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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagccttcgcagtctcagctttcgtgtctgtttgctgtgtttcttttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG

Basic information

species Zea mays
transcript GRMZM2G348697_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|18450409|gb|BM428687.1|BM428687
EST:     CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGG                         GTGAAAATATTAGGATTGATCAACTGGGGATCTG
genomic: CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTG
EST: gi|18649492|gb|BM498311.1|BM498311
EST:     CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGG                         GTGAAAATATTAGGATTGATCAACTGGGGATCTG
genomic: CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTG
EST: gi|18649402|gb|BM498221.1|BM498221
EST:     CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGG                         GTGAAAATATTAGGATTGATCAACTGGGGATCTGGTATGATGGGTTGACAC
genomic: CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACAC
EST: gi|18649243|gb|BM498062.1|BM498062
EST:     CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGG                         GTGAAAATATTAGGATTGATCAACTGGGGATCTGGTATGATTG
genomic: CTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTG

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), 48 (downstream exon)
Score: 54

TGGCACCTGCCTTTCTGGGGTTTTTTAGGTGCCGGTGCTGACGCACCAGCCTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 36

TGGCACCTGCCTTTCTGGGGTTTTTTAGGTGCCGGTGCTGACGCACCAGCCTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG


Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 41

TGGCACCTGCCTTTCTGGGGTTTTTTAGGTGCCGGTGCTGACGCACCAGCCTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 28

TGGCACCTGCCTTTCTGGGGTTTTTTAGGTGCCGGTGCTGACGCACCAGCCTTCGCAGTCTCAGCTTTCGTGTCTGTTTGCTGTGTTTCTTTTCCAGAGGgtcagccttc ... tttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcagccttcgcagtctcagctttcgtgtctgtttgctgtgtttcttttccagaggGTGAAAATATTAGGATTGATCAACTGGGGATCTGGGATGATTGGTTGACACTTGATTAGCACAGAAAATACGTGGGATTAGG
                                   ctgtgtttcttttcc  CT-rich tract
                                        tttctttt  TA-rich tract