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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctactctgaagctgctgttgaccgccgcctcgggtacttgtttcgcctcttagcgccgactattcgtttgttatttgatctgctgcctggattcg...

Basic information

species Zea mays
transcript GRMZM5G862959_T01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G862959_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os12g19350.2 (Oryza sativa), 5'ss of exon 1
GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctactc-tgaagc-tgctgttgaccgccgcct-cgggtacttgtttcgcctcttagcgccgac-tattcgtttgttatttgatctgctgcctggattcg
|  ||||||||||| |||||||||||  ||||||||||    ||||| ||||||||  | ||  |||| ||||||||||| ||||||||| ||||| | ||||||   |||   | ||  ||   ||   || |  | ||  | | || |   |   ||   |||||  | || | || |  ||  |  |   |   | |    
GCGAGCCTGCTGGATAAGGCCAAGGAGCTGGACCAGCTGCGCAAGGAGCAGGACGAGGTGGTCACCGAGATCAACAAGATGCACAAGAAGATCCTCTCCTgtaagtagctcgccatgcgcgcgcgtgggtgctgttttcgtttccgtgctgttcgaattgttgccgaggtgttggattatatttgtagataacggacgaa----
















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|211484297|gb|FL254347.1|FL254347
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|4753396|gb|AI657306.1|AI657306
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337492|gb|FL098066.1|FL098066
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAAC-AGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|88753184|gb|DY537325.1|DY537325
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCCAGTTGACACCATTTTTGCTCAAGCTTCG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACC-AGTTGACACCATTTT-GCTCAAGCTTCG
EST: gi|211048260|gb|FL393106.1|FL393106
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|148974314|gb|EE025087.2|EE025087
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|29944945|gb|CB815389.1|CB815389
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484295|gb|FL254345.1|FL254345
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGARATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|31358058|gb|CD442415.1|CD442415
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484293|gb|FL254343.1|FL254343
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337495|gb|FL098069.1|FL098069
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484294|gb|FL254344.1|FL254344
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|50326336|gb|CO521462.1|CO521462
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337493|gb|FL098067.1|FL098067
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484292|gb|FL254342.1|FL254342
EST:     GGACGAAATCGTTGCCGATATCAACGAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211384387|gb|FL373404.1|FL373404
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484291|gb|FL254341.1|FL254341
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|32914541|gb|CF019353.1|CF019353
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTCGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337491|gb|FL098065.1|FL098065
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|28873324|gb|CB329328.1|CB329328
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211484296|gb|FL254346.1|FL254346
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211043059|gb|FL422974.1|FL422974
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGGCACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|93012241|gb|EB637761.1|EB637761
EST:     GACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337489|gb|FL098063.1|FL098063
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAKTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
EST: gi|211337490|gb|FL098064.1|FL098064
EST:     GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCAT                         CCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG
genomic: GGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTG

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: 208

GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 163

GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 136

GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 138

GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctact ... tgttttgtagCCCCAGAGATGGTTGATAAACCAGTTGACACCATTTTGCTCAAGCTTCGTGGTTTATATGCACGTGCAAAGGAGCTCTCTGAGAATGAAATCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCAGCCTGCTGGAGAAGGCCAAGGATTTGGACCAGCTAAAGAAGGAACAGGACGAAATCGTTGCCGATATCAACAAGATTCACAAGAAGCTCCTCGCATgtaagctactctgaagctgctgttgaccgccgcctcgggtacttgtttcgcctcttagcgccgactattcgtttgttatttgatctgctgcctggattcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC