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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA

Basic information

species Oryza sativa
transcript LOC_Os05g09360.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G350818_T02 (Zea mays), 3'ss of exon 7
gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA
|| | |   |||||||   | || |||   ||  | |||| |||||||| |  ||     | ||   |||||| ||| ||  ||||| ||||| ||||||| || ||||| ||||||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||||||||| |||||||
gt-gaaatccattctgttgtgctgattcccttaat-aagccgtggtgtggtcatttctaatgtt-actgaaatttctgctattgtggcagGTATTGGAAACAAACAGGGCAGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGCCCAAACACCTTCAGTGAACCTTGGCATCTCCCACACA

upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA05G36070.2 (Glycine max), 3'ss of exon 15
gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA
||     | ||   ||      | |    |       | || |||   | |         |||   ||   || |||  | || |   || |  ||||||| || ||    || ||||||||  |||||||||||||| ||||||||   || || || || ||||||||||||||||||||||  ||  
gtccataaccaacttgtgaatttcagggatactcaccaactttggaacgttacaatcaaatttaactttgcatttctg-tgatctttcagATTATGGAAACAAACAGAAGTGAGGAATCTCAGAGTCATGTGCACAGGTTGTATTTCCATGGCCCAAATACATTCAGTGAACCTTGGCATCTACTTCATT

upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GLYMA08G03550.1 (Glycine max), 3'ss of exon 16
----gtagcagaa--cattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA
     || |  |   | || || ||| |     |  |  ||     ||   ||| |   | |   |||  | |||||   | |  | |  |   || |  ||||||| || ||    || |||||||   |||||||||||||| ||||||||  ||| || || || ||||||||||||||||||||||| ||  
gtccataactaacttccttgtgaatttcagggatactcattacctttggaatgttaccat-caaatttaactttgaa---ttttgtgagctttcagATTATGGAAACAAACAGAAGTGAGGAATCTCCGAGTCATGTGCACAGGTTGTATTTCCAGGGCCCAAATACATTCAGTGAACCTTGGCATCTACCTCATT

upper sequence: LOC_Os05g09360.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT5G11700.1 (Arabidopsis thaliana), 3'ss of exon 14
-----------gtagcagaacattctgcattcctaatttgtttctttaagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA
            |   |  ||||  | ||     |   |    |    |    |  | | |  ||  ||   |   ||| | |    |  || | ||  ||||  ||||||| ||||| || ||  |||||||  |||||||||| || |||||||| |||||||| || || ||||||||||| ||||||||  ||||||
agtaatgtttgttcaaaagacataattcagcgaaataatccgccaaacactccttatattacagtgttgtgctgctgtttataatgttattctt-tgtcagGTGTTGGAAACAAATAGAGCTGAGCAATCTCAGAGTCATGTGCATAGAATGTATTTTATGGGTCCTAATACATTCAGTGAACCGTGGCATCTCTCACACA

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|88372007|gb|CI681524.1|CI681524
EST:     ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAG                         GTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
genomic: ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAGgtagcagaac ... catgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
EST: gi|88579210|gb|CI688188.1|CI688188
EST:     ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAG                         GTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
genomic: ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAGgtagcagaac ... catgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
EST: gi|88577560|gb|CI674156.1|CI674156
EST:     ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAG                         GTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
genomic: ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAGgtagcagaac ... catgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
EST: gi|88463656|gb|CI696131.1|CI696131
EST:     ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAG                         GTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG
genomic: ATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAGgtagcagaac ... catgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATG

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: 66 (upstream exon), 32 (downstream exon)
Score: 14

GATGAAGTTTGTTGGCACTGATGAGTTGCCTGGACCAGCACCAACTCAACATAGCTCCCAAATTGATCACTCTTTTCCCTTCCTCGAATCACTCAATGAGgtagcagaac ... catgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taagctgtggtgtgattgttctggtttttcgttgaaatctctcctcatgtggtagGTACTGGAAACCAATAGGGCCGAAGAATCTCACTGTCATGTGCACAGGATGTATTTCATGGGTCCCAACACCTTCAGTGAACCTTGGCATCTACCACACA
                                     tctctcctcat  CT-rich tract
                               ttgaaat  TA-rich tract