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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgaaagtaaattattgtatatttgtatgttcagtcgttaatatgaaatagcattttgcaaggcaaaactgcctgatatctaaatttacccattttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG

Basic information

species Zea mays
transcript GRMZM2G045331_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G045331_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os04g52340.1 (Oryza sativa), 3'ss of exon 2
---------tgaaagtaaattattgtatatttgtatgttc-agtcgttaatatgaaatagcattttgcaaggcaaaactgcctgatatctaaatttacccattttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG
            |   |||| |||||| | ||  |||||| |||| |||| |||| |   || |||    ||  |||       | |  | |||   ||  | |||||||||||| ||||| ||||||||||| || || || |||||||| || ||||| ||| |||||||  | || |||
gtaattttcctgatcaaaataattgtagactt-catgttccagtcattaacatgataagccagtttatttggtcaaa------aaaaattcaat---cctttcttttcagAAAAGAGAGATATTTCAAGATCTGGCCCCACTTCTTTGGCATTCTTTTGGAACAGTTGCTGCACTTCTTCAG
















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|78123053|gb|DV541437.1|DV541437
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|76281973|gb|DV021541.1|DV021541
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|78088708|gb|DV517101.1|DV517101
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|60350887|gb|DN217860.1|DN217860
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|149048884|gb|EE048384.2|EE048384
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|31351237|gb|CD435594.1|CD435594
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|78091209|gb|DV519583.1|DV519583
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|211374626|gb|FK958606.1|FK958606
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|9731640|gb|BE510392.1|BE510392
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|71445883|gb|DR826933.1|DR826933
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|211374623|gb|FK958603.1|FK958603
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|31356490|gb|CD440847.1|CD440847
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGTANNNNNNNGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|211374624|gb|FK958604.1|FK958604
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|76936740|gb|DV174858.1|DV174858
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|31354815|gb|CD439172.1|CD439172
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|211371968|gb|FK958598.1|FK958598
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCATTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|74233595|gb|DT641509.1|DT641509
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
EST: gi|91056772|gb|EB167190.1|EB167190
EST:     AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAG                         AAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC
genomic: AACTCTGCGACCCTGAACTGCGCGAGAACGCTTTACTTGAGCTCTCCAAGgttgcttcca ... attttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatagcattttgcaaggcaaaactgcctgatatctaaatttacccattttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG
                               atctaaa  putative branch site (score: 3)
                                      tttacccattttttc  CT-rich tract
                           tgatatctaaattta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgaaagtaaattattgtatatttgtatgttcagtcgttaatatgaaatagcattttgcaaggcaaaactgcctgatatctaaatttacccattttttcagAAAAGGGAGATTTTTCAAGATCTTGCTCCGCTGCTTTGGCACTCATTTGGCACAATTGCTGCGTTACTCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC