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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatgttctttatcccaaatgataagatacttaaaagggttttctcaacatagcttgaattgagcaacaaaaggcaggatgggattgtattttatctaatttgagatgcacaccaatggaagaataagttcgttgagtaatgctgtttaatgttgtactcactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGAATGGTTATTCAAG

Basic information

species Zea mays
transcript GRMZM2G179696_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g44970.1 (Oryza sativa), 3'ss of exon 2
gtaagcatgttctttatcccaaatgataagatacttaaaagggttttctcaacatagcttgaattgagcaacaaaaggcaggatgggattgtattttatctaatttgagatgcacaccaatggaagaataagttcgttgagtaatgctgtttaatgttgtactcactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGAATGGTTATTCAAG
                                                           | | || | ||    |   || | |        | |  |   | ||      |   |  | ||||| |  ||          ||||| |||| | ||  ||  | | |||| ||||||| ||||||||  |||| ||||||||||||||| | |||||||| || ||||| || ||| | ||||| ||||||||||||||| |    |||||||
-----------------------------------------------------------taattttatcagtgga---caagttcaa----caatccacaaacttgacagagttaattagtggaacacaaaac-------ataatgatgttaagtgacgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGGTTCTGGTTTGCTTCAATGGATTGAGTTTACCAAACTAAATGGAGTATCAATTCAAG

upper sequence: GRMZM2G179696_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g45060.1 (Oryza sativa), 3'ss of exon 2
gtaagcatgttctttatcccaaatgataagatacttaaaagggttttctcaacatagcttgaattgagcaacaaaaggcaggatgggattgtattttatctaatttgagat-gcacaccaatggaagaataagttcgttgagtaatgctgtttaatgttgtactcactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGAATGGTTATTCAAG
                                                           | | || | ||        | |||   | |   |  |   | || |||| |  |   |  | ||||| |  ||          | ||| |||| | || |||  | | |||| ||||||| ||||||||  |||| ||||||||||||||| | |||| ||| || ||||| || ||| | ||||| || |||||||||||| |    |||||||
-----------------------------------------------------------taattttatca--------ctggacaagttcaaaaatccacaaacttgacacagttaattagtggaacacaaaac-------atgatgatgttaagtgatgtgtttattttgtagCTGGATGGAACAATTGTAGCCCCAACCAGTGCTAAAGCTTGGGATTCTGGTTTGCTTCAATGGATTGAGTTTACAAAACTAAATGGAGTATCAATTCAAG
















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|148957360|gb|EC903409.2|EC903409
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAG                         CTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
EST: gi|22819893|gb|BU499983.1|BU499983
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAACCGAATATTGTCTTTCAG                         CTGGAAGGAACAATCCTAGCTCCAACCCAGTGCTAAATCCTGGGGTTCAGG
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACAATCCTAGCTCCAACC-AGTGCTAAATCCTGGGGTTCAGG
EST: gi|87157047|gb|DY401836.1|DY401836
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAACCGAATATTGTCTTTCAG                         CTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
EST: gi|87156563|gb|DY401352.1|DY401352
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAACCGAATATTGTCTTTCAG                         CTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
EST: gi|148980217|gb|EE027018.2|EE027018
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAG                         CTGGAAGGAACA
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACA
EST: gi|26560071|gb|CA832306.1|CA832306
EST:     GGCCAATCTCGTTCTCTGGGCCTTACTGCAAACCGAATATTGTCTTTCAG                         CTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC
genomic: GGCCAATCTCGTTCTCTGGGCCTTACTGCAAATCGAATATTGTCTTTCAGgtaagcatgt ... cactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatggaagaataagttcgttgagtaatgctgtttaatgttgtactcactttgcagCTGGAAGGAACAATCCTAGCTCCAACCAGTGCTAAATCCTGGGGTTCAGGCTTGCTCCAGTGGCTCGAGTTCACCAAACTAAATGGAATGGTTATTCAAG
                                         tactcac  putative branch site (score: 1)
                                           ctcacttt  CT-rich tract
                               tttaatgtt  TA-rich tract