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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtatcttatgtgacctcatcacccgattataattttcgatttggattatatagtttcttgaattcacaaacctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG

Basic information

species Zea mays
transcript GRMZM2G100707_T01
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|32933286|gb|CF038098.1|CF038098
EST:     TGAAACGGTTACAACAGATACTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCTGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
EST: gi|93015870|gb|EB641390.1|EB641390
EST:     TGAAACGGTTACAACAGATACTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
EST: gi|211442681|gb|FL456308.1|FL456308
EST:     TGAAACGGTTACAACAGATACTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
EST: gi|37398356|gb|CF636490.1|CF636490
EST:     TGAAACGGTTACAACAGATANTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
EST: gi|5915101|gb|AW052742.1|AW052742
EST:     TGAAACGGTTACAACAGATACTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
EST: gi|149097072|gb|EE182879.2|EE182879
EST:     TGAAACGGTTACAACAGATACTAGGTCGGAAGCATNNNNNNNNTCTTCAT                         ACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG
genomic: TGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCG

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: 90

ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 82

ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 87

ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 61

ACAGCCTGATTTAGGATTCATGAAACGGTTACAACAGATACTAGGTCGGAAGCATAAAAAAAATCTTCATgtgagtatct ... acctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattataattttcgatttggattatatagtttcttgaattcacaaacctttacagACTATATACATACTCCACCCGACACTGGGACTGAGAACAGCCGTTATGGCGATGCAACTTTTTGTTGACGGGGAG
                                              cctttac  CT-rich tract
                    attatatagtttctt  TA-rich tract