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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaaatgtcactccttttctctgccttgaattaagtgataacaatcttaggcccgattgtctggtttctgattatctacttgtgaatattatgatag

Basic information

species Zea mays
transcript GRMZM2G089484_T01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G089484_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 5'ss of exon 8
CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagat-caaatgtcactcc-ttttctctgccttgaattaagtgataacaatcttaggcccgattgtctg-gtttctgattatctacttgtgaatattatgatag---
||||||| ||||||||||| |||||||||||||||||||||||||||||||||||||| |||| | ||||||||||||| |||||||| ||||| ||  ||| ||||    || | | |   |||| | || | || |||||  |||   | |  |||  ||  |||  |   |   ||||| |  |||    | |||| |        
CAGTAGACCATTTTAAAAAACAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCAACAGCAGCTCCACCTGAGAGACAACATAACTCATTACCAAGgtaagatatttattttattttattttatatgacatggattaaccgatggaacttgtagctccagttgaatatatacttgattcttgactatctactattgtatcgacag
















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|60397061|gb|DN229880.1|DN229880
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCTGACAACCGATCACAAACCACAGCCAGCATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|14245174|gb|BG873756.1|BG873756
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|32835922|gb|CD975600.1|CD975600
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCGCAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|211150023|gb|FL261061.1|FL261061
EST:     AGGGAATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCTGAACAACCGATCACAAACCACAGCCAGCATCA
genomic: AGGGA-TCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGA-CAACCGATCACAAACCACAGCCAACATCA
EST: gi|32835600|gb|CD975278.1|CD975278
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCGCAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|60351950|gb|DN218923.1|DN218923
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCTGACAACCGATCACAAACCACAGCCAGCATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|32835454|gb|CD975132.1|CD975132
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCGCAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|32833224|gb|CD972902.1|CD972902
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCGCAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|71763203|gb|DR961140.1|DR961140
EST:     AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
genomic: AAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC
EST: gi|9742842|gb|BE518990.1|BE518990
EST:     GGGATCTACAGGAACTCCACCTGAGTATGTTTTCATAATTCATTGCCGCG                         GCCGTCTGTTGTCTATTCTGACAACCGATCACAAACCACAGCCAGCATCAC
genomic: GGGATCTACAGGAACTCCACCTGAG-A-GGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCAC

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: 48 (upstream exon), 48 (downstream exon)
Score: 203

CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 112

CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 193

CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 136

CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaa ... attatgatagGCCGTCTGTTGTCTATTCCGACAACCGATCACAAACCACAGCCAACATCACCGAGGATCTTTCCAAGTGTATGCTCAGAGAAAATACACAGAAGACACAT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAGATCATTTTAAAAAGCAGTTTGCATACCTTGAAGAACATTATGCCAAGGGATCTACAGGAACTCCACCTGAGAGGCAACATAATTCATTGCCGCGgtgagatcaaatgtcactccttttctctgccttgaattaagtgataacaatcttaggcccgattgtctggtttctgattatctacttgtgaatattatgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG