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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgtgcgtgcgtgacttgttggactgcgaaattctccatggttttcttgggctctcttctccatcaaacggcctcgggctggtcctctgttttcacgcgcctcaccgcacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACACACATCCGCAAGAAGCTCGTCCGGATGGGGATC

Basic information

species Zea mays
transcript GRMZM2G048910_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G048910_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g14670.1 (Oryza sativa), 3'ss of exon 2
gtgcgtgcgtgcgtgacttgttggactgcgaaattctccatggttttcttgggctctcttctccatcaaacggcctcgggctggtcctctgtt-ttcacgcgcctcaccgcacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACACACATCCGCAAGAAGCTCGTCCGGATGGGGATC
  | |||  || |||   |||  ||   ||      | |||||        || | |||| || ||         |  || | || ||| ||   | |   || || |||   | ||||||||||||||||||||||||| ||| || || ||||||||||||||||||||||||||||||||||||||||||   |||||||||  |  |||||| |||
--gtgtgtttgtgtg---tgtgagatcacg------ttcatggc-------ggatttcttttcgatt--------tttggttcgttctcggtgactgattggcgtcgccggtgggcgcagGTGGTCCAAGATCGCGGCGCGGCTCCCCGGGAGGACGGACAACGAGATCAAGAACCACTGGAACACACACATCAAGAAGAAGCTCCGCAAGATGGGCATC
















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|211063758|gb|FL078031.1|FL078031
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|67021186|gb|CO449935.1|CO449935
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063761|gb|FL078034.1|FL078034
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCA
EST: gi|211063764|gb|FL078037.1|FL078037
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063762|gb|FL078035.1|FL078035
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063766|gb|FL078039.1|FL078039
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGG
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGG
EST: gi|148958717|gb|EC904989.2|EC904989
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|76934017|gb|DV173689.1|DV173689
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063767|gb|FL078040.1|FL078040
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063760|gb|FL078033.1|FL078033
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|149085462|gb|EE174968.2|EE174968
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
EST: gi|211063759|gb|FL078032.1|FL078032
EST:     GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAG                         GTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA
genomic: GACGACGAGGAGAGGCTCGTCATCGACCTGCACGCGCAGCTCGGGAACAGgtgcgtgcgt ... cacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atcaaacggcctcgggctggtcctctgttttcacgcgcctcaccgcacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACACACATCCGCAAGAAGCTCGTCCGGATGGGGATC
                                    gcctcac  putative branch site (score: 3)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgtgcgtgcgtgacttgttggactgcgaaattctccatggttttcttgggctctcttctccatcaaacggcctcgggctggtcctctgttttcacgcgcctcaccgcacgacgcagGTGGTCCAAGATCGCGGCGCAGCTACCGGGCAGGACGGACAACGAGATCAAGAACCACTGGAACACACACATCCGCAAGAAGCTCGTCCGGATGGGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC