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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagtttcagttctcatcttagacgctttccccttttgatacaaataacttcgaatgccagctatgtttccagtaaaagatcgattttctgtaattttctcgatgttgcatatttaaccctgtatgtgtgattattatgatgatgccatccattgttttgtag

Basic information

species Zea mays
transcript GRMZM2G080652_T01
intron # 7
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|211040785|gb|FL108285.1|FL108285
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|32837961|gb|CD977639.1|CD977639
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|166668460|gb|EG154724.1|EG154724
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGAACACTCTCCTC
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGA-CACTCTCCTC
EST: gi|71309452|gb|DR791013.1|DR791013
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|24768059|gb|CA403191.1|CA403191
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|61119643|gb|DN560604.1|DN560604
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGATACTCTCCT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCT
EST: gi|78117500|gb|DV535887.1|DV535887
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|71330843|gb|DR802223.1|DR802223
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|18169407|gb|BM339247.1|BM339247
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         GAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT
EST: gi|71309454|gb|DR791014.1|DR791014
EST:     GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATG                         -AATACAACGACACTCTCCTCATGACCTACTTTGCAATGGCCACTAATTGT
genomic: GAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGT

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), 49 (downstream exon)
Score: 87

TGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 94

TGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

TGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGTTCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 148

TGACATTCCATTAGATAATTCGCTGCTTAGGCAAGTCTCAAGCCTCGTAAGAAGGCTACCAGCTATGGAGTCACAGAAATTCCAAGACGACTTCTTAATGgtatgctagt ... tgttttgtagGAATACAACGACACTCTCCTCATGACCTACCTTGCAATGGTCACTAAATGTTCAAG