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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgacctccctccctctccctagatctgcgcgcgaaggcgcgacgacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG

Basic information

species Zea mays
transcript GRMZM2G092459_T03
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g38340.1 (Oryza sativa), 3'ss of exon 1
-----gtacgacctccctccctctccctagatctgcgcgcgaag-gcgcg-acgacggtgagtc--acgctgctgatctgctcctactctcgctcgcg-gcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAG--CCGGCG
        |   ||| ||| ||||  | ||||||||||||| || ||| |  |  ||| || ||  | || | ||||  |       |  ||| |||| ||||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||  ||||  ||||  ||| ||||  ||  | 
gtaagcctccctctctctctctctttccagatctgcgcgcggagagcgtgcgccgcggcgaatctgaggcgggtgatgagaatggg-tggcgcgcgcgcgcagGTACACGAAGATGGGGTTCGCCGGGAACGTGGAGCCCTGCTTCATCACCCCCACCGTCGTCGCCGTCAACGACACCTTCGCCGGC-CAGACCAGGGCCAAC-

upper sequence: GRMZM2G092459_T02 (Zea mays), 3'ss of exon 1
lower sequence: PP1S85_160V6.1 (Physcomitrella patens), 3'ss of exon 1
------gtacgacctccctccctctccctagatctgcgcgcgaaggcgcgac--gacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG-
        |   | ||  |     ||   |||  ||         || | |   |||||    |   ||     ||    ||  ||           | ||||| ||||||||||| ||||| ||||| ||||||||||| || || |  || || || || ||  |||| || |||||||  ||  ||| |    |     
gtctttaaagatcgtctttaaagatcgtgagacatggtatttgtagctcaatttgacggcatattgagcc-tacatagaatctcacgacatgaatatgtagGTATACGAAGATGGGATTCGCAGGGAATGTGGAGCCCTGTTTTATTATTCCTACAGTAGTGGCACTCAATGAGTCCTTTTTGGGC-CAGTCGGCTCCAAAG
















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|71448010|gb|DR829060.1|DR829060
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACTAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|71304657|gb|DR788445.1|DR788445
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|50332359|gb|CO527485.1|CO527485
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|78093378|gb|DV521752.1|DV521752
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|50332366|gb|CO527492.1|CO527492
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
EST: gi|71448011|gb|DR829061.1|DR829061
EST:     GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGG                         GTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC
genomic: GCCATGGACGCCTTGTCCCGCCCCGCTGTTGTCATCGACAACGGCACCGGgtacgacctc ... ctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcgcgacgacggtgagtcacgctgctgatctgctcctactctcgctcgcggcagGTACACGAAGATGGGGTTCGCGGGGAACGTGGAGCCCTGCTTCATCACCCCCACTGTCGTCGCCGTCAACGATTCCTTTTCCGGTTCAGGCCAGCCGGCG
                       tgctgat  putative branch site (score: 3)
                                 ctcctactctcgctc  putative PPT