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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtttgcaagatatctgtggcgttgctaaatttttttcccttagtggggaagtcggaatctgaagacctgaaccaagtttgatttacttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC

Basic information

species Zea mays
transcript GRMZM2G003692_T07
intron # 4
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|211527525|gb|FL409928.1|FL409928
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGA
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGA
EST: gi|211174932|gb|FL421412.1|FL421412
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAANAACATCCTCA                         GCAAGAATCCAGATAG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAG
EST: gi|37397592|gb|CF636096.1|CF636096
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|149101270|gb|EE187382.2|EE187382
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|40337101|gb|CK371171.1|CK371171
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|211280391|gb|FL376816.1|FL376816
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|211267130|gb|FL426696.1|FL426696
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|211126709|gb|FL428259.1|FL428259
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|211245303|gb|FL400469.1|FL400469
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGATTTGAAATGTTACCCATG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATG
EST: gi|211070635|gb|FL369038.1|FL369038
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACC-ATGGA
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGA
EST: gi|71759817|gb|DR957754.1|DR957754
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|32919174|gb|CF023986.1|CF023986
EST:     ATCTGCACGTAACAAGGACGCACTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
EST: gi|71438969|gb|DR820019.1|DR820019
EST:     ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGNNNNNNNNCATCCTCA                         GCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG
genomic: ATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTG

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: 48 (upstream exon), 48 (downstream exon)
Score: 208

GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 523

GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 431

GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 505

GGGAGGTTCTTGCAATGCACTTCGCAAATTTAGGAGCAAAGCTGATACTATCTGCACGTAACAAGGACGCGCTTGCGAGAGTGAAAAAAAACATCCTCAgtaagtttgc ... cttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtggggaagtcggaatctgaagacctgaaccaagtttgatttacttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC
                                   gtttgat  putative branch site (score: 505)
                                         tttacttttc  CT-rich tract
                                    tttgatttactttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtttgcaagatatctgtggcgttgctaaatttttttcccttagtggggaagtcggaatctgaagacctgaaccaagtttgatttacttttcaaagGCAAGAATCCAGATAGCAGAGTTGAAATGTTACCCATGGATTTATCAGCTGGTGAAGAATCTCTGAAAGAAGTCGTACATGTGGCAGAATCATTTTTTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT