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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATTGAATAATCCTTGGATGGTATTACTCATTATGATAATACAATTCTCATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgccattttcagagggctctgttcccatcaacattttcaagtatttatggattgttgaatgtgaagtttacttaaatatttgcaaggatgttta...

Basic information

species Zea mays
transcript GRMZM2G036902_T01
intron # 4
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|40337056|gb|CK371126.1|CK371126
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
EST: gi|33092496|gb|CF052490.1|CF052490
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
EST: gi|50331608|gb|CO526734.1|CO526734
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCCCCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
EST: gi|32834165|gb|CD973843.1|CD973843
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
EST: gi|71762324|gb|DR960261.1|DR960261
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
EST: gi|37397514|gb|CF636057.1|CF636057
EST:     CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAG                         GTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA
genomic: CATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAA

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), 44 (downstream exon)
Score: 54

ATAATTGAATAATCCTTGGATGGTATTACTCATTATGATAATACAATTCTCATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAATTCAGACTTTCGTTTGGGTTCTTATACGAACAGGAATTGTCCTGTGTGA


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 92

ATAATTGAATAATCCTTGGATGGTATTACTCATTATGATAATACAATTCTCATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAATTCAGACTTTCGTTTGGGTTCTTATACGAACAGGAATTGTCCTGTGTGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 128

ATAATTGAATAATCCTTGGATGGTATTACTCATTATGATAATACAATTCTCATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAATTCAGACTTTCGTTTGGGTTCTTATACGAACAGGAATTGTCCTGTGTGA


Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 81

ATAATTGAATAATCCTTGGATGGTATTACTCATTATGATAATACAATTCTCATAATCTTTCAAATGAAGTGTGCCTGGCAATTTCTTTCCATGGCTTAAGgtatgctgcc ... ctactgacagGTCGGCATGGACATCACCAGGAAATGTGTATGGGTTTTGATTGATTACTAATTCAGACTTTCGTTTGGGTTCTTATACGAACAGGAATTGTCCTGTGTGA