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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagttgtagctggtagaaaatataaaataatgtgatcactgagtcgagcctctattttgtgcgtggctgcttatctcccaaatattccctatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG

Basic information

species Zea mays
transcript GRMZM2G174730_T02
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G174730_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 3'ss of exon 1
------ctagttgtagctggtagaaaatataaaataatgtgatcactgagtcgagcctctattttgtgcgtggctgcttatctcccaaatattccctatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG
      |  |||||| ||||| | | | | |   ||   || |||     |    |  ||| ||||||  |   |  ||  ||  ||| |  ||| ||| |||||||||||||||||||| ||||||| ||||||||| ||| ||||||| || ||||| || |||||||| |||||||||||||||||||| ||||| || |||
aaaaatcgtgttgtaactggttgcacaca-agcctataatgttcatgttatttt-ctactactttgtgatt---tatttgccttgcaattcctcc-tatattgcagGGAGGAAGTGTTCCTCCTGCCAACAATTCTCGACTCCCACCTCTCTCCCATGAGCCAGCTGATTTTTACAATGTGGACATTCCTCTTGACTCGTCTAAG
















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|211137750|gb|FL292365.1|FL292365
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|91876331|gb|EB406288.1|EB406288
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|149015443|gb|EE045301.2|EE045301
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211341624|gb|FL411903.1|FL411903
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA
EST: gi|211137751|gb|FL292366.1|FL292366
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138689|gb|FL292372.1|FL292372
EST:     GGAAGCACGTGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138692|gb|FL292375.1|FL292375
EST:     GAAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: G-AAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138694|gb|FL292377.1|FL292377
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
EST: gi|211138693|gb|FL292376.1|FL292376
EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 357

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 256

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 409

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgagcctctattttgtgcgtggctgcttatctcccaaatattccctatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG
                                        ttccctatctt  CT-rich tract
                                   aaatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagttgtagctggtagaaaatataaaataatgtgatcactgagtcgagcctctattttgtgcgtggctgcttatctcccaaatattccctatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - gtagctg
- - - - - - -gtagaaaa
- - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtgcgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gctgctt