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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tccaattgcctcgttttgtcccagatgttttttttgttgaaattagaagggtgtataatgcactcatttaatgtgcgttatgttgactttaattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG

Basic information

species Zea mays
transcript GRMZM2G017305_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g49000.1 (Oryza sativa), 3'ss of exon 5
tccaattgcctcgttttgtcccaga-----tgttttttttgttgaaattagaagggtgtataatgcactcatttaatgtgcg--ttatgttgactttaattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG
       ||   ||||||   ||||        |||| || ||    |||       | |   ||  |  ||  ||  |     |  |     ||| | |  | ||| |||||||||||||||||||||||||||||||||||| |||||||||| ||||||||||| ||||| ||||| |||| ||| ||| ||
-------gctatgttttgggacagaggaagcacttttgttcttacttttaatcttccgaacggtgtccgtatacaacctctaactcttacattcttgattcactcagACGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAAATTTTGAAAGCAGAAAGGCACTCATCAATATTAACCTTAAAACTGTTGAG

upper sequence: GRMZM2G017305_T02 (Zea mays), 3'ss of exon 2
lower sequence: AT1G80350.1 (Arabidopsis thaliana), 3'ss of exon 5
tccaattgcctcgttttgtcccagatgttttttttgttgaaattagaagggtgtataatgcactcatttaatgtgcgttatgttgactttaattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG
       |  |   | |        |   |    | || | | | |       ||||||| | |   | | | ||      | | || ||  |    |||| ||||| |||| || ||||| ||||| ||||||||||||||||||||| | ||||| |||||||| || ||||| ||||||||| ||
-------gtttaaatattctttgagttaatgccgtctttagacttgctcta-atataatgaaattgctgattctgga----gctcacgttggtg---cagGAGGAGGTTGGAAAAACGTATATATATCCCACTTCCAGATTTTGAAAGTCGTAAGGCTCTTATCAATATCAATCTGAGAACAGTTGAG
















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|13178314|gb|BG349572.1|BG349572
EST:     GGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: GGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|28985682|gb|CB350761.1|CB350761
EST:     ATGGGATATTGATGAGGCACTGAG                         NCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|211478494|gb|FL368092.1|FL368092
EST:     CCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: CCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|67021540|gb|CO450289.1|CO450289
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|18174356|gb|BM349744.1|BM349744
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|5055466|gb|AI734353.1|AI734353
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGAAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|67015406|gb|CO444155.1|CO444155
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|28984876|gb|BQ539249.2|BQ539249
EST:     TGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: TGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|24767871|gb|CA403006.1|CA403006
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAAGCACTGAG                         GCGGAGGCTCGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|211038213|gb|FL329861.1|FL329861
EST:     CCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: CCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|78024488|gb|DV492875.1|DV492875
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|31360569|gb|CD444926.1|CD444926
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAAGCACTGAG                         GCGGAGGCTCGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|213192745|gb|FM193924.1|FM193924
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|17929404|gb|BM266364.1|BM266364
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|61119244|gb|DN560205.1|DN560205
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCGCTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|60344133|gb|DN211106.1|DN211106
EST:     ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
genomic: ATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAG
EST: gi|20301545|gb|BQ164488.1|BQ164488
EST:     TGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGATG                         GCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTA
genomic: TGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGA-Ggttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTA

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: 124

ATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCAAAAATTGTTATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 62

ATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCAAAAATTGTTATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 91

ATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCAAAAATTGTTATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 93

ATGGTGTAAACAATAGCTCCACCACTGATGATGGCCAGCCAAAAATTGTTATGGTTCTGGCTGCTACAAATTTTCCATGGGATATTGATGAGGCACTGAGgttggcaaac ... aattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaagggtgtataatgcactcatttaatgtgcgttatgttgactttaattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG
                  tcatttaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tccaattgcctcgttttgtcccagatgttttttttgttgaaattagaagggtgtataatgcactcatttaatgtgcgttatgttgactttaattgcccagGCGGAGGCTGGAGAAGCGTATTTATATTCCACTTCCAGATTTTGAAAGTAGAAAGGCACTTATCAACATTAATCTTAGAACAGTTCAG

- - - tgcctcg
- - - - - - - - - - - - -tgttttt
- - - - - - - - - - - - - - - - tttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -taatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atgttga