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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAGCAGCAATACGCTACCTGAGGAAGAACGGAGGTTCTATCTCTACAATGATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaatttaatcttggcactggcagcactaccttttcatttctttcttccatcatcagtcagaattcgggtcagtttacattagtttttttggac...

Basic information

species Zea mays
transcript GRMZM2G138425_T02
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G138425_T04 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g42420.3 (Oryza sativa), 5'ss of exon 7
TAGCAGCAATACGCTACCTGAGGAAGAACGGAGGTTCTATCTCTACAATGATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaatttaatcttggcactggcagcactacctttt--catttctttcttccatcatcagtcagaattcgggtcagttt---acattagtttttttggac-
|   || ||| |       ||||| || || || ||||| || || |||||||||||||||||||||||||||||||||||||||||||||||||||||||||  ||       ||      | ||  | ||  | ||      |   ||||||||     ||  ||     |    |||||||   || |||  | | | | |  
TGATAGTAATGCCGCGAAAGAGGACGATCGCAGATTCTACCTTTATAATGATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtatgca----cccattccaatattgtgaacatcatctaccagtacagctttcttctggtttctttcttggat--aatcagtttctcactttacatatatagaaat
















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|5361059|gb|AI795674.1|AI795674
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|94480225|gb|EB709183.1|EB709183
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGGGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|211522640|gb|FL444084.1|FL444084
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|78108347|gb|DV526765.1|DV526765
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|211411772|gb|FL439050.1|FL439050
EST:     ATCTTAGAGTTCTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|50337951|gb|CO533077.1|CO533077
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|78104409|gb|DV522827.1|DV522827
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|78022366|gb|DV490753.1|DV490753
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|16926570|gb|BM079638.1|BM079638
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|50337952|gb|CO533078.1|CO533078
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|13178288|gb|BG349546.1|BG349546
EST:     TTTAGAGTTGTATTTCCTCAAAGGGCAGCTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: CTTAGAGTTGTATTTCCTCAAA-GGCA-CTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
EST: gi|13178547|gb|BG349805.1|BG349805
EST:     ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAG                         CTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC
genomic: ATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaa ... tttgttgcagCTGCGAGTGGAGCATGATTTCCCCGCCGATCCCAAGTACTTTGACATAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAGCAGCAATACGCTACCTGAGGAAGAACGGAGGTTCTATCTCTACAATGATCTTAGAGTTGTATTTCCTCAAAGGCACTCAGATGCAGATGAAGGCGAGgtacacaaaatttaatcttggcactggcagcactaccttttcatttctttcttccatcatcagtcagaattcgggtcagtttacattagtttttttggac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG