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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccgcaatctgagtagagcagtgtcttgacatcgttgaatctctgctgtttctttgtttgccttatccctgacagtgggttcaccatcgttgcag

Basic information

species Zea mays
transcript GRMZM2G098714_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098714_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 5'ss of exon 11
CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccgcaatctgagtagagcagtgtcttgacatcgt-tgaatctctgctgtttctttg--tttgc-cttatccctgacagtgggttcaccatcgttgcag
|||||| |||||||| ||||| ||| | ||| ||||||| || || ||||||| |||  |||||||||| || || |||||||||||||| ||||| ||||||| ||   |||||  |    | |  ||  |   | |||| | |||    |   ||  |||   ||||  |  || || | | || | ||||   | ||     
CTCCGACCCTACTGGTGAGGCCTGGCTTTCTCTGTTCAATGATCAGGCAGAGAGGATTGTTGGCTGCAGTGCAGATGAGCTTGATCGGATTAGGAAGGAGgtaattttgccaatcccacagtaactttgattcaccttcgtgtaaattctaggctttagtttaactttgtgcgaattccaggctgtag-ttcaagcttgtg----
















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|211343900|gb|FL063189.1|FL063189
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGCTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|12969502|gb|BG266446.1|BG266446
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGCTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|60348547|gb|DN215520.1|DN215520
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|14244513|gb|BG842483.2|BG842483
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|14245218|gb|BG873800.1|BG873800
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|32826816|gb|CD966494.1|CD966494
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|29945005|gb|CB815420.1|CB815420
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|211343908|gb|FL063197.1|FL063197
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|71759809|gb|DR957746.1|DR957746
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|29945324|gb|CB815582.1|CB815582
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
EST: gi|211341514|gb|FL063180.1|FL063180
EST:     AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAG                         GAGGGGGACGACAGTTATGCTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT
genomic: AGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCT

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), 48 (downstream exon)
Score: 357

CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCTCACCTGTTCCGCGTCAGCGTCACACAGCATGAATACAATAACGAGAAAA


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 136

CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCTCACCTGTTCCGCGTCAGCGTCACACAGCATGAATACAATAACGAGAAAA


Block sizes: 49 (upstream exon), 37 (downstream exon)
Score: 96

CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCTCACCTGTTCCGCGTCAGCGTCACACAGCATGAATACAATAACGAGAAAA


Block sizes: 49 (upstream exon), 42 (downstream exon)
Score: 62

CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccg ... atcgttgcagGAGGGGGACGACAGTTATGTTCTGAAGCTCAAGGAAGCCACCTGGGTTCCTCACCTGTTCCGCGTCAGCGTCACACAGCATGAATACAATAACGAGAAAA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGATCCTACTGGCGAGGCATGGTTCTCTGTGTTCAACGAGCATGCAGAGAAGATCATTGGCTGCAGCGCCGACGAGCTTGATCGGATCAGGAAAGAGgtaaattccgcaatctgagtagagcagtgtcttgacatcgttgaatctctgctgtttctttgtttgccttatccctgacagtgggttcaccatcgttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT