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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccatctaccctgaactctgagatgttcctgagttggctgcctttctccattagatcaaattaaattctgttggcaccttactatgttcttggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG

Basic information

species Zea mays
transcript GRMZM2G114570_T04
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G114570_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g36690.2 (Oryza sativa), 3'ss of exon 1
ccatctaccctgaactctgagatgttcctgagttggctgcctttctcca---ttagatca-aattaaattctgttggcaccttactatgttcttggaact-gcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG---
        |   |  |||   || |       ||  |||| |    | |   ||||||   |  ||||||  | |   | || || | ||||||| |||| |||| | ||||||| || || || || || || || |||||||||||||| || ||||||||||||||||| || || ||||||||||| || |||||||||||   
-------gctcaagttcttcaatttcatgcctttttctgcatccaacaaagcttagatttcagctaaattaagctcctagctgacga-gttcttgaaacttgcagcagCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTGCGT

upper sequence: GRMZM2G114570_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os10g36690.3 (Oryza sativa), 3'ss of exon 1
ccatctaccctgaactctgagatgttcctgagttggctgcctttctcca---ttagatca-aattaaattctgttggcaccttactatgttcttggaact-gcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG
     || |   |  |||   || |       ||  |||| |    | |   ||||||   |  ||||||  | |   | || || | ||||||| |||| |||| | ||||||| || || || || || || || |||||||||||||| || ||||||||||||||||| || || ||||||||||| || |||||||||||
----gtagctcaagttcttcaatttcatgcctttttctgcatccaacaaagcttagatttcagctaaattaagctcctagctgacga-gttcttgaaacttgcagCAGCCATGGCTAAAGAGTATCCTGCCTCCCCCAAAGCTCAGCAGCTGCAAGAATCCAAGAAGCAGCGGCTCACCTACATCCTCGTGGTGAGCGCGCTCTG
















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|76922466|gb|DV169016.1|DV169016
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415875|gb|FL279557.1|FL279557
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211408230|gb|FL279520.1|FL279520
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410777|gb|FL279531.1|FL279531
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|50332938|gb|CO528064.1|CO528064
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410776|gb|FL279530.1|FL279530
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|149001077|gb|EE038332.2|EE038332
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|148973580|gb|EE024687.2|EE024687
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410774|gb|FL279528.1|FL279528
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|149009582|gb|EE041548.2|EE041548
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410768|gb|FL279522.1|FL279522
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|71445088|gb|DR826138.1|DR826138
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415869|gb|FL279551.1|FL279551
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415873|gb|FL279555.1|FL279555
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415874|gb|FL279556.1|FL279556
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|148932006|gb|EC875298.2|EC875298
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415878|gb|FL279560.1|FL279560
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|93013484|gb|EB639004.1|EB639004
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410769|gb|FL279523.1|FL279523
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211413318|gb|FL279536.1|FL279536
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|149067458|gb|EE157667.2|EE157667
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410778|gb|FL279532.1|FL279532
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410780|gb|FL279534.1|FL279534
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211410772|gb|FL279526.1|FL279526
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|149090063|gb|EE179357.2|EE179357
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211413328|gb|FL279546.1|FL279546
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|211415867|gb|FL279549.1|FL279549
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTGCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
EST: gi|78109569|gb|DV527985.1|DV527985
EST:     CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAG                         GATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG
genomic: CTTGGCGTCCTCCAGCGCTCTGCCTTCCTGAGCTGGCTTCTTGTCCGCAGgtcaggttcc ... ggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccattagatcaaattaaattctgttggcaccttactatgttcttggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG
                             accttac  putative branch site (score: 3)
     tagatcaaattaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccatctaccctgaactctgagatgttcctgagttggctgcctttctccattagatcaaattaaattctgttggcaccttactatgttcttggaactgcagGATCCATGGCGAAGGACTACCCAGCTTCTCCGAAAGCTCAGCAGCTCCAGGAATCCAAGAAGCAGCGCCTGACATACATCCTCGTCGTAAGCGCGCTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - -ccctgaa
- - - - - - - - - - - -gttcctg
- - - - - - - - - - - - - - - - -tggctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - gatcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgttgg