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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGGGGATACTGAGTTGAATATGATCTCAAATCCGGTGGACTGGTATAGTTTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcagttcatgaattccttctctctttctttttgtgaaaagtttcggaatttcttgataaacgtagcatctcacttctatttgtaagccactgca...

Basic information

species Zea mays
transcript GRMZM2G093096_T02
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G093096_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g27019.1 (Oryza sativa), 5'ss of exon 3
CTGGGGATACTGAGTTGAATATGATCTCAAATCCGGTGGACTGGTATAGTTTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcagttcatgaattccttctctctttctttttgtgaaaagtttcggaatttcttgataaacgtagcatctcacttctatttgtaagccactgca
|||||||| |||||||||||||||| |||||||||||| | ||||| |||||||| ||||||||||||| |||| ||||| ||||||||||||| | |||||||||||  ||  |              ||  |  || |      ||   || | | |      |  | ||||     |  |  || || |      | 
CTGGGGATCCTGAGTTGAATATGATATCAAATCCGGTGAATTGGTACAGTTTCGGTCCCGGATAGAATTTGTAGTGATGCCAGATTGGAGGGTGGGCGAGgtaatctcttttttttttcaataagaaaattaatcattttcttgccttcttgattgtatatgggcatatggcatggtgataattcttatatgattgatct
















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|211099742|gb|FL268173.1|FL268173
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|60399400|gb|DN232214.1|DN232214
EST:     GGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: GGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|211097273|gb|FL268169.1|FL268169
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTGGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|211097275|gb|FL268171.1|FL268171
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|211097270|gb|FL268166.1|FL268166
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|211099741|gb|FL268172.1|FL268172
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
EST: gi|211097272|gb|FL268168.1|FL268168
EST:     TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAG                         TTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT
genomic: TTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcag ... gcttttacagTTCGAAGGTAAATTCACTGATGAGTTTGCCCACAGCAGTAGCAACGAACAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGGGGATACTGAGTTGAATATGATCTCAAATCCGGTGGACTGGTATAGTTTCGGACCCGGATAGAATTGGTAGGGATGCAAGATTGGAGGGTGCGTGAGgtaatctcagttcatgaattccttctctctttctttttgtgaaaagtttcggaatttcttgataaacgtagcatctcacttctatttgtaagccactgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG