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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcaccgctctagcttcattcgttcatcagtcaagcctggtacatatagtgtgataaatctaaatcatttggaattg...

Basic information

species Oryza sativa
transcript LOC_Os01g59730.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv13s0064g00850.t01 (Vitis vinifera), 5'ss of exon 2
AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcaccgctctagcttcattcgttcatcagtcaagcctggtacatatag----tgtgataaatcta--aatcatttggaattg--------------
|     ||    ||||||||||||||    || ||||||||||||||||||||||| ||||||||||||||||| ||||||| |||| | | |||||| |||   |  |  |||  |||| || | |  |||  || |   |||  || ||   ||    ||||   | | |    |||||| |    |  ||   || |||| |               
ACTCAAGAAAACATCAACAACAAGCTCGCTCTCGTGATGAAGAGCGGCAAGTACACGCTCGGCTACAAGACCGTGCTCAAGAGCCTCAGAAGCTCCAAGGgtttgttatacatttttttcatattaagagctacagatcttttc--tcttcttgcatttttggtgtgtttggggtttgtgattatcggattaagttttgggaaatacttgatgatggcag

upper sequence: LOC_Os01g59730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EDP06387 (Chlamydomonas reinhardtii), 5'ss of exon 2
AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcaccg-ctctagcttcattcgttcatcagtcaagcctggtacatatagtgtgataaatctaaatcatttggaattg--------------------------------------------------------------
| |  ||||   ||||||  |   |||  ||||||||||||||| ||||||||||| || ||||||||||||  ||| |||||||| |||     ||| ||||  | |  | |            | ||| ||   ||||| |     |      |  |||   |       |||||     ||   | |    |                                                                    
ACCCAGGAGAACATCAACGCCCGTCTGGCGCTGGTGATGAAGAGTGGCAAGTACACTCTGGGCTACAAGACCTGCCTGAAGACCCTGCGCTCGGGCAAGGgtaagtttgcgctcgcgccgacgcccgccgactggtgcttcctcaacccgcaccccctgccccttgtgccctgtgtgg-ggctcagcaccgcacgctgccttctccaccagaaaactgcacatctatctcaccaactttgtctcctcttcttgcccaccgcag

upper sequence: LOC_Os01g59730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ14031 (Selaginella moellendorffii), 5'ss of exon 1
AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcacc-gctctagcttcattcgttcatcagtcaagcctggtacatatagtgtgataaatctaaatcatttggaattg
| |  |||| | ||||||||||   ||  ||||||||||||||||||||||||||| || ||||||||||| || |||||  | || ||||     ||||||     |   || | | |     || |  ||  | | | |||| |  |||  |    ||                                         
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGCTACAAGACGGTGCTCAAATCGCTGCGCAGTGGAAAAGgtg----tgaaatccctctttgtttctcttgcgattgatccattggcgcattgggtgcgcag---------------------------------------

upper sequence: LOC_Os01g59730.1 (Oryza sativa), 5'ss of exon 2
lower sequence: EFJ13021 (Selaginella moellendorffii), 5'ss of exon 1
AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctctttgattcgtttcctagtcacc-gctctagcttcattcgttcatcagtcaagcctggtacatatagtgtgataaatctaaatcatttggaattg
| |  |||| | ||||||||||   ||  ||||||||||||||||||||||||||| || || |||||||| || |||||  | || || |     ||||||   | |   || | | |     || |  ||  | | | || | |  |||  |    ||                                         
ACCCAGGAGAGCATCAACAACAGATTGGCGCTGGTGATGAAGAGCGGCAAGTACACGCTGGGGTACAAGACGGTGCTCAAATCGCTGCGGAGTGGAAAAGgtg--tgtgaaatccctctttgtttctcttgcgattgatccagtggcgcattgggtgcgcag---------------------------------------

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|88213116|gb|CI212780.1|CI212780
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTGATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88364526|gb|CI644604.1|CI644604
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88736541|gb|CI760049.1|CI760049
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88735499|gb|CI759007.1|CI759007
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|42591806|gb|CK738292.1|CK738292
EST:     AGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: AGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88375923|gb|CI528227.1|CI528227
EST:     GTACACCCTCGGGTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|58687548|gb|CK076235.1|CK076235
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|427564|gb|D23632.1|D23632
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88722313|gb|CI745823.1|CI745823
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|88690331|gb|CI734410.1|CI734410
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|287274|gb|D16076.1|D16076
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|58585744|gb|CF984052.1|CF984052
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACGGNCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
EST: gi|87004301|gb|CI298833.1|CI298833
EST:     GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAG                         GGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA
genomic: GTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAA

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: 64 (upstream exon), 63 (downstream exon)
Score: 12

AACGCGGAGGGGATCAACAACAAGCTGCAGCTGGTGATGAAGAGCGGCAAGTACACCCTCGGCTACAAGACCGTCCTCAAGACCCTCCGCAACTCCAAAGgtagctcttt ... gaatcttcagGGAAGCTAGTTATCGTTGCAAACAACTGCCCTCCACTTAGGAAGTCTGAAATTGAGTACTATGCTATGCTGGGAAAAGTTAGTGTGTATCACTTCAATGG




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