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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactcttttttaccaccttgatgtttttccagttgaaatgttctcagaagatccttttatagttttttagttgtatttctggcattctatagttaccca...

Basic information

species Zea mays
transcript GRMZM2G057329_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G057329_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g59700.1 (Oryza sativa), 5'ss of exon 4
AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactcttttttaccaccttgatgtttttccagttgaaatgttctcagaagatccttttatagttttttagttgtatttctggca-----ttctatagttaccca
   ||||||||||||||||| |||||||| ||||||||||||||||||||||| || || ||||||||||| || ||||| || || || |||||| | ||  |  ||||||       ||| || |||||||  | | |||| ||  |       |  | || |  | |    | ||     |||||  |||     
GGGGATGGTACTGGATGCACGTCAATCTATGGTACCAAATTTGATGATGAAAACTTCATTGCAAAGCATACTGGTCCTGGCCTACTTTCTATGgtattattcctctccacctga-----ttttcaattgaaatactgttagaaaatattacctctctaatgtaatcttgtgcaggacaactatttctagtgtttggtg
















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|211112964|gb|FL394568.1|FL394568
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211023124|gb|FL428614.1|FL428614
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|19057931|gb|BM736598.1|BM736598
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|19058424|gb|BM737091.1|BM737091
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|32858929|gb|CD998610.1|CD998610
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACATTGGTANTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|60349165|gb|DN216138.1|DN216138
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|60349812|gb|DN216785.1|DN216785
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|60394638|gb|DN227508.1|DN227508
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|24766439|gb|CA401593.1|CA401593
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211360429|gb|FL377716.1|FL377716
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GGCAA-CAGTGGGATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagG-CAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211357849|gb|FL385252.1|FL385252
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGSTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|87152302|gb|DY397091.1|DY397091
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|32925862|gb|CF030674.1|CF030674
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211438423|gb|FL465204.1|FL465204
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211073855|gb|FL392646.1|FL392646
EST:     ATTATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211027097|gb|FL381991.1|FL381991
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211099687|gb|FL379428.1|FL379428
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|22490292|gb|BU050215.1|BU050215
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211206179|gb|FL469079.1|FL469079
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|32933536|gb|CF038348.1|CF038348
EST:     ATGATGAAAATTTTATAGCAAAGCATACAAGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGGTCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|6695399|gb|AW288507.1|AW288507
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|32926451|gb|CF031263.1|CF031263
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|32940102|gb|CF044921.1|CF044921
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|8577336|gb|BE129973.1|BE129973
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211433999|gb|FL392548.1|FL392548
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|12047274|gb|BF729413.1|BF729413
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211254561|gb|FL409666.1|FL409666
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAAT
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAAT
EST: gi|78179385|gb|DV549758.1|DV549758
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|60398036|gb|DN230852.1|DN230852
EST:     ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: ATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|113800830|gb|DW922816.1|DW922816
EST:     CTGCTCTCGATG                         GCAAACAGTGGAATTAACTCTAATGGATCTCAG
genomic: CTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG
EST: gi|211042680|gb|FL406379.1|FL406379
EST:     TGATGAAAATTTTATAGCAAAGCATACAGGGNCCTGGACTGCTCTCGATG                         GCAAACAGTGGAANTTAACTCTAATGGATCTCAG
genomic: TGATGAAAATTTTATAGCAAAGCATACAGGG-CCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAA-TTAACTCTAATGGATCTCAG

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), 49 (downstream exon)
Score: 270

AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG


Block sizes: 46 (upstream exon), 33 (downstream exon)
Score: 123

AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG


Block sizes: 49 (upstream exon), 33 (downstream exon)
Score: 199

AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG


Block sizes: 48 (upstream exon), 33 (downstream exon)
Score: 115

AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactctttt ... ttttttccagGCAAACAGTGGAATTAACTCTAATGGATCTCAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATGATGGTACTGGATGCACATCAATCTACGGTACCAAATTTGATGATGAAAATTTTATAGCAAAGCATACAGGGCCTGGACTGCTCTCGATGgtactcttttttaccaccttgatgtttttccagttgaaatgttctcagaagatccttttatagttttttagttgtatttctggcattctatagttaccca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG