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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattgagctgtgtattctgttcaatactcttgacactgatgttccttctgtttattcattgcatttttgtaaccgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATTGTTAGTTTGGTTCCTGATGGGCTAGAAATACCAAG

Basic information

species Oryza sativa
transcript LOC_Os04g11880.2
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G134115_T01 (Zea mays), 3'ss of exon 1
gtaattgagctgtgtattctgttcaatactcttgacactgatgttccttctgtttattcattgcatttttgtaaccgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATTGTTAGTTTGGTTCCTGATGGGCTAGAAATACCAAG--------------
|||| |||    |  ||  || | |||  |    | ||||| |   ||||||||     | | || |||     | |||| |||||| || |  || ||||||||||| |||||||||||||||||| |||||||||| ||||||| |||||||||  ||||||||||  |              
gtaactgaa--ataaatgatgcttaatcttgcctagactgaggcatcttctgtt---ctagttcaatttctagtctgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGGTCCTGATGGCTTAGAAATACCTCGGTATGTTCCATCAA

upper sequence: LOC_Os04g11880.3 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM2G040247_T01 (Zea mays), 3'ss of exon 16
gtaattgagctgtgtattctgttcaatactcttgacactgatgttccttctgtttattcattgcatttttgtaaccgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATTGTTAGTTTGGTTCCTGATGGGCTAGAAATACCAAG
|||| |||    |  ||  |||| |||  |  | | ||||| |   ||||||||| ||  ||  |||| | |  | |||| |||||| || |  || ||||||||||| |||||||||||||||||| |||||||||| |||||||||||||||||  ||||||||||  |
gtaactgaa--ataaatgatgtttaatcttgcttagactgaggcatcttctgtttcttagttcaatttctatgtctgttgggcagGTAGGGAATCTATTGGAACATACAGTTGGCAATCTTGATCCTCTGTACATTGTCAGTTTGGTTCCTGATGGCTTAGAAATACCTCG
















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|55409184|gb|CV721560.1|CV721560
EST:     GAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATG                         GTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
genomic: GAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATGgtaattgagc ... cgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
EST: gi|58688189|gb|CK076876.1|CK076876
EST:     ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATG                         GTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
genomic: ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATGgtaattgagc ... cgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
EST: gi|58692342|gb|CK081029.1|CK081029
EST:     ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATG                         GTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
genomic: ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATGgtaattgagc ... cgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
EST: gi|218492660|gb|FG966164.1|FG966164
EST:     ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATG                         GTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT
genomic: ATGAGTTATGGGAGGAATTGATAAGACAGTGCCTCCAAAAACCTGAGATGgtaattgagc ... cgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgacactgatgttccttctgtttattcattgcatttttgtaaccgttgagcagGTTGGAATGCTGTTGGAACATACTGTTGGCAATCTTGATCCTTTGTACATTGTTAGTTTGGTTCCTGATGGGCTAGAAATACCAAG
                                      ttgtaac  putative branch site (score: 2)
                      tttattcatt  TA-rich tract