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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgttactactttccatccatctttcttccttgcttgcttgtttgttttcaaccctagtttcgcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGGGTTCCAAGAAGAAGGAGAAGAAAAGGCAAGACCGAGAGGCCCAGCGTCA

Basic information

species Oryza sativa
transcript LOC_Os07g01320.1
intron # 2
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|88766005|gb|CI775095.1|CI775095
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|58597244|gb|CK007772.1|CK007772
EST:     GAGGCCGGTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|88742256|gb|CI765764.1|CI765764
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|88743875|gb|CI765385.1|CI765385
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|66917239|gb|CX104087.1|CX104087
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|12404832|gb|AU166433.1|AU166433
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|88333113|gb|CI640956.1|CI640956
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
EST: gi|218488561|gb|FG963885.1|FG963885
EST:     GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATG                         TCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG
genomic: GAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGG

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: 37 (upstream exon), 57 (downstream exon)
Score: 24

GTGCTCCGCGGCGGTCCCGCTCCCGGTCCGGCGGCGCGCCGCATGCGCCGGAGGCCGCTCTCCACTTCGGCTGACGCTTCCACCAGCCGCGACCGCGATGgtactgttac ... gcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGGGTTCCAAGAAGAAGGAGAAGAAAAGGCAAGACCGAGAGGCCCAGCGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatctttcttccttgcttgcttgtttgttttcaaccctagtttcgcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGGGTTCCAAGAAGAAGGAGAAGAAAAGGCAAGACCGAGAGGCCCAGCGTCA
                        tttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgttactactttccatccatctttcttccttgcttgcttgtttgttttcaaccctagtttcgcatctgcagTCGACGACGCTGACAGTGACCTAGAGGAGGAGATCCAGGATGTCCCCAGGGGTTCCAAGAAGAAGGAGAAGAAAAGGCAAGACCGAGAGGCCCAGCGTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG