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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggatctgcccttgagatctaggaccctttacaccggatatcgcaccgttaccacttaatctcgtatattcacttagtgccgttgtgctgttgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA

Basic information

species Zea mays
transcript GRMZM2G152573_T04
intron # 1
splice site 3'
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|9733580|gb|BE512332.1|BE512332
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211381965|gb|FL156730.1|FL156730
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379324|gb|FL156711.1|FL156711
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|58029444|gb|CX724871.1|CX724871
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|60398264|gb|DN231080.1|DN231080
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379336|gb|FL156723.1|FL156723
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|5006078|gb|AI712140.1|AI712140
EST:     GCACAGCTACGCCCCCAAATCGAACCAGACCCGCGTCGTCAACCCACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|5108109|gb|AI739822.1|AI739822
EST:     CGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: CGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|15208979|gb|BI430863.1|BI430863
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211086698|gb|FL459706.1|FL459706
EST:     CAAGACCACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAG
genomic: CAAGA-CACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAG
EST: gi|15100525|gb|BI396316.1|BI396316
EST:     GCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211381974|gb|FL156739.1|FL156739
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211384599|gb|FL156742.1|FL156742
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211384597|gb|FL156740.1|FL156740
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|15100606|gb|BI396397.1|BI396397
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211415047|gb|FL462002.1|FL462002
EST:     CGAACCAGACCCGGGTTGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: CGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379329|gb|FL156716.1|FL156716
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379335|gb|FL156722.1|FL156722
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379328|gb|FL156715.1|FL156715
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211086700|gb|FL459708.1|FL459708
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379333|gb|FL156720.1|FL156720
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211492551|gb|FL462928.1|FL462928
EST:     GCACAG-TACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211381961|gb|FL156726.1|FL156726
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379337|gb|FL156724.1|FL156724
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379330|gb|FL156717.1|FL156717
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211379326|gb|FL156713.1|FL156713
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|6031583|gb|AI668485.2|AI668485
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|60397406|gb|DN230222.1|DN230222
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211381962|gb|FL156727.1|FL156727
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|67017356|gb|CO446105.1|CO446105
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|67011017|gb|CO439766.1|CO439766
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|211381966|gb|FL156731.1|FL156731
EST:     GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
EST: gi|30705607|gb|CD058843.1|CD058843
EST:     GCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTG                         GTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT
genomic: GCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGT

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: 744

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 800

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 781

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 480

GAAGCAGCGGCTGGGAGCAAGATGGTGCAGCGCCTCACCTACCGGAAGCGGCACAGCTACGCCACCAAATCGAACCAGACCCGCGTCGTCAAGACACCTGgtaagatcag ... tgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgttaccacttaatctcgtatattcacttagtgccgttgtgctgttgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA
       acttaat  putative branch site (score: 480)
                  tatattca  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggatctgcccttgagatctaggaccctttacaccggatatcgcaccgttaccacttaatctcgtatattcacttagtgccgttgtgctgttgctgattagGTGGGAAACTTGTGTACCAGTACACCAAGAAGCGCGCGAGCGGACCGAAGTGCCCAGTCACCGGGAAGAAGATCCAAGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG