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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcatttgtagtttgcagtctgagtttttttttcctgcttcattcctgggatttgagaaataataattaacatcacaataattgtgaacttgcttttaagaacaatcccatttctatatagattaatcatcagccctgctttgcgtgaacag

Basic information

species Zea mays
transcript GRMZM5G819212_T05
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G819212_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os11g47930.1 (Oryza sativa), 5'ss of exon 3
---AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcatttgtagtttgcagtctgagtttttttttcctgcttcattcctgggatttgagaaataataattaacatcacaataattgtgaacttgc-ttttaagaacaatcccatttctatatagattaatcatcagccctgctttgcgtgaacag
   |||||||||| || || ||||||||| ||||||||||||||||||||||||||||| |||||||||||  || |           |||||  | |  |  ||             || | |  ||| |||  | |         || |  ||||| |||| | | |||  | || ||| ||||| ||        || || ||||  ||||||||
AAGAGGAAGTCAATGACTTGGGAGTCAATGTGGCACTATCCATGCTAAAATTTTACAAAAgtaagttcattcttact-----------gttttcatcttgtattta------------tgtgcagcaatcattggcct---------tgcgcccttgccttttgatatcaa--ctatatctctatagctt--------gctctcctttatgtgaacag

upper sequence: GRMZM5G819212_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g15970.3 (Oryza sativa), 5'ss of exon 3
---AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcatttgtagtttgcagtctgagtttttttttcctgcttcattcctgggatttgagaaataataattaacatcacaataattgtgaacttgc-ttttaagaacaatcccatttctatatagattaatcatcagccctgctttgcgtgaacag
   |||||||||| || || ||||||||  ||||||||||||||||||||||||||||| || ||||||||      |||| || |   | ||     | ||  |           | || | |  ||| |||  | |         || |  ||||| |||| | | |||  | || ||| ||||| ||        || || ||||  ||||||||
AAGAGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAAgtgagttcattc-----ttgctgttttcatcttaaacccttgtatt----------tatgtgcagcaatcattggcct---------tgcgcccttgccttttgatatcaa--ctatatctctatagctt--------gctctcctttatgtgaacag

upper sequence: GRMZM5G819212_T05 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os02g15970.4 (Oryza sativa), 5'ss of exon 3
AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcatttgtagtttgcagtctgagtttttttttcctgcttcattcctgggatttgagaaataataattaacatcacaataattgtgaacttgc-ttttaagaacaatcccatttctatatagattaatcatcagccctgctttgcgtgaacag
|||||||||| || || ||||||||  ||||||||||||||||||||||||||||| || ||||||||      |||| || |   | ||     | ||  |           | || | |  ||| |||  | |         || |  ||||| |||| | | |||  | || ||| ||||| ||        || || ||||  ||||||||
AGGAAGTCAATGACTTGGGAGTCAACGTGGCACTATCCATGCTAAAATTTTACAAAAgtgagttcattc-----ttgctgttttcatcttaaacccttgtatt----------tatgtgcagcaatcattggcct---------tgcgcccttgccttttgatatcaa--ctatatctctatagctt--------gctctcctttatgtgaacag

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|211286457|gb|FL309059.1|FL309059
EST:     CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAAATTTACAAAC                         GAGAAATATCACCTTTACTACCTT
genomic: CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTT
EST: gi|211290851|gb|FL314522.1|FL314522
EST:     AAAGATTTTRGAGTCAATATGGCACTATCCATGCTAAAATTCTYACAAAC                         GAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGC
genomic: AAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTT-ACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGC
EST: gi|33467473|gb|CF244522.1|CF244522
EST:     CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC                         GAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
genomic: CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
EST: gi|211269504|gb|FL311290.1|FL311290
EST:     CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC                         GAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
genomic: CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
EST: gi|5296116|gb|AI782991.1|AI782991
EST:     GCTAAAATTTTACAAAC                         GAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
genomic: GCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
EST: gi|211336107|gb|FL367026.1|FL367026
EST:     CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAAC                         GAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA
genomic: CAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCA

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: 47 (upstream exon), 49 (downstream exon)
Score: 93

AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 115

AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 42

AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTC


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 64

AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcat ... gcgtgaacagGAGAAATATCACCTTTACTACCTTCAAGCTGCCGATATGTACCAACTTGCAGTGAGTACTCTATGCAGGCGTACAAACGATATGGTGTTGTAAAGGGTTC


Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGAAGTCAAAGATTTTGGAGTCAATATGGCACTATCCATGCTAAAATTTTACAAACgtaagttcatttgtagtttgcagtctgagtttttttttcctgcttcattcctgggatttgagaaataataattaacatcacaataattgtgaacttgcttttaagaacaatcccatttctatatagattaatcatcagccctgctttgcgtgaacag

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