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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcacaatgctgactacttggtgttctacatacatacacacgcatgggccattataacatcaattctgtttgagtaactagagcccctccatctttacttgcatagtggctatgactatttctttctgattgcactccag

Basic information

species Zea mays
transcript GRMZM2G133959_T03
intron # 10
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|211416883|gb|FL440253.1|FL440253
EST:     ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|12058307|gb|BF729165.2|BF729165
EST:     CAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: CAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|71445212|gb|DR826262.1|DR826262
EST:     ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|78179633|gb|DV550006.1|DV550006
EST:     CAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: CAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|78080386|gb|DV508798.1|DV508798
EST:     ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|76290046|gb|DV029614.1|DV029614
EST:     ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|71431548|gb|DR812598.1|DR812598
EST:     ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: ACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
EST: gi|9954002|gb|BE640600.1|BE640600
EST:     CAGAGTTCCAAAAG                         CTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG
genomic: CAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATG

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), 42 (downstream exon)
Score: 24

TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 9

TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 31

TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 57

TACAACACAATGCGCAATGTCCTTTTCATGGCAATGACAGAGTTCCAAAAGgtaactcaca ... tgcactccagCTTACTGAAGAACCAGACTGGACTTTCATCAGAGCACAAGAGGACAAAATGGCCTTTTTGTTCGGTGTGGATGATCACTGGGGCCCACTATCTCACTTAG