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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag

Basic information

species Oryza sativa
transcript LOC_Os11g03900.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G005849_T01 (Zea mays), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttcacctcttgcag
|||| |||||||| ||||| || |||||||| || || || || || ||||| || ||||| || ||||| |||||||| || || || |||||||||||||||      |  | |  |    |  ||  ||   || |  ||  |  |   ||||   |  |      ||   |||||||||||
GCGAGGGCATGCTCGCTGGCGAGATGAAGCACGGGCCGCTGGCCCTCGTGGACGAGAACCTCCCCATCATTGTCATTGCGACCCGCGACGCGTGCTTCAGgtaa---tgataaagaagcatgggcccagctttggttaccctttttggtagcaggaaaccaacctcttttcaaaacctcttgcag

upper sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 9
lower sequence: GLYMA09G38460.1 (Glycine max), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctttggacagactacagagcacgttcattttcttttcatttttcaaggagttcctctaaacat-cttcacctcttgcag
| ||||| |||||||||||||||||||||||||| ||  | ||| ||||||||||||| || || ||    ||  | ||||| |||||||| ||||||||||  |   |       ||||   ||| |  || ||| |||         | | |   ||  | |  ||||  || | || |  |||
GTGAAGGGATGCTTGCTGGTGAAATGAAGCATGGTCCTTTGGCATTAGTGGATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgt-------gactgtcgagtagctttattatctgaaa-----ttaggagtttgatattgacatattttatctttgacag

upper sequence: LOC_Os11g03900.1 (Oryza sativa), 5'ss of exon 9
lower sequence: Vv13s0064g00050.t01 (Vitis vinifera), 5'ss of exon 9
GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagc-gctttggacag----actacagagcacgttcattttcttttcatttttcaaggagttcctctaaacatcttc-acctcttgcag
| ||||| ||  |||| ||||||||||| ||||| ||  | || ||||| |||||||| ||||| ||  | || |||||||| |||||||| |||||||||| ||    |||  |       | |  |   |    | | ||  ||  |||| |||  |   ||  | |  |||| ||| |   ||  |||
GTGAAGGAATAATTGCAGGTGAAATGAAACATGGTCCTTTGGCTCTAGTTGATGAAAATCTTCCAATTGTTGTTATTGCTACCCGTGATGCTTGCTTCAGgttagttattttttatttttttattgaaagacttaataagttgtttgacattcttcttgc--tttgtattgacattttctaatgctgacag

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|88220725|gb|CI220285.1|CI220285
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33681120|gb|CF309359.1|CF309359
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33822256|gb|CF336942.1|CF336942
EST:     TCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: TCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58669396|gb|CK058082.1|CK058082
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33689236|gb|CF317475.1|CF317475
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|27548069|gb|CA766086.2|CA766086
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|58591908|gb|CF990216.1|CF990216
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|33794922|gb|CF323341.1|CF323341
EST:     ATGAAAACCTTCCGATCATCGTCATTGCTACACGTGNATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGC
genomic: ATGAAAACCTTCCGATCATCGTCATTGCTACACGTG-ATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGC
EST: gi|112785889|gb|EE591621.1|EE591621
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAACAGTCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86430525|gb|CI082948.1|CI082948
EST:     GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|86489453|gb|CI132086.1|CI132086
EST:     GTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
EST: gi|88226050|gb|CI225966.1|CI225966
EST:     GATG-AAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAG                         CAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT
genomic: GATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGAT

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: 20 (upstream exon), 70 (downstream exon)
Score: 5

GCGAAGGCATGCTTGCTGGTGAAATGAAGCATGGACCACTTGCACTAGTGGATGAAAACCTTCCGATCATCGTCATTGCTACACGTGATGCGTGCTTCAGgtaagcgctt ... cctcttgcagCAAGCAGCAATCAGTGATTCAGCAGCTCCTTTCTCGCAAGGGGCGTCTGATAGTGATGTGCTCAAAGGGAGACGCATCTGCCGTTTGCCCTAGTGGATCT




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