Skip to another splice site:
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 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaaagtttgccctttcgttttccgtccccgattgtattcggctcgtgttctatgcgtttactgatgaatataggtaaaatcccctctctcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCTGTCCTACAGCTCCATGGCTCCAATCTTTCTCAACCTTATCCAATGGATG

Basic information

species Zea mays
transcript GRMZM2G058450_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G058450_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g67850.1 (Oryza sativa), 3'ss of exon 1
ggaaaagtttgccctttcgttttccgtccccgattgtattcg----gctcgt--gttctatgcgtttactgatgaatataggtaaaatcccctctctcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCTGTCCTACAGCTCCATGGCTCCAATCTTTCTCAACCTTATCCAATGGATG
    |  | ||   ||  || ||   |     |  | ||| |    | | ||  |||||  | |||   |||   |||    || |     || | | || || ||||||||||||||||||||||| |||||||||||||| ||||||||||||||||| ||||||||||||||||||||| | || ||||| ||||| ||||||
----atttctgattttgagtatttttttaaaaaaagaatttgtggggatagttcgttcttggtgttc-ttgagtgatactaatagatgattctgtttgttttc-agGGCGCATGCTATACACAGGGCCTATGGGGGTGCCTGTGTGCAGATGAGGCTGTCTTACAGCTCCATGGCTCCAATCATCCTTAACCTCATCCAGTGGATG
















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|211287515|gb|FL360425.1|FL360425
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211372879|gb|FL335377.1|FL335377
EST:     C-GGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|101401307|gb|EB822331.1|EB822331
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211535303|gb|FL356758.1|FL356758
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211049886|gb|FL343175.1|FL343175
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211165711|gb|FL359023.1|FL359023
EST:     -GGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACTCTT                         KBCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGC
genomic: GGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACAC-CCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGC
EST: gi|211010674|gb|FL358964.1|FL358964
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|28931313|gb|CB334674.1|CB334674
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|19351555|gb|BM896087.1|BM896087
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211425705|gb|FL364983.1|FL364983
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|33467297|gb|CF244346.1|CF244346
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211523414|gb|FL361955.1|FL361955
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATNAG-CT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211078311|gb|FL342740.1|FL342740
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211213423|gb|FL335729.1|FL335729
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211282867|gb|FL309979.1|FL309979
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|50325950|gb|CO521076.1|CO521076
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211185710|gb|FL321585.1|FL321585
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211086863|gb|FL356810.1|FL356810
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211453267|gb|FL341700.1|FL341700
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|148930523|gb|EE285118.2|EE285118
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211021655|gb|FL358094.1|FL358094
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211488646|gb|FL313372.1|FL313372
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211083699|gb|FL340081.1|FL340081
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211180683|gb|FL313564.1|FL313564
EST:     C-GGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCKTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|108824167|gb|EC278175.1|EC278175
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211398188|gb|FL404159.1|FL404159
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGC--GCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211147996|gb|FL325032.1|FL325032
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211173505|gb|FL323750.1|FL323750
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|149109824|gb|EE293619.2|EE293619
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211335091|gb|FL315546.1|FL315546
EST:     CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
EST: gi|211529046|gb|FL347500.1|FL347500
EST:     C-GGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCT                         GGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT
genomic: CGGGGGTCTCTCAAGGCGCTTGAAGCTGATATCCACCATGCCAACACCCTgtaagtcctc ... tcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgttctatgcgtttactgatgaatataggtaaaatcccctctctcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCTGTCCTACAGCTCCATGGCTCCAATCTTTCTCAACCTTATCCAATGGATG
               tactgat  putative branch site (score: 2)
                                    tcccctctctcttctc  putative PPT
                       aatataggtaaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaaagtttgccctttcgttttccgtccccgattgtattcggctcgtgttctatgcgtttactgatgaatataggtaaaatcccctctctcttctccagGGCGCATGCTATACACAGGGCGTATGGGGGTGCCTGCGTGCAGATGAGGCTGTCCTACAGCTCCATGGCTCCAATCTTTCTCAACCTTATCCAATGGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC