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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtagatacattaatgcaattgactgcatcgtttcgagaatttaccaatgctgcttgtgattgactaatggctgcttgattaatgttatgccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG

Basic information

species Zea mays
transcript GRMZM2G147500_T02
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 3
agtag-atacattaatgcaattgactgcatcgtttcgagaatttaccaatgctgcttgtgattgactaatggctgcttgattaatgttatgccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG
 |||| ||  | ||||      |  |  | |   |   |  |     |   |||    |   || ||||||| | | ||| | ||  | | | |||||||| ||||| |||||||| ||  |  | ||||| |||||||| |||||||||||||||||||| || |||||||| ||||| |||||  | ||| |||||
tgtagcatttaataatttttaaggttctaccaagtgttgcttacttaatcactgag-atatatgtctaatggatacatgactcatagtttacaatgttcagTATGCAGTCTGATATTTCTAGATTAGAAGCCAAGATTGAAAGAATGGATGCTCAATTAGCTGCAAAAGATCGCGAGCTGGCCACATTGACTAGAACG
















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|31611780|gb|CD568402.1|CD568402
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122097|gb|FL004251.1|FL004251
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|33094171|gb|CF054165.1|CF054165
EST:     CGACAAAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122868|gb|FL004257.1|FL004257
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122100|gb|FL004254.1|FL004254
EST:     GACAGAGGGACATTTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: GACAGAGGGACATT-GAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|33102758|gb|CF062718.1|CF062718
EST:     CGACAAAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124438|gb|FL004293.1|FL004293
EST:     GACAGAGGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: GACAGAGGG-ACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124442|gb|FL004297.1|FL004297
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|22715261|gb|BU197668.1|BU197668
EST:     CGGCAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124431|gb|FL004286.1|FL004286
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122872|gb|FL004261.1|FL004261
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122877|gb|FL004266.1|FL004266
EST:     -ACAAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCASST                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: GACA-GAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211123651|gb|FL004271.1|FL004271
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGWTGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124436|gb|FL004291.1|FL004291
EST:     GACAGAGGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAAGAATGGATG
genomic: GACAGAGGG-ACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGA-GAATGGATG
EST: gi|211123653|gb|FL004273.1|FL004273
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122095|gb|FL004249.1|FL004249
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124441|gb|FL004296.1|FL004296
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124440|gb|FL004295.1|FL004295
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|26559425|gb|CA831660.1|CA831660
EST:     CGGCAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122101|gb|FL004255.1|FL004255
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|33095529|gb|CF055523.1|CF055523
EST:     CGACAAAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211123664|gb|FL004284.1|FL004284
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211125213|gb|FL004301.1|FL004301
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211122098|gb|FL004252.1|FL004252
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTC
EST: gi|211124432|gb|FL004287.1|FL004287
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211124434|gb|FL004289.1|FL004289
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|211123652|gb|FL004272.1|FL004272
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATAGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|148964224|gb|EE015404.2|EE015404
EST:     CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
EST: gi|26558350|gb|CA830585.1|CA830585
EST:     CGGCAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCG                         GATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC
genomic: CGACAGAGGGACATTGAGTTCAGGGAGTCTACAAATGACCAGCGGCAGCGgtgcgtgcca ... ccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatgctgcttgtgattgactaatggctgcttgattaatgttatgccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG
                              ttgattaatgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtagatacattaatgcaattgactgcatcgtttcgagaatttaccaatgctgcttgtgattgactaatggctgcttgattaatgttatgccatgttcagGATGCAATCTGATATCTCACGGCTGGAAGCTAAGATTGAGAGAATGGATGCTCAATTAGCAGCGAAAGATCGAGAGCTAGCCACTCTTACTCGAACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT