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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttacatcataaataaacaatcttggtagattttaattttcacgtctccaagttttaaatcattatttatcataacatctttgctcttttctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA

Basic information

species Zea mays
transcript GRMZM2G090087_T03
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G090087_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g45960.1 (Oryza sativa), 3'ss of exon 4
gttacatcataaataaacaatcttggtagattttaattttcacgtctccaagttttaaatcattatttatcataacatctttgctcttttctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA
     |  |||  |||||       ||| |  |  |   | ||     ||   || | | || |  | ||    |    ||  |    |||  ||     || |||| |||||||| ||||||||||||||||||||||| ||||||||  | ||||| || |||||||  
----tactatatttaaacttgtactgtataact-gacactgacagtggcag--ttaacaacaatgctcatgt--atgctttgacgaacttcggtat----ctttaatatgcagGTATCTCATGTATGGAGATATATCTGCCAAAGCTGCAAACATGCTTGGTCAACCTGTG
















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|67040057|gb|CO466312.1|CO466312
EST:     GCGAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         CTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|148958687|gb|EC904955.2|EC904955
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         -------GT--A----CCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|94472231|gb|EB701189.1|EB701189
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         -------GT--A----CCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|60399068|gb|DN231882.1|DN231882
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCC----AG                         -----A---G-AGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|60346857|gb|DN213830.1|DN213830
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         -------GT--A----CCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|28576035|gb|CB281927.1|CB281927
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         CTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|149071327|gb|EE159720.2|EE159720
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         -------GT--A----CCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
EST: gi|60339011|gb|DN205984.1|DN205984
EST:     TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAG                         -------GT--A----CCTCATGTATGGAGATATATCTGCAAAAGCTGCGC
genomic: TCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGC

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), 49 (downstream exon)
Score: 444

CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 235

CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 165

CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 239

CCATTCGTGGAGAGTTTATCTAAATGCCCAAAGCATGGACTTCACAACCCACTTAAAGCTCCAGAGAGgtgtgtttga ... ctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctccaagttttaaatcattatttatcataacatctttgctcttttctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA
                        tcataac  putative branch site (score: 239)
                              catctttgctcttttc  CT-rich tract
       ttttaaatcattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttacatcataaataaacaatcttggtagattttaattttcacgtctccaagttttaaatcattatttatcataacatctttgctcttttctttaaaaagCTCTAATGTGCAGGTACCTCATGTATGGAGATATATCTGCAAAAGCTGCGCATATGCTGGGCCAACCTGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - aaataaa