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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattttctatctggtatagtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG

Basic information

species Oryza sativa
transcript LOC_Os04g59494.1
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 22
gtaagtattt------tctatctggtat-agtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG
||||| ||||      ||||| ||   | | |||||       |||||| | |||||   |  |  ||||   ||||||| || | ||||||||| || || ||||| |||||||| ||||||||||| |||||||||||||||||||||
gtaagcatttctgtggtctatatgtcgttattataattatcttgattcatttctcactcaacttcattgc---agAACCCTCAGTCTGTGAAGGATGCGGTATCAGTAGCTAACAATGCCTGTTGGGCTATTGGAGAATTAGCAATCAAG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 22
lower sequence: GRMZM5G869572_T01 (Zea mays), 3'ss of exon 2
gtaagtattttctatctggta----------tagtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG
|| || |  |||| | ||||           ||  |||| |     |||||| |||||||     |   |||||||||||||| |||| ||||||||| || || ||||| |||||||| || |||||||| |||||||||||||||||||||
gtgagcaaattctgtgtggtccatatgtcgttatcataataatcttgattcattcctcac---tcgactttgctgcagAACCCTCAATCTGTGAAGGATGCGGTATCAGTAGCTAACAATGCTTGTTGGGCTATTGGAGAATTAGCAATCAAG

upper sequence: LOC_Os04g59494.1 (Oryza sativa), 3'ss of exon 22
lower sequence: Vv03s0038g02830.t01 (Vitis vinifera), 3'ss of exon 22
------------------------gtaagtattttctatctggtatagtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG
                          || |||||| ||  |  |    | |    | ||  ||  | |      | |   |  ||  | |||||| |        |||||||  |||| |||||||| || || ||||||||||||||||||||||||||| | |||
gtaataaattcatttcactaactgaaaaatattttttaggtattg-gtttttttttttcttataaattttatgtaatgaatgatttatacagAACACTTCTAAGCTGAAGGAAACTGTTTCAGTGGCGAATAATGCCTGTTGGGCAATTGGAGAATTAGCAGTTAAG

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|58608072|gb|CK036105.1|CK036105
EST:     ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTG                         AGGCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
genomic: ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTGgtaagtattt ... gttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
EST: gi|58671684|gb|CK060370.1|CK060370
EST:     ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTG                         AACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
genomic: ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTGgtaagtattt ... gttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
EST: gi|29623086|gb|CB628097.1|CB628097
EST:     ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTG                         AACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
genomic: ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTGgtaagtattt ... gttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
EST: gi|86850485|gb|CI307714.1|CI307714
EST:     ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTG                         AACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
genomic: ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTGgtaagtattt ... gttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
EST: gi|58592654|gb|CF990962.1|CF990962
EST:     ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTG                         AACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG
genomic: ATCTGCATCCCCGCCTTCAAGAATTCCTTAATGTTGCTGCGAAGCAACTGgtaagtattt ... gttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctggtatagtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG
                              tcctcac  putative branch site (score: 2)
      tatagtataa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtattttctatctggtatagtataacatctcggattcactcctcacattatgttgttgctgcagAACCCGCAATGTGTGAAGGAGGCTGTGTCAGTGGCTAACAACGCCTGTTGGGCAATTGGAGAATTAGCAATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA