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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttagataccagtatcaaaccgggtccgcattcaacattcgcttcacattgtctatactaaagcacaccaatgttctgcttaagttccaatttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC

Basic information

species Zea mays
transcript GRMZM2G157384_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G157384_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os08g43320.1 (Oryza sativa), 3'ss of exon 1
ttagataccagtat-caaaccgggtccgcattcaacattcgcttcacattgtctatactaaagcacaccaatgttctgcttaagttccaattt---ttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC
    ||||   | |  ||  ||  |  ||| |  |  ||   || | | |||  | |  || |        |  |      |||||      |   |||  ||| ||||||||||||||||| ||  ||||||| || || |||||| |||||||||  ||||| |||||||||||||||||||| |||||||||||| | |||
---catactgttctgtaatacgcctgtgcagtttat-ttattttgatagtgttaagaacaaggggggttcttagtgctaacaagttgtttgctccattggccagTTTGGAGAAGATGGGAGCACTAGACTGGGCGAAGGTTGTTCATCAGCACCAAGCATGGCGTCTCATTAGCTGTATCTGGCTACATGCTGGCCTAATCCAC
















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|86468307|gb|DY234677.1|DY234677
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCCC                         CTTGGAAAAGATGGGAGCTCTCATCTGGGCCAAAGTATTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|148933642|gb|EC877531.2|EC877531
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211216399|gb|FL012231.1|FL012231
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAACATGGGAGCTCTCAACTGGGCCAAAGTAGT
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGT
EST: gi|74241938|gb|DT649852.1|DT649852
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|149080701|gb|EE169761.2|EE169761
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|76289252|gb|DV028820.1|DV028820
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|71446277|gb|DR827327.1|DR827327
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213833|gb|FL012222.1|FL012222
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|78088539|gb|DV516932.1|DV516932
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213838|gb|FL012227.1|FL012227
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213830|gb|FL012219.1|FL012219
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAACATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|149055187|gb|EE156106.2|EE156106
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211216397|gb|FL012229.1|FL012229
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211216398|gb|FL012230.1|FL012230
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAACATGGGAAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACC
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGA-GCTCTCAACTGGGCCAAAGTAGTTCATGAGCACC
EST: gi|148941581|gb|EC886518.2|EC886518
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|71448535|gb|DR829585.1|DR829585
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213837|gb|FL012226.1|FL012226
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAASA-GGGAGCTCTCAACTGGGCCAAAGTAGTTCATGA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGA
EST: gi|74236232|gb|DT644146.1|DT644146
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213839|gb|FL012228.1|FL012228
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213835|gb|FL012224.1|FL012224
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|71447543|gb|DR828593.1|DR828593
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
EST: gi|211213836|gb|FL012225.1|FL012225
EST:     TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCAC                         CTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA
genomic: TCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCA

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: 48 (upstream exon), 46 (downstream exon)
Score: 46

CGCTCGGCGGCGGCGCCGGGTGCGTGGCGGCCGGTCTCCTCCGCCGGTTCTCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 72

CGCTCGGCGGCGGCGCCGGGTGCGTGGCGGCCGGTCTCCTCCGCCGGTTCTCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 55

CGCTCGGCGGCGGCGCCGGGTGCGTGGCGGCCGGTCTCCTCCGCCGGTTCTCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 54

CGCTCGGCGGCGGCGCCGGGTGCGTGGCGGCCGGTCTCCTCCGCCGGTTCTCCTTCCAGCCGCTCCGCGAGAACCCGCTCTTCGGGCCTTCCTCCGCCACgtacgcctcg ... ttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgtctatactaaagcacaccaatgttctgcttaagttccaatttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC
         tactaaa  putative branch site (score: 54)
                                            tttttgt  putative PPT
       tatactaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttagataccagtatcaaaccgggtccgcattcaacattcgcttcacattgtctatactaaagcacaccaatgttctgcttaagttccaatttttgtgcagCTTGGAGAAGATGGGAGCTCTCAACTGGGCCAAAGTAGTTCATGAGCACCAAGGGTGGCGCCTCATTAGCTGTATCTGGCTCCATGCTGGCCTAGTTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - gcattca
- - - - - - - - - - - - - - - - - - - -gcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacacca