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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactttctacactcttgccatttagaatttgtttaattttggtggacaagaattcatcctgacttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG

Basic information

species Zea mays
transcript GRMZM5G896731_T03
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G896731_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g22610.2 (Oryza sativa), 3'ss of exon 7
gtactttctacactcttgc-catttagaatttgtttaattttggtggacaagaattcatcctgacttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG
|||  ||| |||    ||  |||||     |   ||||| | | |  | |    |  |   | ||||||| |||||||||||||||| ||||||| ||||| || ||||| ||||| || |||||||| |||| ||| ||||| ||||||
gtaggttcgacatctgtgttcatttcc--ctcccttaatgtggataaatattcttatactttaacttattcagGAATTGGACGGCCACCTGGCCAAATGGACCCCAAAGCTTTTGTGCTCCAGAAGTTTAATAAGACCGGTCGAGAACGG

upper sequence: GRMZM5G896731_T02 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os03g22610.1 (Oryza sativa), 3'ss of exon 6
gtactttctacactcttgc-catttagaatttgtttaattttggtggacaagaattcatcctgacttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG-----------------------
|||  ||| |||    ||  |||||     |   ||||| | | |  | |    |  |   | ||||||| |||||||||||||||| ||||||| ||||| || ||||| ||||| || |||||||| |||| ||| ||||| ||||||                       
gtaggttcgacatctgtgttcatttcc--ctcccttaatgtggataaatattcttatactttaacttattcagGAATTGGACGGCCACCTGGCCAAATGGACCCCAAAGCTTTTGTGCTCCAGAAGTTTAATAAGACCGGTCGAGAACGGGTAAATATCTATATGGCTAGTAC
















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|32933882|gb|CF038694.1|CF038694
EST:     TGTTATATACCACTTCCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGGTCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|60358732|gb|DN225705.1|DN225705
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|71438321|gb|DR819371.1|DR819371
EST:     TGTTATATACCACTTTCGTAGGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCC
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCC
EST: gi|78085319|gb|DV513712.1|DV513712
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATCG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|89250808|gb|DY622594.1|DY622594
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|86468848|gb|DY235218.1|DY235218
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
EST: gi|78109135|gb|DV527552.1|DV527552
EST:     TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTG                         GAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA
genomic: TGTTATATACCACTTTCGTAAGAATCGAGAATTTTGCCGATTAAGGATTGgtactttcta ... acttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccatttagaatttgtttaattttggtggacaagaattcatcctgacttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG
                                        tcctgac  putative branch site (score: 2)
                                              cttattt  CT-rich tract
     ttagaatttgtttaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactttctacactcttgccatttagaatttgtttaattttggtggacaagaattcatcctgacttatttagGAATTGGACGGCCAGCTGGCCAGATGGATCCTAAAGCCTTTGTTCTTCAGAAGTTCAATAGGACTGGTCGTGAACGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT