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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaagtgcataatcctttgatgccattttgaacattataattgggcttctaagttttaataaacaatttggcttatctgaaaagttaaaactttagtctgtactatatagctccttcctatattttcatgaatatgacataatgtttaatgtgccttcttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA

Basic information

species Zea mays
transcript GRMZM2G044237_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G044237_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g17120.2 (Oryza sativa), 3'ss of exon 12
------------------------gttaagtgcataatcctttgatgccattttgaacattataattgggcttctaagttttaataaacaatttggcttatctgaaaagt-taaaactttagtctgtactatat--agctccttcctatattttcatgaatatgacataa-tgtttaatgtgcct-tcttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA----------------------
                         ||     ||| | | |   ||||    ||     |||  ||   |  |  | ||||  ||| |||| |||  |||||||  || |     | |  | | |  |  ||||  |  | | |    || |||| |   | ||||| ||   | ||| |||||  |   || || |||||||||||  ||| ||||| || ||||| ||||| |||||||||||||||||||| |||||||| ||  ||||||||                      
gttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgttt-gatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAAGTATGATACTGTTTAGCAGCAA

upper sequence: GRMZM2G044237_T02 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os03g17120.1 (Oryza sativa), 3'ss of exon 12
------------------------gttaagtgcataatcctttgatgccattttgaacattataattgggcttctaagttttaataaacaatttggcttatctgaaaagt-taaaactttagtctgtactatat--agctccttcctatattttcatgaatatgacataa-tgtttaatgtgcct-tcttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA
                         ||     ||| | | |   ||||    ||     |||  ||   |  |  | ||||  ||| |||| |||  |||||||  || |     | |  | | |  |  ||||  |  | | |    || |||| |   | ||||| ||   | ||| |||||  |   || || |||||||||||  ||| ||||| || ||||| ||||| |||||||||||||||||||| |||||||| ||  ||||||||
gttaagcgcttagcatttcattcacttcgcaccatcagcatagtatgctgcattttcttttagcatgatgacttgacgttt-gatatacaaattgagttatctggcaactgctgcattcaattattcatcatatcaaatttcctttcttaatttcttcggtgtgacacaagcttctaaagtgcccattccctttgtagGTTACTGTAGCTGGTGCCAATAATGAGGCTGAAGCAGCTAAAATTGCTCGTTCAGTGGCATCTTCCTCCCTGGTTAAA
















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|32934567|gb|CF039379.1|CF039379
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|32835096|gb|CD974774.1|CD974774
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|20802518|gb|BQ293568.1|BQ293568
EST:     GCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: GCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|32928445|gb|CF033257.1|CF033257
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|60348874|gb|DN215847.1|DN215847
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|78543892|gb|DV621390.1|DV621390
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|32833027|gb|CD972705.1|CD972705
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
EST: gi|76917242|gb|DV166726.1|DV166726
EST:     TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAG                         GTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT
genomic: TTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGT

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: 226

GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 273

GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 128

GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 152

GTAATGCAAAGTCTTGCAAAATCCATAGCATGGGATGGTGAGGGTGCAACATGCCTAATTGAGgttaagtgca ... ttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttcctatattttcatgaatatgacataatgtttaatgtgccttcttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA
                              gtttaat  putative branch site (score: 152)
                                      tgccttcttct  CT-rich tract
     tatattttcatgaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaagtgcataatcctttgatgccattttgaacattataattgggcttctaagttttaataaacaatttggcttatctgaaaagttaaaactttagtctgtactatatagctccttcctatattttcatgaatatgacataatgtttaatgtgccttcttctgtgcagGTTACTGTAAGTGGCGCCAACAACGAGGCAGAAGCTGCTAAAATTGCTCGTTCAGTAGCATCTTCTTCTTTGGTTAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT