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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtactcgggttcttgcgcgggtcaaagtgggttcttcgggcggattccttctcaaggatcgctgggaaggtgggatcttggcgctgattcgtttggtcttgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGAGATGTCGGCGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTG

Basic information

species Zea mays
transcript GRMZM2G151050_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G151050_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os11g09329.2 (Oryza sativa), 3'ss of exon 1
gtgagta-ctcgggttcttgcgcgggtcaaagtgggttcttcgg--gcggattccttct--------caaggatcgctgggaaggtgggatcttggcg-ctgattcgtttggtc---ttgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGAGATGTCGGCGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTG--------------------
|||||   |||||||||||||| ||   ||  || ||| || ||  ||||||||    |           |||     || |||||||||  |||| | |||||| |  ||||    ||  | ||  |  |  ||| |||||| |    || ||||||  ||            ||  | ||| || |||| ||||||||||||||||||||||| | ||||||||||                    
gtgaggggctcgggttcttgcggggtggaagatgtgtttttggggggcggattcgggttgggggcgttggggaggtgcggaaaggtgggaatttgggggctgatttgggtggtttgtttttgttgttgtttgcagGATTTAGG-GTTTTTGGTGGTGAGAGG------------GGGAAAATGGCGACGGCCGTGGCGTGCGCGGAGAGGGCGACGAGCGACATGCTGATCGGGCCGGATTGGGCGGT
















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|148954553|gb|EC899991.2|EC899991
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|149100088|gb|EE186140.2|EE186140
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|91871540|gb|EB401497.1|EB401497
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|93012296|gb|EB637816.1|EB637816
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|89247370|gb|DY619156.1|DY619156
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|29168003|gb|CB411263.1|CB411263
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|33942576|gb|CF349176.1|CF349176
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|211038878|gb|FL017021.1|FL017021
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|74233431|gb|DT641345.1|DT641345
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|28873357|gb|CB329357.1|CB329357
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|93013764|gb|EB639284.1|EB639284
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|148962190|gb|EE013005.2|EE013005
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|149106511|gb|EE188403.2|EE188403
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|31909129|gb|CD650764.1|CD650764
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
EST: gi|71449169|gb|DR830219.1|DR830219
EST:     CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTG                         GATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA
genomic: CTCTTTGGTGGTTCCTAAGGGCGAATCTCGTGGCGATTCGCTCAGATTTGgtgagtactc ... tgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatcgctgggaaggtgggatcttggcgctgattcgtttggtcttgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGAGATGTCGGCGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTG
                           cgctgat  putative branch site (score: 4)
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtactcgggttcttgcgcgggtcaaagtgggttcttcgggcggattccttctcaaggatcgctgggaaggtgggatcttggcgctgattcgtttggtcttgcgctgcagGATTTAGGGTTTAGGAGGCGGTGCTGGTGATCGGTTTGTGCCGCCGGGAGAGATGTCGGCGGCTGTGGCGTGCGCGGAGAGGGCGACTAACGACATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG