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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaagccccgcttgaatcgatagttcatttccctctgcataattcgaaattctccttcagtgaccgataccaatcggtccagtttgctgtggactagtgtgatgattggcggagtgctaatagatgttaattttctttaattttggtcccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC

Basic information

species Zea mays
transcript GRMZM2G037469_T01
intron # 1
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|76283454|gb|DV023022.1|DV023022
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|71426896|gb|DR807946.1|DR807946
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211350011|gb|FL351961.1|FL351961
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211138264|gb|FL356409.1|FL356409
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|76909710|gb|DV163496.1|DV163496
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|71448489|gb|DR829539.1|DR829539
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|149102413|gb|EE287775.2|EE287775
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|76020236|gb|DT947406.1|DT947406
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGT-CTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|148967248|gb|EE018449.2|EE018449
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211023709|gb|FL334122.1|FL334122
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211390911|gb|FL318340.1|FL318340
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|32797663|gb|CD949899.1|CD949899
EST:     GATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211263391|gb|FL364894.1|FL364894
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|89756347|gb|DY686397.1|DY686397
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211218567|gb|FL341027.1|FL341027
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211342751|gb|FL350520.1|FL350520
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|94472953|gb|EB701911.1|EB701911
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
EST: gi|211017810|gb|FL312940.1|FL312940
EST:     GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCG                         GTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC
genomic: GCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTC

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: 29 (upstream exon), 34 (downstream exon)
Score: 3

AGACGCCCTCGCATCTCTCGCCCTTCCGGCATCGTATCCCCTGGGCGGCAGCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC


Block sizes: 42 (upstream exon), 48 (downstream exon)
Score: 23

AGACGCCCTCGCATCTCTCGCCCTTCCGGCATCGTATCCCCTGGGCGGCAGCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 27

AGACGCCCTCGCATCTCTCGCCCTTCCGGCATCGTATCCCCTGGGCGGCAGCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 112

AGACGCCCTCGCATCTCTCGCCCTTCCGGCATCGTATCCCCTGGGCGGCAGCGGAGTAAAGATCCGACCCGCTTGGGATTGTTTGCTTCTCCTTTTTGCGgtaaggaagc ... cccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgattggcggagtgctaatagatgttaattttctttaattttggtcccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC
               taatagatgttaattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaagccccgcttgaatcgatagttcatttccctctgcataattcgaaattctccttcagtgaccgataccaatcggtccagtttgctgtggactagtgtgatgattggcggagtgctaatagatgttaattttctttaattttggtcccgcgttagGTGCGCCGCTGGACTCCAGTGCTGCACATGCTCGACGACGGTGCTGAGCTCCTGCAATGGCCCGAAGAAATGCCGGCGCAATGCAGCGGGAGGGTTCCGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA