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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTTTATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatcttaaggtgcacattaaaacaatggatagttagtcataataatgatgcaaaattttcttgtgtacttcaatttcgaaatttgatgcattactg...

Basic information

species Zea mays
transcript GRMZM5G862959_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g19350.1 (Oryza sativa), 5'ss of exon 7
TCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTTTATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatcttaaggtgca-cattaaaacaatggatagtt----agtcataataatgatgcaaaattttcttgtgtacttcaatttcgaaat-ttgatgcattactg
|||||| |||||||| ||||||||||||||||||||||| ||||||||||||||| ||||||||||| |||| |||||||| || || ||| ||||||||||||||||||||  |    ||| ||  | ||| | |  |    |||| | | | | ||   |  |||  || |||  |  | |   |   | |  ||   |     
TCCTTCCAGTGCCCCAGATTTTGGGCAGGGTCGACAAGTCTTAGCTGTTTATCCTAGCACAACAGCACTATATAGAGCTACTGTTGCCTCTAATCGTAAGgtaacatcttaaaatctttcatgaatcctatgtaaatcttttaagtcttgacagtaatttgag-tttctttctgtgttctagtcctgtcctgtccatatgt-----
















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|78118927|gb|DV537311.1|DV537311
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|13126562|gb|BG317132.1|BG317132
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|78116253|gb|DV534640.1|DV534640
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|67011782|gb|CO440531.1|CO440531
EST:     ATCCTGNCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AAGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|78084340|gb|DV512733.1|DV512733
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|71332524|gb|DR803227.1|DR803227
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|13126563|gb|BG317133.1|BG317133
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|149071365|gb|EE159760.2|EE159760
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|148974313|gb|EE025086.2|EE025086
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|67025991|gb|CO454740.1|CO454740
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|113703551|gb|EE681055.1|EE681055
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|60345456|gb|DN212429.1|DN212429
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA
EST: gi|60396327|gb|DN229196.1|DN229196
EST:     ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAG                         AGGAAGTCTGATGA
genomic: ATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatctt ... aatattccagAGGAAGTCTGATGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTTCGAGTGCCCCGGATTTTGGGCAGGGTCGACAAGTTTTAGCTGTTTATCCTGGCACAACAGCATTATACAGAGCTACCGTAGCTTCTCATCGTAAGgtaacatcttaaggtgcacattaaaacaatggatagttagtcataataatgatgcaaaattttcttgtgtacttcaatttcgaaatttgatgcattactg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT