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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggttctttcttgatttccgcaagtttggtcgacacaagtgtctgattgtctgaatagcagagggcttggaacttcctttctcgggaatcttgtt...

Basic information

species Zea mays
transcript GRMZM2G147882_T01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G147882_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g09300.2 (Oryza sativa), 5'ss of exon 1
AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggttctttcttgatttccgcaagtttggtc-gacacaagtgtctgattgtctgaatagcagagggcttggaacttcctttctcgggaatcttgtt
| |     ||||||||||| || | ||||||||||| || |||||||||||||||||||  |||||| ||  | ||||||| || ||||||||||||||||||  |  | | ||||||   | ||| | |||  |  | |   | |       ||  || || |  |   |  | |   |  |  ||| |  |   | |  
AGGGAGGGAGAGCATGGAGTGCTCCATCTCGAGGACGAATCTGAATTGCATCAGCCTGGGTGACCCGGACACCAAGAAATCGGTCGCGCTCCTCAAGCAGgtcttct-tcccttcttggaattcgcgattttctttaggctgtactactactctggatggatggatggatggattgtcttgacactctggataggatagca
















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|211501569|gb|FL375241.1|FL375241
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|211210380|gb|FL427965.1|FL427965
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|211498686|gb|FL368195.1|FL368195
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|88756322|gb|DY540463.1|DY540463
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|74241070|gb|DT648984.1|DT648984
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|78117759|gb|DV536146.1|DV536146
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|211054808|gb|FL419520.1|FL419520
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCWGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|78078284|gb|DV506699.1|DV506699
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|88756286|gb|DY540427.1|DY540427
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|93014970|gb|EB640490.1|EB640490
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|211054809|gb|FL419521.1|FL419521
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|71299023|gb|DR785502.1|DR785502
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|71429426|gb|DR810476.1|DR810476
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|50323931|gb|CO519057.1|CO519057
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
EST: gi|211382338|gb|FL400551.1|FL400551
EST:     TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAG                         GCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA
genomic: TCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAA

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), 49 (downstream exon)
Score: 17

AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 890

AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1100

AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 28

AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggtt ... tatttggtagGCATGCCTGGATTCAGGCTTCTTCTATGTTGTGGATCATGGGATAAGCCAAGAGTTCATGGATGAAGTTTTTGCCCAGAGCAAGAAGTTCTTTGACCTTC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCGCACAGAGCATGGAGAGCCCGATCTCGAGGACTAACCTGAATTGCATCAGCCTGGCGGACCCGAACGTCCAGAAATCAGTGGCGCTCCTCAAGCAGgtccgcggttctttcttgatttccgcaagtttggtcgacacaagtgtctgattgtctgaatagcagagggcttggaacttcctttctcgggaatcttgtt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC