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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaaacgctagatgtatgtatgcccactttgacgtaaacgtactgttccgttactgatttcatgcaagtgctgccag

Basic information

species Zea mays
transcript GRMZM2G102161_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G102161_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g11614.1 (Oryza sativa), 5'ss of exon 6
GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaac--------taaaaacgctagatgt--atgtatgc-ccactttgacgtaaacgtac---tgttccgttactga--tttcatgcaagtgctgccag-
|| ||| || |||| ||||||||||||||| | ||||||||||||||          |  || ||  | ||   ||  |||  || | |   |  ||| |||   | || | || || |  |  ||  || |  ||      
GAGCAACAGCTGCAAGATCTCAACAAAGACTTGAGGAAAAAGgtaacacagccatcgatcaccctgaaagtcattgcgtgcatcagtattcggacaacatacatctttttccttgctaaagtcccaaccatgatcttttcat
















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|32828018|gb|CD967696.1|CD967696
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32837918|gb|CD977596.1|CD977596
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847423|gb|CD987104.1|CD987104
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|18178380|gb|BM379590.1|BM379590
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACTTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|67011315|gb|CO440064.1|CO440064
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32810400|gb|CD962634.1|CD962634
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847744|gb|CD987425.1|CD987425
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32845819|gb|CD985500.1|CD985500
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|16917809|gb|BM073443.1|BM073443
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|211408737|gb|FL193400.1|FL193400
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32824768|gb|CD964490.1|CD964490
EST:     GATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCTGCAGAATGTGATCCACGACGTCTCCTGGGAGAAA
genomic: GATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32866292|gb|CF005974.1|CF005974
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
EST: gi|32847872|gb|CD987553.1|CD987553
EST:     GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAG                         CTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA
genomic: GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAA

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: 47 (upstream exon), 48 (downstream exon)
Score: 328

GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 193

GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaa ... gtgctgccagCTGCAAGAAACAAGTCCGCAGAATGTGATCCACGACGTCTCCTGGGAGGAAGGCGGGCACAGTGGGAGTAGTGTTCTTGGTCCGTTCCAGGGACTCCTTC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAGAGTTGCAGGATCTCAACAAAGACCTAAGGAAAAAGgtaactaaaaacgctagatgtatgtatgcccactttgacgtaaacgtactgttccgttactgatttcatgcaagtgctgccag

- - - - - - - - - - - - - - - - AAGGAA