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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca...

Basic information

species Zea mays
transcript GRMZM2G115424_T03
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G115424_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT1G14510.1 (Arabidopsis thaliana), 5'ss of exon 3
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca--
||||||| ||| | ||  | |||||||| || |||||||| ||||| || |||||||||||||| ||||| ||| | || ||||| | |||| |    |||||    ||| |||   ||   ||   | | ||||||    || |      |   |   ||         |  |  ||      |||| ||  |  | |   
AAAAAGACTGGATTTCTTTGGTTGCAGTTCACAGTGATTCATGGCTTATCTCTGTTGCATTTTACTTTGGTGCACGTTTCGGATTTGGCAAGAATGAGAGgtaa--gtttctttctctgctcagtgttctgtgtttgttaattttgcttgtttggtaaagcttcaatgactagtatagtagctgcataattctagcatccaa
















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|60396717|gb|DN229583.1|DN229583
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60400143|gb|DN232950.1|DN232950
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|93282514|gb|EB674778.1|EB674778
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|149088114|gb|EE177273.2|EE177273
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|94476635|gb|EB705593.1|EB705593
EST:     CTGTTGCATTTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATAT
genomic: CTGTTGCATTTT-ATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATAT
EST: gi|91869344|gb|EB400345.1|EB400345
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|29130260|gb|CB380964.1|CB380964
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|76935015|gb|DV174136.1|DV174136
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60342995|gb|DN209968.1|DN209968
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60343251|gb|DN210224.1|DN210224
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|148979152|gb|EE026541.2|EE026541
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|18964582|gb|BM661089.1|BM661089
EST:     TCTG-TGCATTTTA-TTTGGAGC-AGGTTTGGATTCGACATGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|149088113|gb|EE287286.2|EE287286
EST:     ACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: ACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|4753351|gb|AI657256.1|AI657256
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|211350088|gb|FL126088.1|FL126088
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCA
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCA
EST: gi|211347696|gb|FL126082.1|FL126082
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATAT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATAT
EST: gi|149013491|gb|EE042992.2|EE042992
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|26457236|gb|CA828819.1|CA828819
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|74232055|gb|DT639969.1|DT639969
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|31354599|gb|CD438956.1|CD438956
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|21390188|gb|BQ528237.1|BQ528237
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|211350087|gb|FL126087.1|FL126087
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCT
EST: gi|86466339|gb|DY232710.1|DY232710
EST:     TCTGTTGCATTTTATTTTGGAGCAGGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|211347688|gb|FL126074.1|FL126074
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCT
EST: gi|31910587|gb|CD651499.1|CD651499
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|28930828|gb|CB334189.1|CB334189
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGNTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|31406449|gb|CD485181.1|CD485181
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAAT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAAT
EST: gi|211347693|gb|FL126079.1|FL126079
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGT
EST: gi|211350089|gb|FL126089.1|FL126089
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCCAGCATAT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCC-AGCATAT
EST: gi|28931208|gb|CB334569.1|CB334569
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGNTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|93017250|gb|EB642770.1|EB642770
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|60355952|gb|DN222925.1|DN222925
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|32857894|gb|CD997575.1|CD997575
EST:     GCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAGACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|149110861|gb|EE294360.2|EE294360
EST:     TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: TCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
EST: gi|78544653|gb|DV622151.1|DV622151
EST:     GGAGCAAGG-TTGGATTCGACAAGGAATCCAG                         GAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT
genomic: GGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGT

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), 33 (downstream exon)
Score: 152

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 80

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 94

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 56

AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccattt ... tgcgttgcagGAAACGTCTCTTCACCATGATCAATAATCTTCCCAGCATATATGAGGTTGTCACAGGAACAGCCAAGAAAGAGTCCAAAGAAAAAACTCCTAAAAGCAGC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAAAGATTGGCTATCACTTGTTGCAGTGCATAGTGATTCTTGGCTAATGTCTGTTGCATTTTATTTTGGAGCAAGGTTTGGATTCGACAAGGAATCCAGgtatccatttgttttattgtaaagatgtttctgtttgactgttatataaaatgtttcttgccaatggacttccttcaggtatctcatagtttcatgagca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA