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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatgagccccccacacacccccaaatctcttcctgccgtgcgaagccgagcatcggatctgatccgagtacaagcgcatacacgcctaccaatc...

Basic information

species Zea mays
transcript GRMZM2G120578_T01
intron # 1
splice site 5'
intron type U2

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|211320667|gb|FL013191.1|FL013191
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|148956445|gb|EC902269.2|EC902269
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|78117805|gb|DV536192.1|DV536192
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|148931937|gb|EC875166.2|EC875166
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|148930370|gb|EE284813.2|EE284813
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211322828|gb|FL013194.1|FL013194
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|149072878|gb|EE161134.2|EE161134
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211320669|gb|FL013193.1|FL013193
EST:     CCRTCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211320668|gb|FL013192.1|FL013192
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211322835|gb|FL013201.1|FL013201
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|89756410|gb|DY686460.1|DY686460
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211322829|gb|FL013195.1|FL013195
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|32865849|gb|CF005531.1|CF005531
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCT-GGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAA
EST: gi|28188224|gb|CB179834.1|CB179834
EST:     CCATCCCCCGGTCTTCGNCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|37424555|gb|CF650010.1|CF650010
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|211322831|gb|FL013197.1|FL013197
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
EST: gi|148963955|gb|EE015081.2|EE015081
EST:     CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAG                         AGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA
genomic: CCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAA

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), 49 (downstream exon)
Score: 164

CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAATGGTTCGAACGAGGCGGTGCAGGCAAAGGGGAGTGGGGGTGATAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 174

CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAATGGTTCGAACGAGGCGGTGCAGGCAAAGGGGAGTGGGGGTGATAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAATGGTTCGAACGAGGCGGTGCAGGCAAAGGGGAGTGGGGGTGATAGCTCC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 271

CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatg ... tttgctccagAGGCTGGGAACTCCAAAGAGGAACAGGGTCCATGGCTGGAGGCGCAGGAAATGGTTCGAACGAGGCGGTGCAGGCAAAGGGGAGTGGGGGTGATAGCTCC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTACCCAGGTCTTCGTCGGTCGCTTCGCCAGCCGCCAGGTCTTCGTCGGCCCATCCCCCGGTCTTCGTCCTTCAATCCTCCGGCGACGAGCACCCACCAGgtacgagatgagccccccacacacccccaaatctcttcctgccgtgcgaagccgagcatcggatctgatccgagtacaagcgcatacacgcctaccaatc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccccac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcctacc