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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttcccagtactgattcactttctttctctacagttgggtaatggagctaatggctgctttaatattttgtactgtag

Basic information

species Zea mays
transcript GRMZM2G329306_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G329306_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os06g11320.2 (Oryza sativa), 5'ss of exon 8
ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttcccagtactgattcactttctttctctac-----agttgggtaatggagctaatggctgct-ttaatattttgtactgtag--------------------
||||| ||||||||  |||||||||||||||||||||| ||||| |||||| |||||||||| || |||||   ||| |||||||||  | | | |  || |   | ||||||   |     | ||   ||     |||    ||   | | ||      |||||   |                    
ATTGCCGACAGAAGGAATCAGGAGCGGAAGGCATTTGCAAGGATGTTCCAACCTTCTGGAAAATCAGACAAAGACAATGAAgtaattctcaaatgccaatccttatcctttcttccccccttaatttcttatccaggctttcagcacttatcaagcaaaggtactaatggctgtttcgttctcctgtag
















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|71329028|gb|DR801213.1|DR801213
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|211484888|gb|FL049377.1|FL049377
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|32930877|gb|CF035689.1|CF035689
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|113703884|gb|EE681388.1|EE681388
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|211517927|gb|FL479799.1|FL479799
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|149051834|gb|EE155961.2|EE155961
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|78124365|gb|DV542749.1|DV542749
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|71443878|gb|DR824928.1|DR824928
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|60350322|gb|DN217295.1|DN217295
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|32930670|gb|CF035482.1|CF035482
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|88756259|gb|DY540400.1|DY540400
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGCCTGAAACTTTGC
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGC
EST: gi|76017867|gb|DT945037.1|DT945037
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|88756258|gb|DY540399.1|DY540399
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|32930642|gb|CF035454.1|CF035454
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|149012518|gb|EE042586.2|EE042586
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
EST: gi|211145441|gb|FL467393.1|FL467393
EST:     CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAA                         GAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT
genomic: CATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCT

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: 47 (upstream exon), 47 (downstream exon)
Score: 146

ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 190

ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 300

ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttccc ... tgtactgtagGAGAATAATTGATCTACAGTTCCTTTCCCCCGTCTGAAACTTTGCTTAGCTTAAATCTGGGGCACATTGGAACAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGCTGACAGAAGAGATCAGGAGCGGAAGGCATTTGCTAGGATTTTCCAATCTTCTGGAAAGTCTGACAAGAGCAACGAAgtaatttcccagtactgattcactttctttctctacagttgggtaatggagctaatggctgctttaatattttgtactgtag

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