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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaacactcccaatgcacagcagaaaaaatataaaatttgttgatcttacaaactataagcaatgttgtgttctttttag

Basic information

species Oryza sativa
transcript LOC_Os03g24220.1
intron # 21
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.3 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G359566_T01 (Zea mays), 5'ss of exon 6
AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaacactc----ccaatgcacagcagaaaaaatataaaatttgttgat-------cttacaaactataagcaatgttgtgttc-tttttag
 ||||   |||||| ||||||||||||||||||||||| ||||||||||| ||||| ||||||||||| ||||| || ||||| || |||   ||  |||||  ||||| | ||    ||  | |    || ||| | ||  || |   ||          ||||  | |||    | |  |  |||   |||| ||
GGTGGCAATAAGAGCTCAGGTGATGGTGGACCAACTCAAAGGGCATCAGCCTTGGCAGCTCTTTCATCCGCATTGAATCCATCGTCGCAAGGAAAACAGgtacggttaataatctcctccgttccgttccaaaaatactaataattcccttcccgtttttccttatcagctaaccaccaaatcctgtgggttttcag

upper sequence: LOC_Os03g24220.3 (Oryza sativa), 5'ss of exon 20
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 21
AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaacactcc----caatgcacagcagaaaaaatataaaattt-------gttgatcttacaaactataagcaatgt----tgtgttctttttag
 ||||   |||| | |||||||||||||| |||||||| ||||||||||| ||||| ||||||||||||||||| || ||||| || |||   ||  ||||| || ||| | |      |  | |    || ||| | ||  || ||         ||  |||||  | |||    | | ||    || ||| |||  ||
GGTGGCAATAAGGGCTCAGGTGATGGTGGGCCAACTCAAAGGGCATCAGCCTTGGCCGCTCTTTCATCTGCATTGAATCCATCGTCGCAAGGAAAACAGgtactgctaataattttcttccctccgtttcaaaaacagtaacaatttccttccggatttttcttagcagctaaccaccaggtcctgtgggttttttccag
















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|58677092|gb|CK065779.1|CK065779
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|396941448|gb|HO188657.1|HO188657
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|33794451|gb|CF323110.1|CF323110
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58661440|gb|CK050120.1|CK050120
EST:     CATTGGCTGCTCTTTCGTCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|38477625|gb|CF961758.1|CF961758
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATGGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58652740|gb|CK041420.1|CK041420
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|56157785|gb|C26501.2|C26501
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAAGCGCGCTTT
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCA-GCGCGCTT-
EST: gi|427570|gb|D23638.1|D23638
EST:     CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGNGCTTCA
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGGACCCACTCAGCGCGCTTCA
EST: gi|58652765|gb|CK041445.1|CK041445
EST:     CATTGGCTGCTCTTTCATCTGAATTCAAACCATCTTCCCAAAAGAATAAG                         GGTAATGATAGGGCTAAAAGCTCTGATGGTGG
genomic: CATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaa ... ttctttttagGGTAATGATAGGCCTAAAAGCTCTGATGGTGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTGGATCTAAGAGTTCAGGTGATGGTGGACCAACTCAGAGGGCATCAGCATTGGCTGCTCTTTCATCTGCATTCAACCCATCTTCCCAAAAGAATAAGgtattgttaacactcccaatgcacagcagaaaaaatataaaatttgttgatcttacaaactataagcaatgttgtgttctttttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA