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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtattcggcggcaaatgctcacgccttgtttcctttccaccgcaccatcggtgggtgctgcagccccgaagcgacggctggcaatgaatggcgatggcgttttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG

Basic information

species Zea mays
transcript GRMZM2G065214_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G065214_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g56470.1 (Oryza sativa), 3'ss of exon 4
gtaggtattcggcggcaaatgctcacgccttgtttcctttccaccgcaccatcggtgggtgctgcagccccgaagcgacggctggcaatgaatggcgatggcgttttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG------
                  |||   | ||| ||| || |  ||| ||   |    |  || |  || ||| | |   | ||    |   | |  || ||||    |   |||||||||||||||||| || ||||||||||| |||||||||||||| |||||      |||| |||| || ||||||||||||| ||| ||||||||||   | |      
----------------gtatgtcaatgccatgtgtcatgaccatcgtctccggcgccggcggcgccgccgcca---gccgtgcagggctcaccggagatgaaaatc--ggtgcagATCGTGAGGGCGCTGGAGGGGGACATGTCGCTGGAGGACCTGAACGA------GGGGATGCGGCCGGGGCAGAGCATGGTGTTCGGCACGGCGGAGACCGGGGGCA
















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|50327066|gb|CO522192.1|CO522192
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148935707|gb|EC879751.2|EC879751
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149000961|gb|EE038201.2|EE038201
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148945502|gb|EC890745.2|EC890745
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149082142|gb|EE171322.2|EE171322
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|71428627|gb|DR809677.1|DR809677
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|76289986|gb|DV029554.1|DV029554
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148951983|gb|EC897765.2|EC897765
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149106764|gb|EE188660.2|EE188660
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149083030|gb|EE172281.2|EE172281
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|91873912|gb|EB403869.1|EB403869
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148939327|gb|EC883844.2|EC883844
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|101396441|gb|EB820147.1|EB820147
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|71430899|gb|DR811949.1|DR811949
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149110480|gb|EE294148.2|EE294148
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149206197|gb|ES701793.1|ES701793
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|101396001|gb|EB819929.1|EB819929
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148995635|gb|EE034843.2|EE034843
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148955911|gb|EC901621.2|EC901621
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|50325030|gb|CO520156.1|CO520156
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148936017|gb|EC880073.2|EC880073
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148961342|gb|EE012071.2|EE012071
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148979230|gb|EE026592.2|EE026592
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149088497|gb|EE177606.2|EE177606
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149088291|gb|EE177386.2|EE177386
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148956647|gb|EC902502.2|EC902502
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACGTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149005317|gb|EE039868.2|EE039868
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|148952040|gb|EC897826.2|EC897826
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149109740|gb|EE293528.2|EE293528
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|91875516|gb|EB405473.1|EB405473
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|74237975|gb|DT645889.1|DT645889
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
EST: gi|149073459|gb|EE161764.2|EE161764
EST:     CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAG                         ATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC
genomic: CCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAAC

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 2 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 38 (downstream exon)
Score: 4

GCTGCGGGGCAACTACGACACCATGGAGATGGCGCGCATGGCCGCCAGCGCCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG


Block sizes: 16 (upstream exon), 49 (downstream exon)
Score: 3

GCTGCGGGGCAACTACGACACCATGGAGATGGCGCGCATGGCCGCCAGCGCCGCGGCAGCCGTGCGCCACTCGGCCAAGAAGCGCCCCAAGATGAGTCAGgtaggtattc ... ttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctgcagccccgaagcgacggctggcaatgaatggcgatggcgttttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG
                          aatgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaggtattcggcggcaaatgctcacgccttgtttcctttccaccgcaccatcggtgggtgctgcagccccgaagcgacggctggcaatgaatggcgatggcgttttgggtgcagATCGTGAGGGCACTCGAGGGGGACATCTCGCTGGAGGACCTCAACGACAACGAGGGGGTGCGACCTGGGCAGAGCATGGCGTTAGGCACGGCGGCCGCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA