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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAACAAATAATGGAGATGCAGCAAAACCAGgtagatttttttgttaaacttccattgttgatgtttctttttcattgcacactaaagatggatacattcctgttttcaaatagtgaatttcagtgcttat...

Basic information

species Zea mays
transcript GRMZM2G157722_T01
intron # 3
splice site 5'
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|71760129|gb|DR958066.1|DR958066
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|71438607|gb|DR819657.1|DR819657
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|148949126|gb|EC894557.2|EC894557
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|78117177|gb|DV535564.1|DV535564
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|93282472|gb|EB674736.1|EB674736
EST:     GAACAAATAATGGAGAGGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|149072702|gb|EE160938.2|EE160938
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|76283483|gb|DV023051.1|DV023051
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|88753387|gb|DY537528.1|DY537528
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|101385967|gb|EB815030.1|EB815030
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|71314118|gb|DR793675.1|DR793675
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|86470887|gb|DY237257.1|DY237257
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
EST: gi|149113009|gb|EE295786.2|EE295786
EST:     GAACAAATAATGGAGATGCAGCAAAACCAG                         GTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG
genomic: GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGG

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: 30 (upstream exon), 48 (downstream exon)
Score: 90

GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGGAGAACATTGACAGGTCCCTGGTAACTGAGTTGTTGTTGATCGGACTCGA


Block sizes: 30 (upstream exon), 48 (downstream exon)
Score: 44

GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGGAGAACATTGACAGGTCCCTGGTAACTGAGTTGTTGTTGATCGGACTCGA


Block sizes: 30 (upstream exon), 48 (downstream exon)
Score: 22

GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGGAGAACATTGACAGGTCCCTGGTAACTGAGTTGTTGTTGATCGGACTCGA


Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 118

GAACAAATAATGGAGATGCAGCAAAACCAGgtagattttt ... ctccgaacagGTCCCGGAATTGGTCAGCAATCCATATGCACAAAAGAAGCGATGCCTGCGGAGAACATTGACAGGTCCCTGGTAACTGAGTTGTTGTTGATCGGACTCGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAACAAATAATGGAGATGCAGCAAAACCAGgtagatttttttgttaaacttccattgttgatgtttctttttcattgcacactaaagatggatacattcctgttttcaaatagtgaatttcagtgcttat

- - - - - TGGAGA
- - - - -  GGAGAT
- - - - - - GAGATG