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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctcccccaaaccctaaactaaaccccccctcttccctctcgcattgtcgcgcgcgctactcgcggtttctgaaggtgtggctgctcaccgctgctctcgccgcggttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATC

Basic information

species Oryza sativa
transcript LOC_Os01g11370.1
intron # 1
splice site 3'
intron type U2

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|29625175|gb|CB630186.1|CB630186
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88362444|gb|CI623784.1|CI623784
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTTGGGTATGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCTGGTGTAC
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagG-TTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCC-GGTGTAC
EST: gi|88356674|gb|CI619160.1|CI619160
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88388923|gb|CI592811.1|CI592811
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|58691453|gb|CK080140.1|CK080140
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88312143|gb|CI580308.1|CI580308
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGGGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88411265|gb|CI564386.1|CI564386
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88727156|gb|CI750811.1|CI750811
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88366515|gb|CI610734.1|CI610734
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88730378|gb|CI753991.1|CI753991
EST:     GGCGGCGTCCTCTTCCTGCCCANAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCCAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|29626953|gb|CB631964.1|CB631964
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|29636300|gb|CB641309.1|CB641309
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88441713|gb|CI599618.1|CI599618
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|29624813|gb|CB629824.1|CB629824
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88324258|gb|CI566071.1|CI566071
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88726049|gb|CI749704.1|CI749704
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88693453|gb|CI737028.1|CI737028
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88430331|gb|CI567350.1|CI567350
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
EST: gi|88430530|gb|CI569553.1|CI569553
EST:     GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGG                         GTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA
genomic: GGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAA

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: 71 (upstream exon), 28 (downstream exon)
Score: 4

GGAGGCCGGGGTCGGAGAAGCCGACGGCGGCGATCGTCGAGGACGAGGAGGGCGGCGTCCTCTTCCTGCCCACAAGCACCAGCTCCTCCTCCTCATCCGGgtgctccccc ... ttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcggtttctgaaggtgtggctgctcaccgctgctctcgccgcggttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATC
                     tgctcac  putative branch site (score: 4)
                                                 tttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctcccccaaaccctaaactaaaccccccctcttccctctcgcattgtcgcgcgcgctactcgcggtttctgaaggtgtggctgctcaccgctgctctcgccgcggttggttttagGTTTGGGTACGCGAGCTTGGAGCGGCAGCGGCAGCGGCTGCCGGTGTACAAGTACCGGAAGGCCATCCTCTACCTGGTGGAGCGGCACGCCACGACCATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG