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 5'  3'   		2  
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 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttgcgaaggttgtttcatagtgtctccttgtatattgccttgcacctaactttttatgacgctcttctctag

Basic information

species Zea mays
transcript GRMZM5G832740_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g49150.1 (Oryza sativa), 5'ss of exon 3
GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttgcgaaggttgtttcatagtgtc-tccttgt-atattgccttgcacctaactttttatgacgctctt-ctctag
|||||||||||||||||| || ||||||||||| || |||||||||||||| ||||||||||||||||||||||| |||||||| ||||| ||||||||||||||||||| ||   || ||| ||  |||| |   |||  |||||| | ||| |||| |||| |||  || | | ||||||
GACTTCTGGAGTAAAAGAGGATCGCATGATGATAACCGGAATGCATACTGTGTCTGATATCTTCTGTGTTGGCTGCGGATCCATTGTTGGATGGAAATATgtaagatttgtga---ttattttatgttgtcatatatgttgtattgcgtagcatctaagtttt-atggtgcccctactctag

upper sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA07G18040.1 (Glycine max), 5'ss of exon 2
GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaaga-----tttgcgaaggt--tgtttcatagt--gtctccttgtatattgccttgcacctaactttttatgacgctcttctctag-------------------------
 |||  ||| |  |||||||| || ||||||||||| ||| |||| |||||   ||| || ||||||||||  ||||| ||||| |||||||||| |||||||||      |||   ||| |  |||||     |   |||  ||   |||      |    |  | ||     |   |  |   ||                          
CACTGTTGGTGAGAAAGAAGAACGGATGATGATCACCGGATTGCACACTGTCGTTGACATATTCTGTGTTGTATGTGGGTCCATTGTTGGGTGGAGATATgtaaggaccagtttctaaagctcatgttttgcgatttatctgtttacttatcaaaacgtcattggcattgggaaatttttgttcttaaaatatttcactttatttcattttag

upper sequence: GRMZM5G832740_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv08s0007g02170.t01 (Vitis vinifera), 5'ss of exon 4
GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg---cgaaggttgtttcatagtgtctccttgtatat-----tgccttgcacctaactttttatgacgctcttctctag--------------
 ||    ||||  || ||||| ||  ||||||| || |||||||| ||||||  ||| || ||||||||||| ||||| ||||| ||||| |||||||||||||||| ||   |  |  || | |   | ||  |   | | ||      |||||   || | |  |  | ||    | |  | | |              
CACAGTCGGAGAGAAGGAAGATCGGTTGATGATGACTGGAATGCACACTGTTGTTGACATATTCTGTGTTGGGTGTGGCTCCATTGTTGGATGGAAATATgtaagatctggttcagaaattctgttgcattgcttgagtttttaactttgtgcctgttacttgatctagtttgggattttaattttgattatcgaaattag

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|211112095|gb|FL402628.1|FL402628
EST:     TTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTT-GGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|30031938|gb|CB833789.1|CB833789
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|149090255|gb|EE179558.2|EE179558
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|18173505|gb|BM348893.1|BM348893
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|14203013|gb|BG836690.1|BG836690
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|29544063|gb|CB604443.1|CB604443
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|32909109|gb|CF013921.1|CF013921
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|116816600|gb|EC859352.1|EC859352
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|211514494|gb|FL430420.1|FL430420
EST:     TTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTTGGAAATAT                         GATGCTGCACATGAGGAAGGG
genomic: TTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGT-GGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAG-AAGGG
EST: gi|60343936|gb|DN210909.1|DN210909
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|29544546|gb|CB604926.1|CB604926
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|30031937|gb|CB833788.1|CB833788
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|211046404|gb|FL436681.1|FL436681
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|5058748|gb|AI737224.1|AI737224
EST:     GATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATNCGGCNCATGAGAAGGGCCAGAGATNCAAGGAAGGCAAGTTTATTCTG
genomic: GATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|50327958|gb|CO523084.1|CO523084
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|149090254|gb|EE179557.2|EE179557
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|16926162|gb|BM079230.1|BM079230
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|211198966|gb|FL379005.1|FL379005
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|18163201|gb|BM333040.1|BM333040
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|5847256|gb|AW000335.1|AW000335
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|78024572|gb|DV492959.1|DV492959
EST:     TCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|33942278|gb|CF348878.1|CF348878
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
EST: gi|211150629|gb|FL420957.1|FL420957
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCTGCACATGAGAAGGGCCAGAGATACAA
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAA
EST: gi|5325164|gb|AI783355.1|AI783355
EST:     TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATAT                         GATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG
genomic: TTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTG

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: 143

GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG


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

GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 182

GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttg ... tcttctctagGATGCGGCACATGAGAAGGGCCAGAGATACAAGGAAGGCAAGTTTATTCTGGAGAG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GACTTCTGGAGTAAAAGAAGACCGCATGATGATCACAGGAATGCATACTGTTTCTGATATCTTCTGTGTTGGCTGTGGATCCATAGTTGGGTGGAAATATgtaagatttgcgaaggttgtttcatagtgtctccttgtatattgccttgcacctaactttttatgacgctcttctctag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA