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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgattataactaaatgtttttacttgtggatgtgtggtgtctataaggcattaagatccaaagaggaggagctgaaatggccacgaaacacatat...

Basic information

species Zea mays
transcript GRMZM2G134889_T01
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G134889_T01 (Zea mays), 5'ss of exon 10
lower sequence: PP1S122_5V6.1 (Physcomitrella patens), 5'ss of exon 12
TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgattataactaaatgtttttacttgtggatgtgtggtgtctataaggcattaagatccaaagaggaggagctgaaatggccacgaaacacatat--------------------------------------------------------------------------------
 | || || || ||||| ||||| |||| ||||||||||||||| ||||||||||||||  ||  || || |    | |  | |     | || | | |  ||  |   | |    |    | |  |||  || | | |    || | |    || |                                                                                
CCCGATGGCTATCCGACTATTCTTTTCTTTCCAGCTGGGAAGAAGAGCTTTGAGCCAgtgcgtctttctatccttttctcctgagcgaggaatttattgc-tcagtgctgaaccttgcatgagattggaacagttcaga--atcatgcagtgaatgttcttcaggacctgataaccttgaagctatgtttgtaaattagaacttcattacttagagttgcaatgcttgacaatgcag
















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|211193716|gb|FL465420.1|FL465420
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|32165106|gb|CD670424.1|CD670424
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACGGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|76014424|gb|DT941594.1|DT941594
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|149077066|gb|EE165722.2|EE165722
EST:     GATACCCGACGATTCTTTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|71767590|gb|DR965527.1|DR965527
EST:     GATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|110965155|gb|EE185055.1|EE185055
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|37392565|gb|CF633534.1|CF633534
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|211190973|gb|FL452316.1|FL452316
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|113701716|gb|EE679220.1|EE679220
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|148938717|gb|EC883049.2|EC883049
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|67020721|gb|CO449470.1|CO449470
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTNTGAGCCA                         ATCACTTTTGNAGGGG-AGCGGACAGTGGTAAATCTGTACAAGTTCATCAA
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTG-AGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAA
EST: gi|37381267|gb|CF627509.1|CF627509
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|91873350|gb|EB403307.1|EB403307
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|148974380|gb|EE025157.2|EE025157
EST:     GATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|211243943|gb|FL442200.1|FL442200
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|76285047|gb|DV024615.1|DV024615
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTCTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|67013918|gb|CO442667.1|CO442667
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|211193717|gb|FL465421.1|FL465421
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|211193715|gb|FL465419.1|FL465419
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|60340788|gb|DN207761.1|DN207761
EST:     GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
EST: gi|78105578|gb|DV523996.1|DV523996
EST:     GATACCCGACGANNNNNNNNNATCCAGCTGGGAAGAAAAGCTTTGAGCCA                         ATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG
genomic: GATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAG

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: 129

TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCGAGAACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 106

TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCGAGAACCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 121

TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCGAGAACCG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 85

TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgatt ... cctttttcagATCACTTTTGAGGGGGAGCGGACAGTGGTAGATCTGTACAAGTTCATCAAGAAACATGCTAGCATCCCTTTCAAGTTGAAGCGCCAGGAGTCGAGAACCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGACGGATACCCGACGATTCTCTTCTATCCAGCTGGGAAGAAAAGCTTTGAGCCAgtaagtgattataactaaatgtttttacttgtggatgtgtggtgtctataaggcattaagatccaaagaggaggagctgaaatggccacgaaacacatat

- - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacaca