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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaggaaatgagttattacttatatgcatttttactttttctgatacattagatgcctcatatcctggttatatttaactgtaacttggccagatttcaacatgtaaatttattttggtgggtaggaaattgatctttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGATGTGAGCATGCCTAACTTTAACATCGTGTTTCA

Basic information

species Zea mays
transcript GRMZM2G116204_T02
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116204_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os12g34450.1 (Oryza sativa), 3'ss of exon 2
gtaaaggaaatgagttattacttatatgcatttttactttttctgatacattagatgcctcatatcctggttatatttaactgtaacttggccagatttcaacatgt--aaatttattttggtggg-taggaaattgatct-------ttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGATGTGAGCATGCCTAACTTTAACATCGTGTTTCA
                                                                                                 |  |||||||   | |||||||||||||| |  | |||| |  |       |||  |||   |||   ||   ||| | | |||||||||||||||||| ||||| || |||||||| ||| ||||| |||||||| | ||||||   ||  |                                
------------------------------------------------------------------------------------------------gtaaaacatgttggattttattttggtgggatgtgcaatttacatcgaagtgtttaattacattatgtttcgattttttatcgcagGTTTGGAATTCTGATGAGCATGAGGATTTGCAGGTTATTGTGGTCATATCGCGCCCGCCTATCAAAGT--------------------------------
















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|211522617|gb|FL101850.1|FL101850
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211437737|gb|FL101814.1|FL101814
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGA
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGA
EST: gi|211528629|gb|FL101884.1|FL101884
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGGAATTCTGACGAGCACGAAGATTTGCAAGGTTCTTGKGATCATAT
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGG-AATTCTGACGAGCACGAAGATTTGCAAG-TTCTTGTGATCATAT
EST: gi|8516405|gb|BE123131.1|BE123131
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTTTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCAT
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCAT
EST: gi|211531634|gb|FL101902.1|FL101902
EST:     TTCTTTCAGAATACCACATTTTCCAATCCCCTGTAATTGATCCACACCAG                         GGTTGGGATTTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATC
genomic: TTCTTTCAGAATACCACATTTTC-AATCCC-TGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATT-CTGACGAGCACGAAGATTTGCAAGTTCTTGTGATC
EST: gi|211522625|gb|FL101858.1|FL101858
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAA
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAA
EST: gi|211537637|gb|FL101922.1|FL101922
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGKGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|29130566|gb|CB381270.1|CB381270
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGC
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGC
EST: gi|211534628|gb|FL101908.1|FL101908
EST:     TTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAAG                         GTTTGGAATTCTGACGAGCACGA
genomic: TTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCA-Ggtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGA
EST: gi|24774056|gb|CA409310.1|CA409310
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATTTCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|71775267|gb|DR973145.1|DR973145
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211531626|gb|FL101894.1|FL101894
EST:     CTTTCTTTCAGAA-ACCACATTTTCAATCCCTGTAA-TGATCCACACCAG                         GTTTGGGATTCTGACGAGCACGAAGATTTGCAGGGTCTTGGGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211528630|gb|FL101885.1|FL101885
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGC
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGC
EST: gi|15100471|gb|BI396262.1|BI396262
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|14717723|gb|BI245373.1|BI245373
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACCAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211522612|gb|FL101845.1|FL101845
EST:     TTTCTTTCAGAATACCCACATTTTCA-TCCCTGTAAATGATCCACACCAG                         GTTTTGGAATTCTGACGAGCACGAAGATTTGNNCA-GT-CTTGTGATCATA
genomic: TTTCTTTCAGAATACC-ACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTT-GGAATTCTGACGAGCACGAAGATTTG--CAAGTTCTTGTGATCATA
EST: gi|211522611|gb|FL101844.1|FL101844
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAG
EST: gi|211519602|gb|FL101834.1|FL101834
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCANACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGC
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGC
EST: gi|15427248|gb|BI543070.1|BI543070
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211522614|gb|FL101847.1|FL101847
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTCGGAATTCTGACGAGCA
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCA
EST: gi|211525622|gb|FL101863.1|FL101863
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211519598|gb|FL101830.1|FL101830
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTWAATGATCCACACCAG                         GTTTGGAATTCTGACGA
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGA
EST: gi|22936024|gb|BU572299.1|BU572299
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATTTCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211525632|gb|FL101873.1|FL101873
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGKAAATGATCCACACCAG                         GTTTGGGADTTCTGACGAGCACGAAGATTTGCAAGT
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAA-TTCTGACGAGCACGAAGATTTGCAAGT
EST: gi|28931186|gb|CB334547.1|CB334547
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|24774132|gb|CA409386.1|CA409386
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATTTCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|14883533|gb|BI273401.1|BI273401
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTT
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTT
EST: gi|211537638|gb|FL101923.1|FL101923
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATC
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATC
EST: gi|24773715|gb|CA408969.1|CA408969
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAACGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATTTCG
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCG
EST: gi|211522616|gb|FL101849.1|FL101849
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGACGAGCACGAAGATTTGC
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGC
EST: gi|211435151|gb|FL101811.1|FL101811
EST:     CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAG                         GTTTGGAATTCTGA
genomic: CTTTCTTTCAGAATACCACATTTTCAATCCCTGTAAATGATCCACACCAGgtaaaggaaa ... tctcttgcagGTTTGGAATTCTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtgggtaggaaattgatctttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGATGTGAGCATGCCTAACTTTAACATCGTGTTTCA
                        tgttaat  putative branch site (score: 3)
                                    catcatctttctctt  putative PPT
                    tttttgttaatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaggaaatgagttattacttatatgcatttttactttttctgatacattagatgcctcatatcctggttatatttaactgtaacttggccagatttcaacatgtaaatttattttggtgggtaggaaattgatctttttgttaatgtatacatcatctttctcttgcagGTTTGGAATTCTGACGAGCACGAAGATTTGCAAGTTCTTGTGATCATATCGAGACCGCCTGCTAAGATGTGAGCATGCCTAACTTTAACATCGTGTTTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG