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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTCCTGGAGATCGAGCCCAAGGCATGGGCGGGGATGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggcccttccatccctcccacccgatcgtgttatatgtgttcacctactttcacagcagttgggtgagggactggattcgaaggtcagtgccgctgg...

Basic information

species Zea mays
transcript GRMZM2G092776_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G092776_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g02170.1 (Oryza sativa), 5'ss of exon 2
GTTCCTGGAGATCGAGCCCAAGGCATGGGCGGGGATGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccctt-ccatccctcccacccgatcgtgttatatgtgttcacctactttca-cagcagttgggtgagggactgga-ttcgaaggtcagtgccgctgg-----------------------------------------------------------------------------------------
||||||||||||||| |||||||| ||| ||||| ||||||||||||| |||||| | || |||   |||||||||||||| |||||||||| ||  |      | |  |||  |||| || ||  ||  |      |||   |||   |   |||| ||  |||   |     ||  |      ||                                                                                          
GTTCCTGGAGATCGATCCCAAGGCGTGGTCGGGGCTGGAGGAGACGGCGGCGTCGTCCGAGGCC---AAGCATCACATCGGCGCGgtacggcactcactgcattttctgccc--tcgtattgtaattggccgtgcgttttggtcagtgttgcagtgatggtttggggcttaggtgtttgattatatgcctacaagactgttcaacttcaatttccgcgtgtgcttgaccagtgaaatttgtgttttcgtagcatctcatatcactctcattttgtag
















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|211249133|gb|FL249388.1|FL249388
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGTTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|149008583|gb|EE040762.2|EE040762
EST:     TGGAGGAGACGGGCGCGTCGCCGGACGCCGCCAAACATCACATCGGTGCG                         TTTATAAACATACTCTTTGAGGAAGACGGGGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|148967634|gb|EE018890.2|EE018890
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|74240503|gb|DT648417.1|DT648417
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|149106667|gb|EE188561.2|EE188561
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|211251350|gb|FL249389.1|FL249389
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|149094696|gb|EE180247.2|EE180247
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|148979722|gb|EE026796.2|EE026796
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|76284885|gb|DV024453.1|DV024453
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|149005261|gb|EE039808.2|EE039808
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|74233199|gb|DT641113.1|DT641113
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGTTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
EST: gi|50325911|gb|CO521037.1|CO521037
EST:     TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCG                         TTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA
genomic: TGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggccct ... ggtttcgcagTTTATAAGCATACTCTTTGAGGAAGACGGCGAGAGCTCTTCAGACAGGCTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTCCTGGAGATCGAGCCCAAGGCATGGGCGGGGATGGAGGAGACGGCCGCGTCGCCGGACGCCGCCAAGCATCACATCGGTGCGgtacggcccttccatccctcccacccgatcgtgttatatgtgttcacctactttcacagcagttgggtgagggactggattcgaaggtcagtgccgctgg

- - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - AGGAGA