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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtcatcgatcagtcatcagtgttctcttcactatttgtccacagcctgcaacgccggccgccggcggataggaagtacttcataggaactgagggtgctctttgtttgcgccttgtgtctcggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGTCATCGTCGACCTGGTGCAGGAGATCGCGGAGGCCGTGTCGGCGTTCACG

Basic information

species Zea mays
transcript GRMZM5G829946_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G829946_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os04g32320.1 (Oryza sativa), 3'ss of exon 8
gtgagtcatcgatcagtcatcagtgttctcttcactatttgtccacagcctgcaacgccggccgccggcggataggaagtacttcataggaactgagggtgctctttgtttgcgccttgtgtctcggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGTCATCGTCGACCTGGTGCAGGAGATCGCGGAGGCCGTGTCGGCGTTCACG
                   | ||||   || | |  || ||         ||   |  | || | || ||   | || |            | ||| | || |||||| ||||   |||  | |   |   ||||||||||| || ||| ||||||| ||||||| |||||||||||||||||||| |||||||||||||||  ||||||||| | ||||||||| | |||| | 
------------------gtgagtgccgtcgtgatcatgtgcttgtg---tgtggctgcagctgacgacgacgacgacg----------acattgatgatg-tctttgcttgcat-ttgcatttgcataatgcagCAACGTGCCGAAGGCGGTGTACTTGCAGCAGCTGATGGGGGTGGACGGCGTGATCGTCGACCTGGTGGCGGAGATCGCCGCGGCCGTGTCCGAGTTCGCC
















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|50328123|gb|CO523249.1|CO523249
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|31355157|gb|CD439514.1|CD439514
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|50326841|gb|CO521967.1|CO521967
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGCCCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCCCCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|93017159|gb|EB642679.1|EB642679
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|78180580|gb|DV550908.1|DV550908
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|26455300|gb|CA826883.1|CA826883
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|87154706|gb|DY399495.1|DY399495
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|12046438|gb|BF728577.1|BF728577
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|71429646|gb|DR810696.1|DR810696
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|24769990|gb|CA405119.1|CA405119
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|6964668|gb|AW433361.1|AW433361
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAN                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|21236541|gb|BQ441992.1|BQ441992
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|6973514|gb|AW438208.1|AW438208
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|71307445|gb|DR789929.1|DR789929
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|110206346|gb|EC888243.1|EC888243
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCCCCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|31349103|gb|CD433460.1|CD433460
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|148964440|gb|EE015554.2|EE015554
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCCCCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|24769781|gb|CA404910.1|CA404910
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCCCCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|74237764|gb|DT645678.1|DT645678
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAA                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
EST: gi|24763547|gb|CA398719.1|CA398719
EST:     AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTCCGGTCAGCTCAC                         CAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT
genomic: AAGATCAAGGAGGCCAACAAACTGTCGCTGATGACCTACGGTCAGCTCAAgtgagtcatc ... ggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttcataggaactgagggtgctctttgtttgcgccttgtgtctcggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGTCATCGTCGACCTGGTGCAGGAGATCGCGGAGGCCGTGTCGGCGTTCACG
                        tttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtcatcgatcagtcatcagtgttctcttcactatttgtccacagcctgcaacgccggccgccggcggataggaagtacttcataggaactgagggtgctctttgtttgcgccttgtgtctcggtctcgcagCAACGTGGCGGAGGTGGTGTACGTGCAGCACCTGATGGGGGTGGACGGCGTCATCGTCGACCTGGTGCAGGAGATCGCGGAGGCCGTGTCGGCGTTCACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC