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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atattcatcaatattcttgtctccatgctttgattctatggcaaagggaatattagttctgcatgctgatctctgattgtatccccctttttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTC

Basic information

species Zea mays
transcript GRMZM2G115939_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115939_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os10g11260.3 (Oryza sativa), 3'ss of exon 1
---atattcatcaatattcttgtctccatgctttgattctatggcaa-agggaatattagttctgcatgctgatctctgattgtatccccctttttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTC
   | || ||  |||     |   |   | || |  |    |  ||  |||  ||| |  || | |   |||||     ||  | ||||| ||| ||||  |||||||||| |||||||| |||||||||||| | ||||||||||  |||||||||||||| |||||||||| ||||| ||||| || |||||||| ||||||
cagagatgcagaaatgcaactaattatgttctcttttgtgctttcatcaggtgatagtgttttttct--ctgattgtaaatcttttccccttttctttg--cagAAAGATGCTTAATCTTATCAAAATAAAGGATAAAAAGAAAGAGCAGGCAGCAAGTGCTGCTGGAAAGGCTCCTGTGAAGAAGCAATCTGCTGGAGAGCTC
















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|211132803|gb|FL366559.1|FL366559
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211373002|gb|FL342998.1|FL342998
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAWAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|9028438|gb|BE238583.1|BE238583
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211398788|gb|FL318386.1|FL318386
EST:     AAGGAAGCCGTTCCACGCTCCTCCAGCGAGCTCCGTGCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|32915063|gb|CF019875.1|CF019875
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTGCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211259767|gb|FL311710.1|FL311710
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|78077789|gb|DV506218.1|DV506218
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|24462527|gb|BM660058.1|BM660058
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTGCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAANAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211350032|gb|FL354315.1|FL354315
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAWAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211320075|gb|FL327296.1|FL327296
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211153912|gb|FL325451.1|FL325451
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|50326390|gb|CO521516.1|CO521516
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211407585|gb|FL360124.1|FL360124
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211505256|gb|FL326165.1|FL326165
EST:     AAGGAAGCCGTTCCACGCTCCTCCAGCGAGCTCCGTGCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|19770077|gb|BQ034798.1|BQ034798
EST:     CGCTCCTCTAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGAAGAGGCAGC
genomic: CGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211472923|gb|FL342170.1|FL342170
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAWAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211118985|gb|FL350356.1|FL350356
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
EST: gi|211090799|gb|FL312054.1|FL312054
EST:     AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAG                         AAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC
genomic: AAGGAGGCCGTTCCACGCTCCTCCAGCGAGCTCCGTTCTGAAGCGGCAAGgtaaacctgc ... ttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gggaatattagttctgcatgctgatctctgattgtatccccctttttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTC
                               ttgtatcccccttttt  CT-rich tract
                                          tttttttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atattcatcaatattcttgtctccatgctttgattctatggcaaagggaatattagttctgcatgctgatctctgattgtatccccctttttttgtgcagAAAGATGATTAATCTTTTCAAAATAAAGGGTCAAAAGAAAGATGAGGCAGCAAGTGCTACTGGAAAGGCCCCTGTTAAGAAACAGTCTGCTGGGGAGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - attcttg
- - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - tgattct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgc