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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtacccaagcttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcag

Basic information

species Zea mays
transcript GRMZM2G437859_T03
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g55500.4 (Oryza sativa), 5'ss of exon 1
GGTAGGGA-AATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgta----cccaagc--ttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatct--gttttgtgttttcgtctttttttttgcttttcatttcag
 |  | ||  ||||| |||||||||||||| ||||| ||| | ||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||     || ||||    |  |||| |  |  ||     | || | || |||  |   ||||||||   || |||  |||| |   |||                   
-GCGGCGACGATGGCTGAGGTGAAGCCGGAAGAGATCAGCTACCCGCCCATGGAGCAGCTGCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtgagagccgaagcggcggcggctgcattgcattttttcctgc-tcgggatttcgcattctgaatccacgtcttggatttttgctgtttcag----------------

upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA04G06750.1 (Glycine max), 5'ss of exon 1
GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtacccaagcttggagctgaaa---cgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttt--tgcttttcatt-tcag---
    |    ||||| |     ||||| |||||||||||||| || || ||||| || || || || || |||||||| || ||||| |||||| ||||||||  |  ||||       | ||| |    |   ||||        ||| || |   || | || || |  ||    |||| || ||  |     || |||  | | | |    
AAAGGAATCATGGCAGCTCCAAAGCCAGAGGAGATAAGCCACCCACCAATGGATCAACTTCAAGGCTTAGAGTACTGTATAGACTCAAACCCTTCCTGGGgtatg--cccacttcctcaactgcattttcagcttcatgaaaagattg-aacttttttgtgtgtatgttgttcacattttggttttaatgagaatgttttgaactgttaacag

upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA06G06840.1 (Glycine max), 5'ss of exon 1
GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtacccaagcttggagctgaaacgagttcacatccgcgttggaattcgg-ttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcag
    |    ||||| |     ||||| |||||||||||||| || || ||||| || || || || || |||||||| |||||||| |||||| ||||||||  |  | ||       | ||| |     ||||  | |        |||    || | ||      ||||| |||||  |   | ||||||       |  |||
AAAGGAATCATGGCAGCTCCAAAGCCAGAGGAGATAAGCCACCCACCAATGGACCAACTTCAAGGCTTAGAGTACTGTATCGACTCAAACCCTTCCTGGGgtatg--ctcacttcctcaactgcatt---ttcagcttcattaaaagattgaacttttttgtgcacattttg-gttttaatgagtgtttttgaaccgtttaacag

upper sequence: GRMZM2G437859_T03 (Zea mays), 5'ss of exon 1
lower sequence: AT2G34190.1 (Arabidopsis thaliana), 5'ss of exon 1
GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtacccaagcttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcag
  |||    ||||     || ||||| ||||||||||| || || || ||||| ||||| ||||| || |||||||| || ||||| |||||||| ||||||    ||  |  |||| | |        || |      |  |     |||  ||  | |||||    |  || | |  |                        
TTTAGAATCATGGATCTTGTAAAGCCAGAGGAGATAAGTCACCCACCAATGGATCAGCTTCAGGGTTTAGAGTACTGTATTGACTCAAACCCTCCATGGGgt----acttagccttgaaaccattctctgtactttattggttgacttttcactttccggaatcctgatgatgatcttattgcag-------------------

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|211100340|gb|FL069921.1|FL069921
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|50339069|gb|CO534195.1|CO534195
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74244049|gb|DT651963.1|DT651963
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|149001123|gb|EE038382.2|EE038382
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|78084450|gb|DV512843.1|DV512843
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102812|gb|FL069930.1|FL069930
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|78081194|gb|DV509606.1|DV509606
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100342|gb|FL069923.1|FL069923
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71439895|gb|DR820945.1|DR820945
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74243489|gb|DT651403.1|DT651403
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|149071736|gb|EE160129.2|EE160129
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102808|gb|FL069926.1|FL069926
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71431026|gb|DR812076.1|DR812076
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|76923378|gb|DV169457.1|DV169457
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74238882|gb|DT646796.1|DT646796
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|74240437|gb|DT648351.1|DT648351
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|33467816|gb|CF244865.1|CF244865
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|91049745|gb|EB160163.1|EB160163
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71449525|gb|DR830575.1|DR830575
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211102810|gb|FL069928.1|FL069928
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACT
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACT
EST: gi|211102809|gb|FL069927.1|FL069927
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|50331687|gb|CO526813.1|CO526813
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|91878994|gb|EB408951.1|EB408951
EST:     GGAGCAGCTCCAGGGGTTCCAGTACTGCATCGACTCCCACCCTCCCTGGG                         GCGAGGCGATCATACTG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTG
EST: gi|93016333|gb|EB641853.1|EB641853
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGG
EST: gi|211100339|gb|FL069920.1|FL069920
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100336|gb|FL069917.1|FL069917
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71310987|gb|DR791795.1|DR791795
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|211100341|gb|FL069922.1|FL069922
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
EST: gi|71438783|gb|DR819833.1|DR819833
EST:     GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGG                         GCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG
genomic: GGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtaccc ... ttcatttcagGCGAGGCGATCATACTGGGCTTCCAGCACTACATACTGGCGCTGGGCACGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGTAGGGAAATGGCGGAGGTGAAGCCGGAGGAGATAAGCCATCCGCCCATGGAGCAGCTCCAGGGGTTCGAGTACTGCATCGACTCCAACCCTCCCTGGGgtgcgtacccaagcttggagctgaaacgagttcacatccgcgttggaattcggttctctgaatctgttttgtgttttcgtctttttttttgcttttcatttcag

- - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC