Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcag

Basic information

species Zea mays
transcript GRMZM2G166345_T02
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G166345_T02 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g60660.1 (Oryza sativa), 5'ss of exon 8
CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcag
||| || |||||||||||||||||||||||||| ||||||| ||||||||||||||| ||||| ||||  | ||||||||| || |||  |||||||| ||| | |||| || | |||  |||| ||  ||  ||||||   |  |||  ||  ||||| | | | | | |||| || ||  || |||| ||| ||    ||| ||||   |||
CCTCTTGGTTGAGGAGATAGATTTGGGAGATGGCAATGTGCATCAAGTTGTTAGTGGGCTTGCCAAGTTCTTCAGCCCAGAGGAACTTGTTgtgagtatttaacagcaacaatggacttgaattattcctgttcatttttcttgccatg-aaattgtttcatccaagattctgttttctgtaataaacaactgcct----tttccttca--cag
















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|18173735|gb|BM349123.1|BM349123
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|32913187|gb|CF017999.1|CF017999
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|31363989|gb|CD448344.1|CD448344
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|213173994|gb|FM188956.1|FM188956
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|32863847|gb|CF003529.1|CF003529
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|149110254|gb|EE294046.2|EE294046
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTATT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211207476|gb|FL411825.1|FL411825
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|56462002|gb|CK986300.1|CK986300
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|83279363|gb|DV943371.1|DV943371
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|91874366|gb|EB404323.1|EB404323
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATTTTACT                         AATCGGCATGTTGTTTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|91873662|gb|EB403619.1|EB403619
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|38229745|gb|CF920058.1|CF920058
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211244774|gb|FL481676.1|FL481676
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|12972445|gb|BG267985.1|BG267985
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211217164|gb|FL385248.1|FL385248
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|213173188|gb|FM191133.1|FM191133
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|32863787|gb|CF003469.1|CF003469
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|67022300|gb|CO451049.1|CO451049
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAAATGATCTTACT                         AATCG-CATGTTGTCTTGA
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGA
EST: gi|32849223|gb|CD988904.1|CD988904
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|88756566|gb|DY540707.1|DY540707
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATTTTATT                         AATCGGCATGTTGTTTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|24934254|gb|CA452472.1|CA452472
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|71758158|gb|DR956095.1|DR956095
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|33095762|gb|CF055756.1|CF055756
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|32944796|gb|CF049615.1|CF049615
EST:     GTCAAGTTGTTAGCGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|93280898|gb|EB673162.1|EB673162
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTATT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211105793|gb|FL432184.1|FL432184
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|91053825|gb|EB164243.1|EB164243
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|166465899|gb|EG190327.1|EG190327
EST:     TTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: TTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|211165085|gb|FL207333.1|FL207333
EST:     AAAGTATTGCAGCCCAGATGATCTTACT                         AATCGSCATGTTGTCTTGATCACGAATGTGAAGCCTGGGAAGCTGCGAGAT
genomic: AAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|76286900|gb|DV026468.1|DV026468
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|17931240|gb|BM268200.1|BM268200
EST:     GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
EST: gi|78112559|gb|DV530953.1|DV530953
EST:     GTCAAGTTGTCAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACT                         AATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT
genomic: GTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagtt ... cttctttcagAATCGGCATGTTGTCTTGATCACGAATGTGAAGCCTGGAAAGCTGCGAGAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTTTTAGTTGAGGAGATAGATTTGGGAGATGGTAATGTGCGTCAAGTTGTTAGTGGTCTTGCAAAGTATTGCAGCCCAGATGATCTTACTgtgagtagttagctgcaagaaggaactcaaattgtttttgaccattttctctctcatttaagatgtttgacctatgttgctgtgttttgctatgaacacctgtctgtcgttttcttctttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG