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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACAAAGCCAGCCGCAACAGATGTCATCGGTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacatttttccccagtccactctgaaatcttccatgtgaccatgtccactctgaaatatgccattttccgttatttgtaaatgtggtgtcgctgtatcc...

Basic information

species Zea mays
transcript GRMZM2G365374_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G365374_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ20961 (Selaginella moellendorffii), 5'ss of exon 1
---------------------CACAAAGCCAGCCGCAACAGATGTCATCGGTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacatttttccccagtccactctgaaatcttccatgtgaccatgtccactctgaaatatgccattttccgttatttgtaaatgtggtgtcgctgtatcc
                       ||||||  || | |   |||||||||||||||||| | |||||||||||||| ||||| || || ||||| || ||||||    | || |   ||   | |    |  |   | |||| || |    |||         || ||   |                             
ATGGCTGCTTGGTGTTGTTGTAGCAAAGCT-GCTGGAGGGGATGTCATCGGTATCGATTTGGGCACAACGAATTCTTGCGTTTCTGTGATGGAGGGCAAGgtaa--ctatcacatttctcttttttcgtgcttgttatgacgattttttttct------cttcacttctag-----------------------------

upper sequence: GRMZM2G365374_T01 (Zea mays), 5'ss of exon 3
lower sequence: EFJ32297 (Selaginella moellendorffii), 5'ss of exon 1
---------------------CACAAAGCCAGCCGCAACAGATGTCATCGGTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacatttttccccagtccactctgaaatcttccatg-tgaccatgtccactctgaaatatgccattttccgttatttgtaaatgtggtgtcgctgtatcc
                       ||||||  || | |   |||||||||||||||||| | |||||||||||||| ||||| || || ||||| || ||||||  | |  |     ||   | |      |   |||  ||  || |      | |  | |                                        
ATGGCTGCTTGGTGTTGTTGTAGCAAAGCT-GCTGGAGGGGATGTCATCGGTATCGATTTGGGCACAACGAATTCTTGCGTTTCTGTGATGGAGGGCAAGgtaactatcacatttctcttttttcgtgcttgttatggcgaaaatttttttcttcacttctag--------------------------------------
















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|148941311|gb|EC886216.2|EC886216
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|149084295|gb|EE173729.2|EE173729
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211323068|gb|FL021672.1|FL021672
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|4753439|gb|AI657349.1|AI657349
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|32935708|gb|CF040520.1|CF040520
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211323069|gb|FL021673.1|FL021673
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|148996233|gb|EE035510.2|EE035510
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|149112242|gb|EE295147.2|EE295147
EST:     GTATCGATCTAGGCACAACGAATACCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211325253|gb|FL021695.1|FL021695
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211296076|gb|FL131064.1|FL131064
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|148970119|gb|EE021057.2|EE021057
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|148940757|gb|EC885578.2|EC885578
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211325246|gb|FL021688.1|FL021688
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|61118988|gb|DN559949.1|DN559949
EST:     CTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: CTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211296070|gb|FL131058.1|FL131058
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ATACCACGGGNGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|38502553|gb|CF972413.1|CF972413
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211323074|gb|FL021678.1|FL021678
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211323071|gb|FL021675.1|FL021675
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211327407|gb|FL021697.1|FL021697
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211323075|gb|FL021679.1|FL021679
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCACAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|148954033|gb|EC899430.2|EC899430
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|76293599|gb|DV033167.1|DV033167
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211325245|gb|FL021687.1|FL021687
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211298204|gb|FL131069.1|FL131069
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAACGCAGAAGGCGCGAGGACAACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211325240|gb|FL021682.1|FL021682
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|211325241|gb|FL021683.1|FL021683
EST:     GTATCGATCTAGGCACTACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
EST: gi|149110606|gb|EE190506.2|EE190506
EST:     GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAG                         ACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT
genomic: GTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacattttt ... gcttgtgtagACACCACGGGTGATTGAAAATGCAGAAGGCGCGAGGACGACACCCTCCATT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACAAAGCCAGCCGCAACAGATGTCATCGGTATCGATCTAGGCACAACGAATTCCTGCGTCTCCGTCATGGAAGGAAAGgtacatttttccccagtccactctgaaatcttccatgtgaccatgtccactctgaaatatgccattttccgttatttgtaaatgtggtgtcgctgtatcc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA