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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaggcacagttctttcttttttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT

Basic information

species Oryza sativa
transcript LOC_Os08g29370.2
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G015967_T01 (Zea mays), 3'ss of exon 5
gtaagtaggcacagttctttcttt----tttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
|| ||||    |||   ||   ||     ||   ||||   |||      |  |||   || |||||| |  || |||  |||||||||  | ||  ||||     ||||||||||||| |||||||||||||||||||| || ||||| || || |||||||||||||| ||||| ||||| 
gtgagtataagcagcctttctcttaaccctttgatttcgtcatcgcttctatttttattcagctgtatttgaataagcccgttcttacatcatacgggatcg-attttcagGAACTTGGTCGCTACAAGGCTCAAACAAAACTCCCTTTCAACGCTTTTGGAACAATGGCTATGGCAAGAGAA

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA13G23850.1 (Glycine max), 3'ss of exon 5
gtaagtaggcacagttctttcttttttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
    | ||   || ||   | | ||||  ||||   || ||        | ||  |  ||  | || ||  | |||  || |    |    || |||       ||||| ||||| |  ||||||||||||||||||||||| |||||||| || || |||||||||||||| ||||||
----gaagtttcactttgatgtattttatgttttcaaacctgttcc---tcttatcttctcaaggtggaaaaactttctcatttgttggcaataatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCCTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 5
gtaagtaggcacagttctttcttttttcagtttcagaatctaccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
          | | |    | | ||||   |||   || ||        | ||| |  ||  | |||||  | |||  || |    |     | |||       ||||| ||||| |  ||||||||||||||||||||||| |||||||| || || |||||||||||||| ||||||
----cactttataatgtgatgtattttatattttcaaacctgttcc---tcttgtcttctcaaggttgaaaaactttctcatttgttggcactaatctgttggacagGAGCTTGGTCTATACAAGGCTCAAACAAAGCTTCCGTTTAATGCTTTCGGTACAATGGCAATGGCAAGAGAT

upper sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 5
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 5
gtaagtaggcacagttctttcttttttcagtttcagaatcta-ccggaaattttggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
     | |  | |  | |||  |        |||| |||||  ||  |||| | |   | ||  |  ||||  |      |||    || |  || |  |     ||||| ||||| |  ||||||||||||||||||||||| ||||||||||||||||||||||| ||||| ||||||
-ctctttgatata--tttttggtcaaaagacttcataatctgtcctaaaatctcgatgattgctt--tgatctgtcaaggcttg--atataattggt-gtttgaacagGAGCTTGGTCTGTACAAGGCTCAAACAAAGCTTCCATTTAATGCATTTGGAACAATGGCCATGGCAAGAGAT

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|86848897|gb|CI295714.1|CI295714
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|88221803|gb|CI221759.1|CI221759
EST:     TCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: TCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|313084044|gb|HO213827.1|HO213827
EST:     AGTTAATGGTCGATGGCGACAAAGCGCCTGTATATGGTGGAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|25804245|gb|CA760206.1|CA760206
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|86500872|gb|CI143505.1|CI143505
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|29658080|gb|CB654355.1|CB654355
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|29613721|gb|CB618734.1|CB618734
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|29657974|gb|CB654249.1|CB654249
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|86831350|gb|CI297619.1|CI297619
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|86257246|gb|CI004064.1|CI004064
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
EST: gi|29622079|gb|CB627090.1|CB627090
EST:     AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAA                         GAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA
genomic: AGTTAATGGTCGATGGTGACAAAGCGCCTGTATATGGTGAAACACTTGAAgtaagtaggc ... atgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggcaactgtatgttgatgagcttgttcttacagtacacatgatcatgcattcagGAACTTGGCCGCTACAAGGCTCAAACAAAGCTTCCTTTTAATGCATTTGGAACAATGGCAATGGCTAGAGAT
                         ttcttac  putative branch site (score: 2)