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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTTGTATTTGCGAGCTATTCTTTTGATGTTTGGGAGAGCTGGACGCTGGAGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctgttatcatcatttatagtacttaacatcaaggtttgagaattaagatgcacccgatcaatgatactaatatccagcgatatcatggaaaga...

Basic information

species Oryza sativa
transcript LOC_Os10g38900.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g38900.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G418294_T01 (Zea mays), 5'ss of exon 6
GCTTGTATTTGCGAGCTATTCTTTTGATGTTTGGGAGAGCTGGACGCTGGAGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctgttatcat---catttatagtact-taacatcaaggtttgagaat-taagatgcacccgatcaatgatactaatatccagcgatatcatggaaaga----------------------------------
| | || || || ||  |||||||||||||||| |||||||||| |||||| ||||   |    || |  |||||  | || || ||||||| | ||  |||| |  |  | ||| |   ||||   || |   |||  | ||  |     ||| |     | |  |   | |    |   |  | ||  |||  ||||    |                                   
GTTCGTCTTCGCAAGTCATTCTTTTGATGTTTGTGAGAGCTGGATGCTGGAAGGGTGCCTTTCAGAATACTGCAAACTTGTTAATCGCAAAAATGCTATGgtacgttcattcatccttgccattctaagcaggataaacttaacatacacaaatatccccagtagtcagacgaaacgaactacttgcactgattccatgtgttgtttatacctttcctggtggttaattttttctgaag
















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|86540669|gb|CI180875.1|CI180875
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|88233198|gb|CI233047.1|CI233047
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|88270455|gb|CI385713.1|CI385713
EST:     AGGGGTCTTTACTGGATTGTGGCAAGGTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATAGTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|86496516|gb|CI139149.1|CI139149
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|87031815|gb|CI272516.1|CI272516
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|88838417|gb|CI374965.1|CI374965
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|86412641|gb|CI067046.1|CI067046
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|86434072|gb|CI094415.1|CI094415
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
EST: gi|86867644|gb|CI342645.1|CI342645
EST:     AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCG                         GTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT
genomic: AGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGAT

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: 60 (upstream exon), 54 (downstream exon)
Score: 4

GCTTGTATTTGCGAGCTATTCTTTTGATGTTTGGGAGAGCTGGACGCTGGAGGGGTCTTTACTGGATTGTTGCAAGTTGGTCAACCGCAAAATTCCTTCGgtatgccctg ... ttttttgtagGTTGTATTGGAGGTCTATATTGAAATCCTCGCAGCTGTGAGTGAAGAAGATGGTGTCACTAGATGGCTAGATTGATCCATCTACCCCAGGAGCCTAGGAC




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