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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAGTTCGTCAATCCTTTGCTCCTCCATCCCGACCTCGTAA

Basic information

species Zea mays
transcript GRMZM2G322953_T03
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G322953_T05 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os05g36270.3 (Oryza sativa), 3'ss of exon 2
gtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAGTTCGTCAATCCTTTGCTCCTCCATCCCGACCTCGTAA
||||  |  |     | | ||       ||       ||||  |   | ||||      |     |||||  || |||||    | ||  ||  |||||||||| || ||||||||||||||||||||||||||  |||||||| |  |||||||||| ||                                      
gtaatacagtac---agattagcagtttatgttttgctacagat---aagttcagtttctgaaacttgacagtgacactccattcctttctg--tgcagTGTGTTCTTGTGTCTGAAGAGAACGAGGAGGCCATTATCGTCGACGCTCCCCTCCGCGGAAA--------------------------------------
















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|87152940|gb|DY397729.1|DY397729
EST:     TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
EST: gi|22490108|gb|BU050031.1|BU050031
EST:     TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAG
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAG
EST: gi|211164076|gb|FL013514.1|FL013514
EST:     TCCTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGAACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
EST: gi|78104993|gb|DV523411.1|DV523411
EST:     TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
EST: gi|211164070|gb|FL013508.1|FL013508
EST:     TCCTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAGG
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGG
EST: gi|18654939|gb|BM499744.1|BM499744
EST:     TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACC                         TGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC
genomic: TACTGTCCAACGAGGTCTTCGTGAAGGCGCTCGTCAGCAGCGGCCGCACCgtaacgcgct ... ttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAGTTCGTCAATCCTTTGCTCCTCCATCCCGACCTCGTAA
                   cattgac  putative branch site (score: 3)
                                 ctctgcgctttctt  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaacgcgctctcctacactacatacacatacacccgtacacgtcccaggttctcggcttaggcattgactttggcactctgcgctttcttgcgtgcagTGTGTCCTCGTGTCTGAAGAGAACGAGGAGGCCATCTTCGTCGACCCGGCCCTCCGCGGGAAGTTCGTCAATCCTTTGCTCCTCCATCCCGACCTCGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC