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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggagtacagtaatatttgttatgaaatatggttcatcttctagaatgctcagttcatggataccataagcattcttggatatgaatgtgatgtgctctcctactgtatctgagttcttgtggcattcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAACCTCAACGGGCTCGAGAGTTATTTCCTTCAATCCCCACGTCAACCTTGTC

Basic information

species Zea mays
transcript GRMZM2G017187_T02
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|26559041|gb|CA831276.1|CA831276
EST:     GCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: GCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
EST: gi|22935977|gb|BU572252.1|BU572252
EST:     GGTTTCGGAACTGCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: GGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
EST: gi|31612183|gb|CD568805.1|CD568805
EST:     ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
EST: gi|87156368|gb|DY401157.1|DY401157
EST:     GCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: GCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
EST: gi|33094675|gb|CF054669.1|CF054669
EST:     ACGATCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGT
genomic: ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGT
EST: gi|32808248|gb|CD960482.1|CD960482
EST:     ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
EST: gi|78074585|gb|DV503019.1|DV503019
EST:     ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTG                         GACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC
genomic: ACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAAC

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: 369

GATGCAGCTAATCCACAATCCCCTCAACCTCCACTAAGGGCTAAGCGTCCACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAACCTCAACGGGCTCGAGAGTTATTTCCTTCAATCCCCACGTCAACCTTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 62

GATGCAGCTAATCCACAATCCCCTCAACCTCCACTAAGGGCTAAGCGTCCACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAACCTCAACGGGCTCGAGAGTTATTTCCTTCAATCCCCACGTCAACCTTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 90

GATGCAGCTAATCCACAATCCCCTCAACCTCCACTAAGGGCTAAGCGTCCACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAACCTCAACGGGCTCGAGAGTTATTTCCTTCAATCCCCACGTCAACCTTGTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 99

GATGCAGCTAATCCACAATCCCCTCAACCTCCACTAAGGGCTAAGCGTCCACGACCCCCAGCTTCACCTTGTATGGTTTCGGAACTGCCTTCAGGTTTTGgtaaggagta ... ttcatgttagGACTCTGGAAATCCCCAATTGAATCATCCTGTACACTCTCATTTTCGGAACCTCAACGGGCTCGAGAGTTATTTCCTTCAATCCCCACGTCAACCTTGTC