Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAACAAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccctgcctacaagacttgctgtttttgctagcatgttacattgctggacggttttgccatgccatgtgagttacgcaattaatcattcttgtctgtcatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g05420.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g05420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G085254_T02 (Zea mays), 5'ss of exon 9
ATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAACAAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccctgcctacaagacttgctg-tttttgctagcatgttaca--ttgctgga------cggttttgccatgccatgtgagt---------tacgcaattaatcattcttgtctgtcatgcag
 || || ||||||||||| ||||| || |||||||||||||| || || || ||  |||||||||||||||||| ||||||||||||||| ||||| ||||||      |  |    || ||    || |||||||   | | | | |  | ||||        | ||  |  | | |  |   |||         |  |||||   |  |||||||  |  ||||||
CTCGCCTTTGGACTTTGTCATTCGTCCACAGTCCAAAATTGACCCTGAGCAGATACGGGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgtttaccttccacacttaaaacagattggtttttgccttcctttaatagctagctgagtttcttccgtgcttgcctactcttgaagtaggaccaaatgagcaatagcttgttcttgttggatatgcag

upper sequence: LOC_Os01g05420.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G100881_T02 (Zea mays), 5'ss of exon 9
ATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAACAAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccctgcctacaagacttgctgtttttgct----------agcatgttaca-ttgctggacggtt-ttgccatgccatgtgag-----ttacgcaat---taatcattcttgtctgtcatgcag
 || || ||||||||||| ||||| || |||||||||||||| || || || ||  | |||||||||||||||| ||||||||||||||| ||||| |||||| |    |   |   || || |  ||  ||||            |||  | ||   || ||  | | || ||| |     | ||  |      |  |||||   | ||  |||| ||  | |||||||
CTCGCCTTTGGACTTTGTCATTCGTCCACAGTCCAAAATTGACCCTGAGCAGATACGAGCTCGTGCTAAGCAGGCTGTCCAAGACCAGCGTCGGCTGAAGgttttccttccatccttaaaacatcttggctttgtctcccttcataagctagctagggttccttcatgcttgttgactgttgaagtaggaccaactgagcaatagctgattcttctcgttggacatgcag
















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|33813166|gb|CF332476.1|CF332476
EST:     GCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: GCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29662253|gb|CB658528.1|CB658528
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGTTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29670427|gb|CB666702.1|CB666702
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29679612|gb|CB675887.1|CB675887
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88220373|gb|CI219933.1|CI219933
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|218504271|gb|FG960657.1|FG960657
EST:     CAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCCAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88413157|gb|CI523718.1|CI523718
EST:     TGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: TGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|218479478|gb|FG952626.1|FG952626
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|88382235|gb|CI533439.1|CI533439
EST:     GCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: GCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|29665319|gb|CB661594.1|CB661594
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
EST: gi|27577848|gb|CB000543.1|CB000543
EST:     AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAG                         ATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG
genomic: AAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAG

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: 68 (upstream exon), 73 (downstream exon)
Score: 31

ATCACCCTTGGACTTTGTTATTCGCCCGCAGTCCAAAATTGATCCCGAACAAATTAGGGCTCGTGCTAAGCAGGTTGTCCAAGACCAGCGCCGGCTAAAGgttctgtccc ... tgtcatgcagATGAACAAGAAATTGCAGCAGCTGAAAGCACCAAAGAAGAAAAACCTTCAGGCGTCAAAACTCAGTGTTGAAGGGCGTGGAATGATCAAGTACTTGTAAA




<











<


<