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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgataaactaatccattcattttattttttaatttaaatgttaccctcaaccactcgtcttttatttaagcgttacttaaatttttttttccatttttttgtaacag

Basic information

species Zea mays
transcript GRMZM2G066440_T01
intron # 4
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|211413817|gb|FL421626.1|FL421626
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211271873|gb|FL420608.1|FL420608
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211453719|gb|FL371690.1|FL371690
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211479925|gb|FL425093.1|FL425093
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211271148|gb|FL388759.1|FL388759
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211089720|gb|FL375370.1|FL375370
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211273933|gb|FL428371.1|FL428371
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211085797|gb|FL424019.1|FL424019
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTNACCTGCACCATTCATGGACATTTCAG
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATG-ACATTTCAG
EST: gi|211059644|gb|FL374516.1|FL374516
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|78120608|gb|DV538992.1|DV538992
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211233915|gb|FL394219.1|FL394219
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211210029|gb|FL411366.1|FL411366
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCAGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211218085|gb|FL424499.1|FL424499
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211485264|gb|FL406762.1|FL406762
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|78122609|gb|DV540993.1|DV540993
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGTATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211450321|gb|FL410319.1|FL410319
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211158229|gb|FL401285.1|FL401285
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211339029|gb|FL403594.1|FL403594
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211204746|gb|FL408304.1|FL408304
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211282425|gb|FL393384.1|FL393384
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211229498|gb|FL371568.1|FL371568
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211179793|gb|FL384665.1|FL384665
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211527411|gb|FL405481.1|FL405481
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211487815|gb|FL394402.1|FL394402
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|149072975|gb|EE161236.2|EE161236
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211374582|gb|FL413733.1|FL413733
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
EST: gi|211521604|gb|FL412478.1|FL412478
EST:     ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATC                         GGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA
genomic: ACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCA

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: 222

TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 236

TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgata ... tttgtaacagGGCAACGAGTCACCTGCACCATTCATGACATTTCAGTCCACATGCTTCCCATCAGATATTCTAAGGGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCACAAAGTGCTCCTTCCACTAATCAAGTTTCTCAGGCTGCCAGTGGAAACCAAATGTCGACAGAAGCATATCGTGCTAAGCATGAGATTACCATCATCgtatgtgataaactaatccattcattttattttttaatttaaatgttaccctcaaccactcgtcttttatttaagcgttacttaaatttttttttccatttttttgtaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC