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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgcacatgacacatgcatctgcatctccctgtcagttttaattaaaaacaacacaatcatagctcacttttcttcaaggtcgagataattggtt...

Basic information

species Zea mays
transcript GRMZM2G041181_T01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G041181_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 5'ss of exon 4
GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgcacatgacacatgcatctgcatctccctgtcagttttaattaaaaacaacacaatcatagctcacttttcttcaaggtcgagataattggtt-----
||||||||||  ||||| |||||||||||||| |||||||||||||||||||||||||||||||||  |        ||| |||||  || ||| |||  | |||| |  |  |  || | |     | |    | |||  |  ||  |   | |  |||||      
GACCTGAAGAATAGGGAAAAGGAGCTGCAAGCTAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtacaccatg---aacatatgcagttgtatcaccc-attagttgtg-tccattacgataggtcaacaaaagagtttgttgtaatctgatgcttcttggtcttaat
















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|76929603|gb|DV172080.1|DV172080
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|88755248|gb|DY539389.1|DY539389
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|71301449|gb|DR786760.1|DR786760
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211171878|gb|FL095747.1|FL095747
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|32906331|gb|CF011144.1|CF011144
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|76018527|gb|DT945697.1|DT945697
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|22819595|gb|BU499685.1|BU499685
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCCAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|37621887|gb|CF674940.1|CF674940
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211170205|gb|FL095740.1|FL095740
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|28566548|gb|CB278196.1|CB278196
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|74239804|gb|DT647718.1|DT647718
EST:     GGGAGAAGGAGCTACAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211171877|gb|FL095746.1|FL095746
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211170209|gb|FL095744.1|FL095744
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGCTGGCATTGT
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAGCTGGCATTGT
EST: gi|42491841|gb|CK700887.1|CK700887
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|149076171|gb|EE164763.2|EE164763
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|50322749|gb|CO517875.1|CO517875
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|37622034|gb|CF675087.1|CF675087
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211170207|gb|FL095742.1|FL095742
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGC
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGC
EST: gi|67033086|gb|CO461835.1|CO461835
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211170208|gb|FL095743.1|FL095743
EST:     GGGAGAAGGAGCTGCAASCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGGAGAGAGGAGGCTGCAGCGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGG-AGAGAGGAGGCTGCAGCGAG
EST: gi|94472178|gb|EB701136.1|EB701136
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211170204|gb|FL095739.1|FL095739
EST:     GGAGAAGGAGCTGCTAGCAAGGGAACGCGGAATTGAACWAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAAGCTGCAGCGA
genomic: GGAGAAGGAGCTGCAAGCAAGGGAA-GCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGA
EST: gi|38568932|gb|CF974817.1|CF974817
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|50325032|gb|CO520158.1|CO520158
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|211171876|gb|FL095745.1|FL095745
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
EST: gi|37361385|gb|CF602674.1|CF602674
EST:     GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAG                         GAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG
genomic: GGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG

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: 44 (upstream exon), 46 (downstream exon)
Score: 57

GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 90

GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 96

GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG


Block sizes: 48 (upstream exon), 46 (downstream exon)
Score: 128

GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgca ... ttttgaatagGAACTAAAACGGAGAGAGGAGGCTGCAGCGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACCTGAAGAGAAGGGAGAAGGAGCTGCAAGCAAGGGAAGCGGAATTGAACAAGAGGGAGAAGgtattctgcacatgacacatgcatctgcatctccctgtcagttttaattaaaaacaacacaatcatagctcacttttcttcaaggtcgagataattggtt

- - - - - - - GGAGAA
- - - - - - - - - AAGGAG
- - - - - - - - - - GGAGCT
- - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaacaa