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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctag

Basic information

species Oryza sativa
transcript LOC_Os06g01850.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G168143_T02 (Zea mays), 5'ss of exon 2
CGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctag
|||||||||||| |||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||  ||||||||||||||||||||||||| ||||||  |   |   ||| ||||| |||  ||  ||||  ||         | |||||      | | |||       | | ||| |   | || |       
CGTCATCGCCGATGGCGTCGACAAGAACGGCAAGCCGCACAAGGTCAGGCTCTACTCCATCGCCAGCAGCGCGATCGGCGACTTCGGCGACTCCAAGACAgtcagtagctagccaatct-ctcctgctttctctctctctctcaagtct---gaatcgactattctccgtcattttct-tgagcatttctgcctgcag------

upper sequence: LOC_Os06g01850.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 5'ss of exon 3
CGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtccccctcttctcttctcctccttattcaatctcattccttctcatcggatcgatctcctttcttcacaccagataatcatcttcacttgtacctctag
 || ||  | || ||  | ||||||||||| |||||||||||||||||||| ||||| ||||| || || ||  | || ||||| || |||||||||||||| ||  |   |  || ||    |  || | | |||   | |  ||  ||    |  ||||| || |  ||     |   |  | | | ||             
AGTGATTCCAGAGGGAATAGACAAGAACGGGAAGCCGCACAAGCTCAGGCTTTACTCTATCGCGAGTAGTGCCATTGGTGACTTTGGAGACTCCAAGACCgtaag--caaataatccctctaacaactaactaaat---aatgatttaca---aaatgatcttctcttatctggaaatggatccttttgcag------------
















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|88671965|gb|CI726081.1|CI726081
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|58695210|gb|CK083897.1|CK083897
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88671055|gb|CI725171.1|CI725171
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88668144|gb|CI722883.1|CI722883
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88955314|gb|CI721886.1|CI721886
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88955313|gb|CI721885.1|CI721885
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|33798466|gb|CF325091.1|CF325091
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|29685685|gb|CB681960.1|CB681960
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88665792|gb|CI715948.1|CI715948
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGAAC                         GTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT
EST: gi|88670049|gb|CI724165.1|CI724165
EST:     TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGAAC                         GTTTCACTCTGCGTNAAGAGGCTCGTTTACACCAACGACCAGNGAGAGATT
genomic: TCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATT

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: 74 (upstream exon), 63 (downstream exon)
Score: 164

CGTCATCGCCGACGGCGTCGACAAGAACGGCAAGCCGCACAAGCTCAGGCTCTACTCCATCGCCAGCAGCGCTCTCGGCGACTTCGGCGACTCCAAGACCgtcagtcccc ... gtacctctagGTTTCACTCTGCGTCAAGAGGCTCGTTTACACCAACGACCAGGGAGAGATTGTCAAAGGAGTCTGCTCCAACTTCCTCT




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