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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagctcttgggaacagcgccaaagaactttttaatccaaagccaaatatcagttaacctactttctcttgcccgtgatctaatacttcgttttcttgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC

Basic information

species Zea mays
transcript GRMZM2G455243_T01
intron # 15
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|211256182|gb|FL476971.1|FL476971
EST:     GAAGAGGGTMCCAAGCMCAAGTTGCAGAAGGTGCAGCTCAACTATCCAAG                         TGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC
EST: gi|211308482|gb|FL124620.1|FL124620
EST:     GAAGA-GGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAG                         TGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC
genomic: GAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC
EST: gi|16920171|gb|BM074535.1|BM074535
EST:     AAGTTGCAGAAGGTGCAGCTCAACTATCCAAG                         TGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC
genomic: AAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATC

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: 48 (upstream exon), 48 (downstream exon)
Score: 152

CTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 46

CTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 59

CTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC


Block sizes: 48 (upstream exon), 44 (downstream exon)
Score: 55

CTGCAAGCTTGGTGAAAGCAAGATCATCCTCTGTGAAGAGGGTACCAAGCACAAGTTGCAGAAGGTGCAGCTCAACTATCCAAGgtcagctctt ... tgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttaacctactttctcttgcccgtgatctaatacttcgttttcttgattgacagTGATGATGTGACATTTGCCCTCAAGGAATCTCCAGATCTTCCTTGGCTATCTAAGTACTTGTGAGGCTCTTATTGCATTAACCATTGATTCCTGGCACTC
                                tacttcgttttctt  CT-rich tract
 atctaata  TA-rich tract