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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaattttcttgtttctgtgtgaaacttatttttatcttcatactattgatggacctcaggatgattctgaatccaactgtttgattcatgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT

Basic information

species Zea mays
transcript GRMZM2G028346_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G028346_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g59600.1 (Oryza sativa), 3'ss of exon 8
-ggaaattttcttgtttctgtgtgaaacttatttttatcttcatactattgatggacctcaggatgattctgaatccaactgtttgattcatgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT
  |  | | |   |  ||       | ||| |  ||   ||   || ||   ||| | |||| ||  |||||| ||||||| ||  | |  |||||| |||||| ||||| |||||||| ||||| |||||||||||||| ||||||||||| || |||||||||||
tagctactgttgagcatccaacattagcttttgcttcgatttgcaccatct-tggtcatcagaatagttctgattccaacttttcaaatgctgtctttcagTGAAATAGAGAAGTTGAAGCTTTCCGAGCTTACCTGCCGGGAAGGCATTGTGGAGGTTGCAAAGAT
















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|211317863|gb|FK969337.1|FK969337
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317862|gb|FK969336.1|FK969336
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGGGGAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317857|gb|FK969331.1|FK969331
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317861|gb|FK969335.1|FK969335
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211404206|gb|FL443972.1|FL443972
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317859|gb|FK969333.1|FK969333
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211079760|gb|FK950720.1|FK950720
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAARTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|32933640|gb|CF038452.1|CF038452
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCAGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211169213|gb|FL479845.1|FL479845
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGWAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317856|gb|FK969330.1|FK969330
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317864|gb|FK969338.1|FK969338
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317854|gb|FK969328.1|FK969328
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317865|gb|FK969339.1|FK969339
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|12969059|gb|BG266004.1|BG266004
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCAGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317860|gb|FK969334.1|FK969334
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
EST: gi|211317855|gb|FK969329.1|FK969329
EST:     AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGAC                         TGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT
genomic: AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGT

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: 171

AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 149

AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 162

AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 163

AAATACTTTGGTGCTGCATTGGGGAAGGGAAGGCAGGCCGCAAAGACgtaagcttac ... tgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattgatggacctcaggatgattctgaatccaactgtttgattcatgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT
                                    tttgatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaattttcttgtttctgtgtgaaacttatttttatcttcatactattgatggacctcaggatgattctgaatccaactgtttgattcatgtcttgcagTGAGATAGAAAAGTTGAAACTTTCGGAGCTTACCTGCCGAGAAGGCATTGTTGAAGTTGCAAAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - -tgtttct
- - - - - - - - - - - - - - - - - - - - - - - attgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgaatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattca