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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcacacgcacatcctctttctcatctcttcgccttaaccttagtactagaaacaaacaacagtctgttttcacctgaaaatagtttagggcgagtgaggtgaggtgttcttcttatcgagtttcatctccatgttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATCTTTGACCATAATGGCTGTAGCTTCTGCCAGTGCACTGTTTTCCGCCAAG

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
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|88329338|gb|CI653252.1|CI653252
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88576463|gb|CI670608.1|CI670608
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88432766|gb|CI690614.1|CI690614
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88422474|gb|CI571456.1|CI571456
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88385975|gb|CI568643.1|CI568643
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTACTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88428516|gb|CI564984.1|CI564984
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGGTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88401622|gb|CI588563.1|CI588563
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTT-CGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88365009|gb|CI616428.1|CI616428
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88363573|gb|CI618134.1|CI618134
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88370937|gb|CI595049.1|CI595049
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88393970|gb|CI684238.1|CI684238
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|58690363|gb|CK079050.1|CK079050
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|58668740|gb|CK057426.1|CK057426
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88370912|gb|CI595024.1|CI595024
EST:     GAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: GAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|2428458|gb|C72921.1|C72921
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88575002|gb|CI666771.1|CI666771
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88361282|gb|CI626386.1|CI626386
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88333029|gb|CI639877.1|CI639877
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88390016|gb|CI590529.1|CI590529
EST:     ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGGCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATA
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
EST: gi|88393415|gb|CI618303.1|CI618303
EST:     ATCCGGCGAGCAT-CCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCG                         GAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC
genomic: ATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATC

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: 47 (upstream exon), 68 (downstream exon)
Score: 9

ACAGATCGCTCGCCTCCCCGTCTCCTCGCCCGCCGCCTTCGCCGATCTCCATCCGGCGAGCATCCCTCCCGCCGCCGTCCTGCTGCTGCTTCCGCCGCCGgtgagcacac ... gttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATCTTTGACCATAATGGCTGTAGCTTCTGCCAGTGCACTGTTTTCCGCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggcgagtgaggtgaggtgttcttcttatcgagtttcatctccatgttgctgcagGAGGGGAGGGATATGTGCCTGTGAAAAATCGGAGGAAAGGGGGTATAAATCTTTGACCATAATGGCTGTAGCTTCTGCCAGTGCACTGTTTTCCGCCAAG
                      ttcttat  TA-rich tract