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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCGTCGATCTCCTCGCGACTTTGCCCGCCGCCGCCGCCGCCGCTCTCCATCCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgcccgcacgcgtgcacatcctctctctcatccctctcgttgtacccaacaccccctattttttgttttttttttccctcgaatttgccttaaac...

Basic information

species Oryza sativa
transcript LOC_Os03g29260.1
intron # 1
splice site 5'
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|88402149|gb|CI614992.1|CI614992
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGCAAGCT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAG-AAGCT
EST: gi|58682390|gb|CK071077.1|CK071077
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|3768112|gb|AU032139.1|AU032139
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88402165|gb|CI615008.1|CI615008
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88339571|gb|CI641280.1|CI641280
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88353429|gb|CI631614.1|CI631614
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88363300|gb|CI643158.1|CI643158
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|25799116|gb|CA755077.1|CA755077
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|58600756|gb|CK011284.1|CK011284
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88347074|gb|CI631154.1|CI631154
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88573347|gb|CI664918.1|CI664918
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88395078|gb|CI609394.1|CI609394
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88584537|gb|CI702099.1|CI702099
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88325561|gb|CI675368.1|CI675368
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|86847825|gb|CI288864.1|CI288864
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88347568|gb|CI630524.1|CI630524
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88354486|gb|CI628857.1|CI628857
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTCGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88358923|gb|CI619427.1|CI619427
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGGG                         ATGGGGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|218480642|gb|FG944950.1|FG944950
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|55432415|gb|CV729228.1|CV729228
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88383970|gb|CI631860.1|CI631860
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
EST: gi|88587802|gb|CI705577.1|CI705577
EST:     CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCG                         ATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT
genomic: CCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTT

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: 58 (upstream exon), 75 (downstream exon)
Score: 23

TCGTCGATCTCCTCGCGACTTTGCCCGCCGCCGCCGCCGCCGCTCTCCATCCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgccc ... ttgtgaccagATGGCGATTACTTTGTCCAATGTCAACTCTGAGGCAGGCCTCCAGAAGCTTGATGAGTACCTCCTTACTCGCAGCTACATCAGTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCGTCGATCTCCTCGCGACTTTGCCCGCCGCCGCCGCCGCCGCTCTCCATCCCGCGAGAAGCTCGTCGCCGGCGTCCCGCTGCATCCATCCTCTCCGGCGgtgagcgcccgcacgcgtgcacatcctctctctcatccctctcgttgtacccaacaccccctattttttgttttttttttccctcgaatttgccttaaac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cgcccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccccc