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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagcccccagtgtttgatgaataccaaaggaaacatattgttaattcagatctgcaggaaagagtttttgttcagttcataacctcatcctgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT

Basic information

species Zea mays
transcript GRMZM2G550865_T01
intron # 12
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|166578693|gb|EG113196.1|EG113196
EST:     ATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: ATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|33095993|gb|CF055987.1|CF055987
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|166642915|gb|EG224379.1|EG224379
EST:     GTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8665781|gb|BE186597.1|BE186597
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8318797|gb|BE025437.1|BE025437
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|87152457|gb|DY397246.1|DY397246
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|113646681|gb|DW803477.1|DW803477
EST:     CATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAAGGG
genomic: CATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAA-GGG
EST: gi|67024360|gb|CO453109.1|CO453109
EST:     GATTGAAAAGATGGAACTGGTAAATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAA
EST: gi|7304567|gb|AW600506.1|AW600506
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|88747083|gb|DY531224.1|DY531224
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|116819483|gb|EC862618.1|EC862618
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|4388094|gb|AI491266.1|AI491266
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|40485947|gb|CK394819.1|CK394819
EST:     TTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: TTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|8318798|gb|BE025438.1|BE025438
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|7216838|gb|AW562960.1|AW562960
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGNTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|19057574|gb|BM736241.1|BM736241
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|19437048|gb|BM953458.1|BM953458
EST:     ATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCCTAACCAAG                         ATGGGCTTCAAAAGGTGGGGCAACTAACCTTGGCAGATCGGTTCCAAGGG
genomic: ATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTC-TAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGG
EST: gi|31357352|gb|CD441709.1|CD441709
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTACCCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|211400405|gb|FL382672.1|FL382672
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|60345367|gb|DN212340.1|DN212340
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|19351198|gb|BM895730.1|BM895730
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|78083755|gb|DV512148.1|DV512148
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|6964703|gb|AW433396.1|AW433396
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|78083754|gb|DV512147.1|DV512147
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGGGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|60349715|gb|DN216688.1|DN216688
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
EST: gi|28188075|gb|CB179685.1|CB179685
EST:     GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAG                         ATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA
genomic: GATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGA

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: 237

GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 146

GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 241

GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 160

GTCCGCACCGCCTCCTAATGGAGCTTCAAGTTCTGATCAACCTGAAAGATGATTGAGAAGATGGAACTGGTAGATTTTTCGTGGCATGAGTCTAACCAAGgtatatctta ... tgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagatctgcaggaaagagtttttgttcagttcataacctcatcctgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT
                               tcataac  putative branch site (score: 160)
                                     cctcatcct  CT-rich tract
                   tttttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagcccccagtgtttgatgaataccaaaggaaacatattgttaattcagatctgcaggaaagagtttttgttcagttcataacctcatcctgttcagcagATGGGCTTCAAAAGGTGGTGCAACTAACCTTGGCAGATCGGTTCCAAGGGACTCGGACAATGGGCTCAATAAAAACAAGCTCAACAGCAGTTTATCCGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- gccccca
- - - - - - tttgatg
- - - - - - - - - - - - - - - aaacata
- - - - - - - - - - - - - - - - - - - - - - - - - tctgcag