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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaagttcaccgatatgctgttgtgtctgtcttgagaagttccacaagcaatcttggagaaagatcatgtagacatcactattttgttttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGGCGTTGGTAATTTGTCAATTTGGCTAGGGGTTTGTTAACCTTATTCAGAT

Basic information

species Zea mays
transcript GRMZM2G382104_T02
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|88750910|gb|DY535051.1|DY535051
EST:     GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAG                         GTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
genomic: GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
EST: gi|211250898|gb|FL454491.1|FL454491
EST:     GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAG                         GTGCTTGTTTG-A-AGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
genomic: GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
EST: gi|40335444|gb|CK369514.1|CK369514
EST:     GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAG                         GTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
genomic: GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
EST: gi|88749210|gb|DY533351.1|DY533351
EST:     GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAG                         GTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG
genomic: GACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGG

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 2 RNA-Seq libraries.


Block sizes: 46 (upstream exon), 24 (downstream exon)
Score: 2

ACAAGAAGCACTCAAGGATGGTTGTAACTTAGAGCAAAGTAGCAGCGGTGGACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGGCGTTGGTAATTTGTCAATTTGGCTAGGGGTTTGTTAACCTTATTCAGAT


Block sizes: 9 (upstream exon), 41 (downstream exon)
Score: 1

ACAAGAAGCACTCAAGGATGGTTGTAACTTAGAGCAAAGTAGCAGCGGTGGACATTGATTGTGAACATATTTGTAGTCCCCAAAATGCACATAATGTCAGgtatatatat ... ttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGGCGTTGGTAATTTGTCAATTTGGCTAGGGGTTTGTTAACCTTATTCAGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaagcaatcttggagaaagatcatgtagacatcactattttgttttgtggccagGTGCTTGTTTGAAGAGAGAGTAATATTGGCTTTGGCTATGGAAGCAGCAGGCGTTGGTAATTTGTCAATTTGGCTAGGGGTTTGTTAACCTTATTCAGAT
                                      ttttgtttt  CT-rich tract
                                    tattttgtttt  TA-rich tract