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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccccaataccctgcgccatgacctcgcatcccgttacatactaaaccaccggtttacgagacttaagttagtttttctttttgcctggacttgtcacag

Basic information

species Zea mays
transcript GRMZM2G472991_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G472991_T03 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g66520.1 (Oryza sativa), 5'ss of exon 1
-CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccccaataccctgcgccatga-cctcgcatcccgttacatacta-aaccaccggtttacgagacttaagttagtttttctttttgcctggacttgtcacag
  || |||||||  ||||||||||||||||||| || || ||||||||| ||||||| |||||||||||||| ||||||||||||||||||||||| |||||||| ||    | ||    | | |  | |||   | || |   |     | ||   | |  |       | | | || ||  |  |  ||   |||| | |      
GGAGGAGGAGGAGGCCATGAAGCTTGACGTGAACGCGCTCCGCTACCTCTCCAAGGATGACTTCCGCGTCCTCACCGCCGTCGAGATGGGCATGCGTAACgtaagttctgatacacttgccacgaccatccttaaacccagcaccgcgtgagaattgctgtgtccttgtgcctgacttggtggtcttgatt--ttggattcgcag---

upper sequence: GRMZM2G472991_T03 (Zea mays), 5'ss of exon 3
lower sequence: PP1S40_20V6.1 (Physcomitrella patens), 5'ss of exon 1
CAGAAGGAGG--ACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccccaataccctgcgccatgacctcgcatcccgtt-------acatactaaaccaccggtttacgagacttaagttagtttttctttttgcctggacttgtcacag
  |  ||||    || ||||||| | ||||||||||| || ||||||||| |||| || || ||||| || ||||| ||||| ||||||||||||   || |||||   |     | ||| |  ||  |  ||   ||  |||        || | | |||| |  |       | ||  |  | |  ||| |     | |   |||    |||
-GGCGGGAGTTTGCAACATGAAGTTAGACGTGAATGCGCTGCGCTACCTCACCAAAGATGAGTTCCGTGTTCTTACAGCCGTGGAGATGGGCATGAAGAATgtaagtcacgtcgaaacctcc-tcagaatttcttgtcgagttcatgagtgcagattgaaccgcgaggaactctgtctgca--tggaatttatgagcactttcgctttgtgcag
















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|93016530|gb|EB642050.1|EB642050
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|18384009|gb|BM417209.1|BM417209
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGA-TGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|18384971|gb|BM418170.1|BM418170
EST:     CAAGGACTGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATTGCCAGACTGAA
genomic: CAAGGAC-GACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|71429251|gb|DR810301.1|DR810301
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|20299997|gb|BQ162940.1|BQ162940
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|20300018|gb|BQ162961.1|BQ162961
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|78120952|gb|DV539336.1|DV539336
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAAAACTTGTCGACGGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|76014878|gb|DT942048.1|DT942048
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|78112924|gb|DV531318.1|DV531318
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|76014835|gb|DT942005.1|DT942005
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|89106284|gb|DY576501.1|DY576501
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|22489226|gb|BU049149.1|BU049149
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|91056420|gb|EB166838.1|EB166838
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAGC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|18383990|gb|BM417190.1|BM417190
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
EST: gi|211277358|gb|FL192926.1|FL192926
EST:     CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAAC                         CACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA
genomic: CCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 145

CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 66

CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 53

CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 77

CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccc ... cttgtcacagCACGAGATTGTTCCAGCAGAACTTGTCGACAGGATCGCCAGACTGAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAAGGAGGACACCATGAAGCTTGACGTGAATGCCCTTCGCTACCTCGCCAAGGACGACTTCCGCGTCCTTACCGCCGTCGAGATGGGCATGCGCAACgtaagatccccaataccctgcgccatgacctcgcatcccgttacatactaaaccaccggtttacgagacttaagttagtttttctttttgcctggacttgtcacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG