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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcgagcaccatccttcatctccatgccgcggcgagcatcgtccatgtcagcttcgttcccgtgtgtttctgacgacggcgtgcgtgtgcatgtgcctgtgcctgtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGAAGGACCTCTTCCTCCCATTCCGCTGCTTCTGCACGCGCAAAGAC

Basic information

species Zea mays
transcript GRMZM2G301647_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G301647_T02 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g54590.1 (Oryza sativa), 3'ss of exon 1
gcgagcac--catccttcatctccatgccgcggcgagcatcgtccatgtcagcttcgttcccgtgtgtttctgacgacggcgtgcgtgtgcatgtgcctgtgcctgtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGAAGGACCTCTTCCTCCCATTCCGCTGCTTCTGCACGCGCAAAGAC
|| | |||  |||||  |    ||  ||||| |  | |      |  ||| | ||   ||  || | | ||||||||           |||| | ||        | | |||||||||| |||| |||||| ||||||||||| |||||| |||||||||||||||||||||| |||||||| |||||||||||||||||||| ||||||
gcaaccactgcatcccccggacccccgccgctgaaatc-----tctcgtcggatt---tcaagtttttctctgacga-----------tgcacgcgc--------gcgtgtgcagGTGGCGTGGAGGACGCGGCCGGGTACAAACAGCCGTCGGACCCGCAGATGAAGGACCTGTTCCTCCCGTTCCGCTGCTTCTGCACGCGGAAAGAC
















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|89760757|gb|DY689040.1|DY689040
EST:     CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
EST: gi|76912619|gb|DV164822.1|DV164822
EST:     CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
EST: gi|78076030|gb|DV504464.1|DV504464
EST:     CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
EST: gi|89762511|gb|DY690058.1|DY690058
EST:     CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
EST: gi|160481517|gb|EY254349.1|EY254349
EST:     CTCGTGCCAC-TCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CTCGTG-CACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
EST: gi|89761195|gb|DY689309.1|DY689309
EST:     CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGG                         GTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA
genomic: CAGGGGCCAGACCATCGTCCTCGTGCACGTCAACACCAAAGGCACCTCGGgcgagcacca ... gtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccgtgtgtttctgacgacggcgtgcgtgtgcatgtgcctgtgcctgtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGAAGGACCTCTTCCTCCCATTCCGCTGCTTCTGCACGCGCAAAGAC
        ttctgac  putative branch site (score: 2)
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcgagcaccatccttcatctccatgccgcggcgagcatcgtccatgtcagcttcgttcccgtgtgtttctgacgacggcgtgcgtgtgcatgtgcctgtgcctgtgcgtgcagGTGGGGTGGCGGACGCCGCCGGGTACAAGCAGCCGACGGACCCGCAGATGAAGGACCTCTTCCTCCCATTCCGCTGCTTCTGCACGCGCAAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG