Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGTGGGCTGGACTCTGAGAAAAATTGCGTGCATGGTTCGGATTCACCAGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttcttcactacttgtttcatatacggaagtgcaaagatcaccccataaaactttcttgaccttattttttttgataatgcag

Basic information

species Zea mays
transcript GRMZM2G060464_T02
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G060464_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os02g35700.2 (Oryza sativa), 5'ss of exon 3
ATGTGTGGGCTGGACTCTGAGAAAAATTGCGTGCATGGTTCGGATTCACCAGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttcttcactacttgtttcatatacggaagtgcaaagatcaccccataaaactttcttgaccttattttttttgataatgcag
||||||||  ||||||| |||||||| || ||||||||||| ||||||||| ||||||||| |||||| || ||||||||||| ||||| | |  ||| ||||||||||||||   |||||| ||||     || |   |||| |    ||  ||| |||||  ||| | || | |  ||||||||||
ATGTGTGGAGTGGACTCAGAGAAAAACTGTGTGCATGGTTCAGATTCACCACAATCTGCAGCCAGAGAAATTTCATTTTTCTTTGGAGATGTTAGATCTGgttggtttcttcat--cttgttccata-----aattttgaagagc----caccaaattttct-aaccctgttctgt--gataatgcag
















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|78106343|gb|DV524761.1|DV524761
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|22542609|gb|BU093047.1|BU093047
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGCGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|60356826|gb|DN223799.1|DN223799
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|120481163|gb|EH211203.1|EH211203
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|16916528|gb|BM072881.1|BM072881
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|91873960|gb|EB403917.1|EB403917
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|60358496|gb|DN225469.1|DN225469
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|78090669|gb|DV519043.1|DV519043
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|78106342|gb|DV524760.1|DV524760
EST:     AGAATCTGCAGACAGAGAGATCTCANNNNNNNNCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|26457519|gb|CA829102.1|CA829102
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|78090668|gb|DV519042.1|DV519042
EST:     AGAATCTGCAGACAGAGAGATCTCANNNNNNNNCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|60351869|gb|DN218842.1|DN218842
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
EST: gi|60339376|gb|DN206349.1|DN206349
EST:     AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCG                         TAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC
genomic: AGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttct ... gataatgcagTAACTGTGGAACATGATGAGCTATAGACGCCACACTGGTATCAGGCAAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGTGGGCTGGACTCTGAGAAAAATTGCGTGCATGGTTCGGATTCACCAGAATCTGCAGACAGAGAGATCTCATTTTTCTTCGGAGAAGCTGAATCCGgttggtttcttcactacttgtttcatatacggaagtgcaaagatcaccccataaaactttcttgaccttattttttttgataatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA