Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattactcttcattcactgaaccacacatgatagctgcaaggctttcttttttgcattaatttatgcctgtgcatgcattagcctgtttataatttgattcgtcaatttcaacctctcaaataggctaaccgttatgtgttggttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g59730.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59730.1 (Oryza sativa), 3'ss of exon 3
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 3'ss of exon 3
gtaagattactcttcattcactgaaccacacatgatagctgcaaggct--ttcttttttgcattaatttatgcctgtgcatgcattagcctgtttataatttgattcgtcaatttcaacctctcaaataggctaaccgttatgtgttggttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG
             | | |  | |  |   | ||| | | |||   |    | |    || |||     | || |  |||  |||||    ||||  | |    |  | |      |  | |  |  |    ||  ||    ||  |   |   | ||||||| ||||| || |||||||||||||||||||||||||| ||  ||   ||     ||  ||| || |
------------gtaagtggcggtcctcaatatgcttgatgcctagtcaataccggcttccatggggctttggcgctgc--gcatttatttgttgttgagcgcacccattgcccgctgctttcctcac---cttccctccgtgcct---tccctccagACAACGTTGACCTGGGCACTGCCTGCGGCAAGTACTACCGCGTCAGCGTGCTGGCCATCACCGACCCCG
















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|88213116|gb|CI212780.1|CI212780
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88364526|gb|CI644604.1|CI644604
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88736541|gb|CI760049.1|CI760049
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88735499|gb|CI759007.1|CI759007
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|42591806|gb|CK738292.1|CK738292
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88375923|gb|CI528227.1|CI528227
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|58687548|gb|CK076235.1|CK076235
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|3761149|gb|C98397.1|C98397
EST:     TGAGTNCTATGCTACGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCNACCT--CTGCGGCAAGTACTACCGAGTGTGCTG
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGC-A-CTGCCTGCGGCAAGTACTACCGAGTGTGCTG
EST: gi|427564|gb|D23632.1|D23632
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88722313|gb|CI745823.1|CI745823
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88690331|gb|CI734410.1|CI734410
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|287274|gb|D16076.1|D16076
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGG-AAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|58585744|gb|CF984052.1|CF984052
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88457930|gb|CI542112.1|CI542112
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88992338|gb|CI035476.1|CI035476
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCCATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|87004301|gb|CI298833.1|CI298833
EST:     TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: TGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
EST: gi|88365679|gb|CI543160.1|CI543160
EST:     CTTCAATGGAA                         ACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC
genomic: CTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTC

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), 24 (downstream exon)
Score: 6

AAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGGAAgtaagattac ... gttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcgtcaatttcaacctctcaaataggctaaccgttatgtgttggttaattcagACAATGTTGATCTTGGCACTGCCTGCGGCAAGTACTACCGAGTGTGCTGTCTCAGTGTCGTCGATCCTG
       aatttcaa  TA-rich tract