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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaggaatcattttcatttatgttcctggaaaaaatggatcattttgtttccttgaatacacaaggaatatgtacattttgcacatgactagttggcgttgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG

Basic information

species Zea mays
transcript GRMZM2G164562_T01
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os03g14990.1 (Oryza sativa), 3'ss of exon 9
gtaaggaatcattttcatttatgttcctggaaaaaatggatcattttgtttccttgaatacacaaggaatatgtacattttgcacatgactagttggcgttgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG
                                        | |||   ||    || | | |    |   || ||  ||||||| ||  ||         ||  |||   |  | |        |  | | || |  ||||||||||||||| |||||| ||||  ||||||||||||||||||||||||||||||||||||||||||||||||||||| ||| |||||||||| ||||||||||| |||
---------------------------------------gtaattgaattaatctgcacataattagttgatttattttttgcaaatagctg--------tgcatgccaactactttgctactggcctcaatactaactaataacttgtgcccagGTACTGACTACACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGAACAAGAACTAATCGTTCAGGCGGTGTGCAG

upper sequence: GRMZM2G164562_T01 (Zea mays), 3'ss of exon 9
lower sequence: GLYMA10G35560.1 (Glycine max), 3'ss of exon 9
gtaaggaatcattttcatttatgt-tcctggaaaaaatggatcattttgtttccttgaatacacaaggaatatgtacattttgcacatgactagttggcgttgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG
|||   || | |  | || ||| | |||  |      ||  | ||  | ||  |  || || ||| |||  |  |  |   ||    |   |  |||      | ||  || ||  |  ||||  |  | | | |     ||| | || |    ||| ||    || ||||| ||||| |||||||||||||||||||| |||||   ||||||    || ||| |||| |||||||| || ||  | |||
gtactaaaacttgcttatgtatatgtccgagtgcccttgtcttatgatattggcc-gactaaacagggatcaattgaacaatgt---tattttcttgatcacttgtgtctgaagtgtgttctaatggcttagtga-----aatta-ttat----agGCACCTTTTTGACTGGGAGTGAACATAATGATGAGTTCTATATAGATGAACATGGAAACACAAGAACAAGAACAAATCGCTCTGGTGGGATACAG
















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|211540751|gb|FL105309.1|FL105309
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|60357187|gb|DN224160.1|DN224160
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|78089033|gb|DV517426.1|DV517426
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|32862616|gb|CF002298.1|CF002298
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|7216715|gb|AW562837.1|AW562837
EST:     GCTTTCTCTTNCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|40335508|gb|CK369578.1|CK369578
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|213172541|gb|FM189510.1|FM189510
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|32808278|gb|CD960512.1|CD960512
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGACGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|113701263|gb|EE678767.1|EE678767
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|32808708|gb|CD960942.1|CD960942
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|18659504|gb|BM500373.1|BM500373
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|148963944|gb|EE015066.2|EE015066
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTTTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|37385128|gb|CF629683.1|CF629683
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|211540749|gb|FL105307.1|FL105307
EST:     AGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: AGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|60352524|gb|DN219497.1|DN219497
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|67042195|gb|CO468450.1|CO468450
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|32793479|gb|CD945715.1|CD945715
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGATG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
EST: gi|5901142|gb|AW042242.1|AW042242
EST:     GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTG                         GTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG
genomic: GCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 289

CTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 677

CTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 588

CTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 835

CTTGGCTCTCCTGTTTTTGACAAACTTGAAGCTGAACTGGCAAAAGCCATGCTTTCTCTTCCTGCAAGCAAGGGGTTTGAGATTGGCAGTGGGTTCGCTGgtaaggaatc ... ttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG
                                      taataac  putative branch site (score: 835)
                                      taataactt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggaatcattttcatttatgttcctggaaaaaatggatcattttgtttccttgaatacacaaggaatatgtacattttgcacatgactagttggcgttgtttgcatgcagcctactctacagtttgactaattcctaataacttgtgccaagGTACGGACTTTACTGGAAGTGAGCATAATGATGAGTTCTATATGGATGAGGCTGGAAATGTGAGGACACGAACTAATCGCTCAGGCGGTGTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA