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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatcctctcgatccaatccacctcaaatccccgccgccgctgccgccacctgaaaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG

Basic information

species Oryza sativa
transcript LOC_Os03g61950.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61950.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G351160_T01 (Zea mays), 3'ss of exon 1
---------------------------------gtaatcctctcgatccaatcc--acctcaaatccc-cgccgccgctgccgccacctga-aaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG
                                 |    |  ||||||||  |||    ||  | || | | |  || ||    | |  | | ||||    || ||| ||      |||||||||||||| ||||| | ||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | ||  |  ||||||||||||| |
gtatccatccagctcctcctcctcctcgccgccggcgccgcctcgatcccgtcctggactggagtctcaccctacccctctaacaaagtaacaacctcacgattttgcgatttcgtgcagCGGGCACACTGCGGTTATCATTGGCAAGTCCAAGGTGGTCGTCTTCGGAGGATTCGCCGACAAGCGCTTCCTCGCTGATGTTTCCGTCTACGACGTCG
















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|88389984|gb|CI590497.1|CI590497
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88423266|gb|CI576391.1|CI576391
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88468919|gb|CI696927.1|CI696927
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|117250064|gb|CT843884.1|CT843884
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88593275|gb|CI709438.1|CI709438
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88355627|gb|CI679350.1|CI679350
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88321948|gb|CI673096.1|CI673096
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88443548|gb|CI597015.1|CI597015
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88396872|gb|CI578021.1|CI578021
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88423265|gb|CI576390.1|CI576390
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88406641|gb|CI603835.1|CI603835
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|29686595|gb|CB682870.1|CB682870
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88361530|gb|CI605311.1|CI605311
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88587351|gb|CI705089.1|CI705089
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88352722|gb|CI678743.1|CI678743
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88397430|gb|CI684346.1|CI684346
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88581551|gb|CI698547.1|CI698547
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88585547|gb|CI703189.1|CI703189
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
EST: gi|88316019|gb|CI618895.1|CI618895
EST:     GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAG                         CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG
genomic: GCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGG

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: 51 (upstream exon), 27 (downstream exon)
Score: 2

TCTGAGAGAGAGCAATGACGCCGCAGCTGCAGCCGAAGCAGATGCACTGGGCGAGGGCCGACTCCTCCGACTTCGGAGGCCAAATCCCCGCCCCTCGGAGgtaatcctct ... gcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atccccgccgccgctgccgccacctgaaaccatgtgaattttcgtgcctctgcagCGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG
                                            tgcctct  CT-rich tract
                                  tgaatttt  TA-rich tract