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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atcaaaccatccctgtaccactgtccttgtaacaagtaaattctctattttgctacgtatgtgtatcattaatcaaacaccttgattttcgtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG

Basic information

species Zea mays
transcript GRMZM2G042818_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G042818_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os01g54860.1 (Oryza sativa), 3'ss of exon 10
----atcaaaccatccctgtac-cactgtccttgtaacaagtaaattctctattttgctacgtatgtgtatcattaatcaaacaccttgattttcgtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG
    | ||| |    || ||   |||||||||  |||||||  |||   || |||| || |  ||    || | ||          ||| | ||  |   ||||||||||||||| |||||| || |||||||||||||| ||| |||| || |||||  || ||||||||||||| ||| |||||||||| || ||  |||||
actcaccaatcaccaccagtcttcactgtcct-ataacaaggcaatcaact-ttttcctgcaaat---cataagtagcgtcttttgttgttgttgttgtttgtagGAATCAGAAGGGAGCATTGATGGAAACCAATGGATCGCTACAGTACTGAAGGGCATGCGAAGATCATCTCCTACTTCACTGAAGATGACTCTTCGATCG
















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|74240479|gb|DT648393.1|DT648393
EST:     TCAACAAATGCTTCTTTGCGGAGACTGTTGAGGATATCATAAAAGCATTT                         GATTCAGAAGCGAGCTTAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|29544823|gb|CB605431.1|CB605431
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|37400624|gb|CF637668.1|CF637668
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|15177481|gb|BI398420.1|BI398420
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAAGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|148959114|gb|EC905254.2|EC905254
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|45568357|gb|CK986026.1|CK986026
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|37392700|gb|CF633603.1|CF633603
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|60352184|gb|DN219157.1|DN219157
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|33092056|gb|CF052050.1|CF052050
EST:     GCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: GCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|32930057|gb|CF034869.1|CF034869
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|71304194|gb|DR788217.1|DR788217
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|29544214|gb|CB604594.1|CB604594
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|37383733|gb|CF628896.1|CF628896
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|40303747|gb|CK348134.1|CK348134
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|149089063|gb|EE178226.2|EE178226
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAGGCGAGCATAGACGGAAACCAATGG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGG
EST: gi|91053743|gb|EB164161.1|EB164161
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|74239819|gb|DT647733.1|DT647733
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|211149870|gb|FL475634.1|FL475634
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|74238393|gb|DT646307.1|DT646307
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAG
EST: gi|37379687|gb|CF626591.1|CF626591
EST:     TCAACAAATGTTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCAAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
EST: gi|71762792|gb|DR960729.1|DR960729
EST:     TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTT                         GAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG
genomic: TCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAG

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: 114

GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 206

GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 151

GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 310

GCTTTCAACTATCAACAAATGCTTCTCTGCAGAGACTGTTGAGGATATCATAAAAGCATTTgtaaggattc ... gtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgctacgtatgtgtatcattaatcaaacaccttgattttcgtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG
                                        ttttcgtc  CT-rich tract
                  tatcattaatcaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atcaaaccatccctgtaccactgtccttgtaacaagtaaattctctattttgctacgtatgtgtatcattaatcaaacaccttgattttcgtcactgtagGAATCAGAAGCGAGCATAGACGGAAACCAATGGATAGCTCCAGTCCTAAAGGGTCTGAGAAGATCATCTCCAACTGCACTGAAGATCACCCTGAGATCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- caaacca
- - - - - ccctgta
- - - - - - - - -ccactgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaaa