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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgcgcatccccttcctcatccctctccacccacgccttctctctacgcggctatgccttaacccttagcttctccttctagatctagaagttg...

Basic information

species Oryza sativa
transcript LOC_Os08g36994.1
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|88402908|gb|CI568682.1|CI568682
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88393317|gb|CI618205.1|CI618205
EST:     NNNNCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|58612036|gb|CK039748.1|CK039748
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88441824|gb|CI597113.1|CI597113
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACGATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88453289|gb|CI565731.1|CI565731
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88420765|gb|CI564601.1|CI564601
EST:     GCGGGCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88315677|gb|CI615549.1|CI615549
EST:     GCGGCCGGGGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|117227378|gb|CT846566.1|CT846566
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCC-----G-------                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|86849717|gb|CI301619.1|CI301619
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
EST: gi|88298796|gb|CI565993.1|CI565993
EST:     GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCC                         ATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG
genomic: GCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAG

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: 45 (upstream exon), 51 (downstream exon)
Score: 3

AGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgc ... gttattgcagATTTGCAGGCCAAAGGCCTGATACAATTACCAAACAGAGGCTGTTTTGAAGACACTATAGTTAGGGGCTTAGAGTAACCTGGTTACAGATAATGTCTGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGACGATCTCCTCCGCCGAGCAGCGCCGATCTCCCCTCCCGCGAGCAGCGGCGGCCGGCGACCTGCTGCTTCTGCCGAATTCTCTCCGGTGAGCATCCCCgtacgtacgcgcatccccttcctcatccctctccacccacgccttctctctacgcggctatgccttaacccttagcttctccttctagatctagaagttg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccccttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccttc