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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttctgttttcagctttcatgcaaatctgagattcacccctgcaatctttgttgtattatttctggcactgaacctcctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT

Basic information

species Zea mays
transcript GRMZM2G058498_T01
intron # 11
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|33104196|gb|CF064156.1|CF064156
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|71310172|gb|DR791375.1|DR791375
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|5055819|gb|AI734706.1|AI734706
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|32868064|gb|CF007746.1|CF007746
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|32915972|gb|CF020784.1|CF020784
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|32823928|gb|CD963650.1|CD963650
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|78092604|gb|DV520978.1|DV520978
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCCCAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|24769686|gb|CA404815.1|CA404815
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAACCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|50339683|gb|CO534809.1|CO534809
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|71756690|gb|DR954627.1|DR954627
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|12969344|gb|BG266288.1|BG266288
EST:     ATCGCAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|211462818|gb|FL454180.1|FL454180
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|78023897|gb|DV492284.1|DV492284
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
EST: gi|67013709|gb|CO442458.1|CO442458
EST:     ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAG                         GAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG
genomic: ATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTG

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), 47 (downstream exon)
Score: 291

GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 353

GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 246

GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 170

GTTTGCTATGACTGGAGCCGTGGGGCCGAAAATCACAACCCTGCAGCTGCAAAGACATCCATCTATCTCCACAGTCCACAGgtgagttctg ... ctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcacccctgcaatctttgttgtattatttctggcactgaacctcctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT
                                         cctcctctt  CT-rich tract
               tttgttgtattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagttctgttttcagctttcatgcaaatctgagattcacccctgcaatctttgttgtattatttctggcactgaacctcctcttaatagGAAACCGAGGTCAAAGGAAAGCCGCGCATTGCAACAGGCAGGAAGTGATTGCATTGAAGGTGTTGCAAGGAACCATGATGTCATCCAGCAGTTTTGTCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA