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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctcccactcgtcatctcttactgtacttcatcgctggatggctccatgattaacccactgctcatctaactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG

Basic information

species Oryza sativa
transcript LOC_Os01g01070.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G147587_T01 (Zea mays), 3'ss of exon 3
-------gtctcccactcgtcatctcttactgtacttcatcgctggatggctccatgattaacccactgctcatctaacta------ttagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG
       |  | | | |       | || || | ||| | | |    ||  |  || ||||   || | ||||||  |  |      | |||||||||||||||||||||| || ||| | ||||| |  |||||||| ||| | |||||||| || ||||||||||| |
gttttttgcatgcgaatttctgcttttttctatcctttaacaccaattgcatgtatcattagttcattactcatcagatcaagtgtttcagGTCAATCATCTCAGAGAGGAGCTGCAAATGTTGTCTAAATCAAATCATGTTTCCATTGTCACTGTTGATGGTAGACCTG

upper sequence: LOC_Os01g01070.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G078711_T01 (Zea mays), 3'ss of exon 3
gtctcccactcgtcatctcttactgtacttcatcgctggatggctccatgat-taacccact-gctcatctaactatt--agGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG
|| |    |  | ||  |  | || |  |  |||  |  |   |      || || |  |||   | |   || | ||  |||||||| ||||||||||||| || ||| | ||||| |  |||||||| |||||||||||||| || ||||||||||| |
gttttttgcatgacaagttctgcttttttctatccttcaacatcaattgcatatatcatactcattaagtcaagtgttccagGTCAATTATCTCAGAGAGGAGCTACAAATGTTGTCTAAATCAAATCATGTTGCTATTGTCACTGTTGATGGTAGACCTG
















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|58593533|gb|CF991841.1|CF991841
EST:     AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAG                         GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
genomic: AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAGgtctcccact ... taactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
EST: gi|88421467|gb|CI618591.1|CI618591
EST:     AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAG                         GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAGATCAACGT
genomic: AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAGgtctcccact ... taactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAA-GT
EST: gi|88315903|gb|CI618779.1|CI618779
EST:     AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAG                         GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCACATCAAGTT
genomic: AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAGgtctcccact ... taactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
EST: gi|58687220|gb|CK075907.1|CK075907
EST:     AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAG                         GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
genomic: AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAGgtctcccact ... taactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
EST: gi|33658119|gb|CF280733.1|CF280733
EST:     AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAG                         GTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT
genomic: AGGATGGCCCATCCACCAGCAGCCCTCACGCTGCTCACTTGCTATCTCAGgtctcccact ... taactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtacttcatcgctggatggctccatgattaacccactgctcatctaactattagGTCAATCATCTCAGAGAGGACCTCCAACTTTTGTCCAGGTCAAATCAAGTTGCTATTGTCACCGTCGATGGTAGACCAG
                                          atctaac  putative branch site (score: 2)
                                       ctcatct  CT-rich tract
                                             taactatta  TA-rich tract