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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttactgcactgttctcccgcccttctttcttactccatctttcgacatatataaataaatgtgtgtgctatcacgttcccactctctgaatgtctgatcattaacttgttgaccttgttcttaaggtaaagctactcactcactcccatctagtactgcaattgattcttgtccccccgtgtatgccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG

Basic information

species Zea mays
transcript GRMZM2G174990_T03
intron # 14
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|211055318|gb|FL438696.1|FL438696
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|16380026|gb|BI993269.1|BI993269
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|211483107|gb|FK977834.1|FK977834
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGA-GTTCTGCTTTCTA-GATCTGACCATGGAGCAGC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTT-CTAAGATCTGACCATGGAGCAGC
EST: gi|31997891|gb|CD661822.1|CD661822
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|31611996|gb|CD568618.1|CD568618
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|71426246|gb|DR807296.1|DR807296
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTTTGCTTTTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60672515|gb|DN475220.1|DN475220
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60336722|gb|DN203695.1|DN203695
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|60336887|gb|DN203860.1|DN203860
EST:     AGGATGAGCTGCTGGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
EST: gi|13557670|gb|BG549026.1|BG549026
EST:     AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGT                         AAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC
genomic: AGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCC

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: 47

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 205

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 357

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 92

GCCCTTTACGATGCTCTGATGCGACAGGATGAGCTGCTCGCGTACATTGACAGGCAGGAGCTGATCAAGTTCCGTgtacgttact ... ccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactcccatctagtactgcaattgattcttgtccccccgtgtatgccttctgcagAAAAAGAAGTTCTGCTTCTAAGATCTGACCATGGAGCAGCTGGTCATGTCCGGAGCCGTTCGTGTATATTGTTGGATCGCGGCTAGTACGGTGAATGATG
                                           tgccttct  CT-rich tract
                   aattgatt  TA-rich tract