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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggtagtaaactaaggccgcatgcccatgctttccgtgtcatcgtttacatcagagaccaaccaaaatgttttgccggccatatgcag

Basic information

species Zea mays
transcript GRMZM2G116427_T01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G116427_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 5'ss of exon 6
GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggtagtaaactaaggccgcatgcccatgctttccgtgtcatcgtttac-atcagagaccaaccaaaatgtt-ttgccggccatatgcag
|||||| |||||||| || |||||||||||||||||||| || || || ||||||||||| ||||||||||||   |||   ||      |   || | || | ||       |||   |  | ||| |     |  |  || |  ||  |||         
GCGCATCCGTGATGAACTCGCCAAGCAGAATGAGGAAACTACAGAACTCACCACAAAGCTAGACAAGgtgagtaa-agtggccttcatgtgtgggctc-tgttatct-cactgtcgggcattaacagggtttgtctgatttgctactgttggcag-------
















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|21330027|gb|BQ485408.1|BQ485408
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|32869175|gb|CF008857.1|CF008857
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|21390796|gb|BQ528845.1|BQ528845
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|21480752|gb|BQ577435.1|BQ577435
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|7227834|gb|AW566475.1|AW566475
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|14324103|gb|BG929580.1|BG929580
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|6851592|gb|AW352602.1|AW352602
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTNCGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|22545270|gb|BU097643.1|BU097643
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|5922394|gb|AW055683.1|AW055683
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|22546799|gb|BU099110.1|BU099110
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|4730313|gb|AI649479.1|AI649479
EST:     TTGCCAAGCAGAATGAGGAAACCCCTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|211128611|gb|FL432588.1|FL432588
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|21481481|gb|BQ578164.1|BQ578164
EST:     TNGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTGGACAAG                         GAAATCCACTCACTGAAAGCCCAGTTGGAGGCAGCAAAGTACGATG
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATG
EST: gi|87154790|gb|DY399579.1|DY399579
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|22546847|gb|BU099158.1|BU099158
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|32906186|gb|CF010999.1|CF010999
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
EST: gi|7238187|gb|AW573409.1|AW573409
EST:     TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAG                         GAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC
genomic: TTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATC

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), 48 (downstream exon)
Score: 54

GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATCAAGTACTGCATAGGTACCATTGTTTCGATCTCAGCCGTCGGCCTCGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATCAAGTACTGCATAGGTACCATTGTTTCGATCTCAGCCGTCGGCCTCGCCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 114

GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATCAAGTACTGCATAGGTACCATTGTTTCGATCTCAGCCGTCGGCCTCGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 125

GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggta ... ccatatgcagGAAATCCACTCACTGAAGGCCCAGTTGGAGGCAGCAAAGTACGATGTCATCAAGTACTGCATAGGTACCATTGTTTCGATCTCAGCCGTCGGCCTCGCCG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCGCATACGTGATGAGCTTGCCAAGCAGAATGAGGAAACCACTGAGCTTACCACAAAGCTTGACAAGgtgagtggtagtaaactaaggccgcatgcccatgctttccgtgtcatcgtttacatcagagaccaaccaaaatgttttgccggccatatgcag

- - - - - - - - - - - - - - - - - - - - -  GAGCTT