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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaggcataagtatcaacgaggtcttcttgtgatatacaccttttgcccctccatgtttacatcatttcatctttaacataacccactttggtttgttagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA

Basic information

species Oryza sativa
transcript LOC_Os02g03060.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G174596_T03 (Zea mays), 3'ss of exon 5
gcaggcataagtatcaacgaggtcttcttgtgatatacaccttttgcccctccatgtttacatcatttcatctttaacataacccactttggtttgttagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA----------------------------------
                                                                                                                                     ||||| |||||||||||||||||||||||||||||  |||||||||||||||||||||| |||||||                                  
-------------------------------------------------------------------------------------------------------------------------------------cTTCTCGGTGCAAGGCATTATTCCACCCCTGTTGATGTGTGGTCAGTTGGTTGCATTTTCGCTGAAATGGTGAACCAGAAGGCGCTTTTTCCTGGCGACTC

upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G174596_T02 (Zea mays), 3'ss of exon 5
gcaggcataagtat-caacgaggtcttcttgtgatatacaccttttgcccctccatgtttacatcatttcatctttaac-ataacccactttggtttgttagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA
|| |||||    ||   |        |    ||||   |  | | ||| |||     |||      ||     |||||    |||  |  |||  || ||||||||||||  | ||||||||||| |||||||| ||||| |||||||||||||||||||||||||||||  |||||||||||||||||||||| |||||||
gctggcatttacatatgatagaactgttacatgatgctccgcatgtgctcctttccttttgagattttgatcatttaattggaactgaacttg--ttattagGTGGTGACGCTTTGGTATAGAGCGCCTGAAATCCTTCTCGGTGCAAGGCATTATTCCACCCCTGTTGATGTGTGGTCAGTTGGTTGCATTTTCGCTGAAA

upper sequence: LOC_Os02g03060.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S25_198V6.6 (Physcomitrella patens), 3'ss of exon 6
gcaggcataagtatcaacgaggtcttcttgtgatatacaccttttgcccctccatgtttacatcatttcatctttaacataacccact--ttggtttgt---tagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA
     | || |  ||||  | ||  |    ||||| ||   |||    | |  |    |   |    || |  || |       || |   ||| ||      ||||||| ||||||||||| |||||||| ||||||||  | ||| |  | || || || || ||||| ||  ||||||| || || |||||||| ||||| |
--gatcttacgattcaa--atgttgttagctgata-acttttttgcatcataaacagctcatttgggtcgtagttcatgggtttcattgtctggcttaaatgcagGTGGTAACATTGTGGTACAGAGCACCAGAAATTCTCTTAGGTTCTCGCCACTACTCTACACCTGTAGATGTGTGGTCTGTAGGATGCATTTTCGCTGAGA

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|33678285|gb|CF306524.1|CF306524
EST:     TTGGGTTGGCCAGGGCATTTGGCATTCCTGTCCGGACATTTACTCACGAG                         GTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCAT
genomic: TTGGGTTGGCCAGGGCATTTGGCATTCCTGTCCGGACATTTACTCACGAGgtacatttta ... ggtttgttagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCAT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcccctccatgtttacatcatttcatctttaacataacccactttggtttgttagGTGGTGACATTGTGGTATAGAGCACCTGAAATTCTTCTTGGTGCAAGGCATTATTCCACCCCTGTTGACATGTGGTCAGTTGGTTGCATTTTTGCTGAAA
                               acataac  putative branch site (score: 3)
                           tttaacataa  TA-rich tract