtttgggaaggtgtctgctgattcaatgtgttgttggtttgtttttgcttatacctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCGAGAACCG

upper sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G033829_T03 (Zea mays), 3'ss of exon 10
ttatg-tagttgttcaaacgttcgatgtgatagggtgtaaaatttttgtgtgggaaccaaacagggccttatttaatttggctg-tgcgttattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA
   || |  |  ||  | |  | ||||||        |  |||     | |    | ||       | ||||  |  ||| ||| | || | | ||  | || | || ||||||||||| || || ||||| || ||||||| ||| |||||||| || |||||||||||||||||  ||||||| | ||| ||   |    
-agtgcttatcattttacctgttgatgtgtggtatcctgtaatcacattattctcagcagtgctatctttatgaacattgactgattcgatgt-gttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG

upper sequence: LOC_Os02g01010.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G033829_T01 (Zea mays), 3'ss of exon 10
ttatgtagttgt---tcaaacgttcgatgtgatagggtgtaaaatttttgtgtgggaaccaaacagggccttatttaatttggctg-tgcgttattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA
 || ||  || |   |  | |  | ||||||        |  |||     | |    | ||       | ||||  |  ||| ||| | || | | ||  | || | || ||||||||||| || || ||||| || ||||||| ||| |||||||| || |||||||||||||||||  ||||||| | ||| ||   |    
gtaagtgcttatcattttacctgttgatgtgtggtatcctgtaatcacattattctcagcagtgctatctttatgaacattgactgattcgatgt-gttggtagGTCACGTTTGAGGGGGAGCGGACAGTGGTAGATATGTACAGGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCAAGAAGGG

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|88908344|gb|CI090937.1|CI090937
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86893336|gb|CI313437.1|CI313437
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|15849945|gb|BI798221.1|BI798221
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGA-CCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86546649|gb|CI186855.1|CI186855
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88970357|gb|CI383859.1|CI383859
EST:     GTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|89179758|gb|CI044037.1|CI044037
EST:     ATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: ATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88295807|gb|CI532768.1|CI532768
EST:     TTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCNTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: TTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86483506|gb|CI126139.1|CI126139
EST:     CAGCAGGAAAGAAAAGTTTGGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: CAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86871789|gb|CI331166.1|CI331166
EST:     ACGATCCTCTTTTATCCACCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGA-GGGGACCCTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: ACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|15850569|gb|BI798845.1|BI798845
EST:     ATTCCCAACGATGCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: ATTCCCAACGAT-CCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|89193503|gb|CI050801.1|CI050801
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|87034915|gb|CI188718.1|CI188718
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|2797997|gb|AA751291.1|AA751291
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACG-TGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86545063|gb|CI185269.1|CI185269
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86837598|gb|CI345781.1|CI345781
EST:     CCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: CCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88276074|gb|CI396678.1|CI396678
EST:     GTTTTGAGCCT                         ATTACTTTTGA-GGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|29660339|gb|CB656614.1|CB656614
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88269895|gb|CI381193.1|CI381193
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGCGTGGTGGAGATGTACAAGTTTATCAA
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACG-GTGGTGGAGATGTACAAGTTTATCAA
EST: gi|88265825|gb|CI376727.1|CI376727
EST:     AAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGCTGGTGGAGATGTACAAGTTTATCAAG
genomic: AAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86511920|gb|CI154553.1|CI154553
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|89184057|gb|CI046622.1|CI046622
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|89175957|gb|CI042978.1|CI042978
EST:     CCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: CCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86845536|gb|CI346893.1|CI346893
EST:     CAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: CAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|58681044|gb|CK069731.1|CK069731
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86493340|gb|CI135973.1|CI135973
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86509792|gb|CI152425.1|CI152425
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|86536022|gb|CI176228.1|CI176228
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGAGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88839098|gb|CI378022.1|CI378022
EST:     GATTCCCAACGATCCTCTTTTATCCACCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88466414|gb|CI529823.1|CI529823
EST:     TCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: TCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
EST: gi|88250194|gb|CI250471.1|CI250471
EST:     GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCT                         ATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG
genomic: GATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAG

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

CCTGATGGATTCCCAACGATCCTCTTTTATCCAGCAGGAAAGAAAAGTTTTGAGCCTgtaagtgccc ... ttgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtgtgggaaccaaacagggccttatttaatttggctgtgcgttattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA
                        atttaat  putative branch site (score: 87)
                      ttatttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatgtagttgttcaaacgttcgatgtgatagggtgtaaaatttttgtgtgggaaccaaacagggccttatttaatttggctgtgcgttattgtgtgcagATTACTTTTGAGGGGGACCGTACGGTGGTGGAGATGTACAAGTTTATCAAGAAGCACGCTAGCATCCCTTTCAAACTGAAGCGGCCGGATTCGTCAGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - tgtgata
- - - - - - - - - - - - - - - - - - - - - - - - - - gaaccaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggctgt