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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggattttgatggtagctcaaaactttgttagcttgactgtctcatgcagcgttttccttttcgaagaaacaaaatgaattttggtgcacgtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT

Basic information

species Zea mays
transcript GRMZM2G011456_T02
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G011456_T03 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g04660.1 (Oryza sativa), 3'ss of exon 2
--aggattttgatggtagctcaaaactttgttagcttgactgtctcatgcagcgttttccttttcgaagaaacaaaat--gaattttggtgcacgtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT
  | |||||   |  | |        ||||  |||| ||||| | |||   || || |      |   |    ||     ||| ||   ||||  | | | ||||| || ||| ||||| | |||| |||||||| ||| | ||| ||||| |||||||||||||| ||||||||||||||||||||| || | 
ataagatttccttacttggcgtg---tttgggagctagactgacccatat-gcattcttgaaaacatggtctgaatcctagaaattgcatgcattttctttcagGCGTGCGTTCTTCCTCCTCCCAAGAGATCTTCTTGTGCCAACTATGCTAGAGTTGTGAATCATATTTTGCAAGGCCTGACCAATTTGCAG
















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|211230907|gb|FL222476.1|FL222476
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTCTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211230912|gb|FL222481.1|FL222481
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|71311078|gb|DR791853.1|DR791853
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|71300983|gb|DR786520.1|DR786520
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|89762829|gb|DY690269.1|DY690269
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|33468108|gb|CF245157.1|CF245157
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAG
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAG
EST: gi|91876145|gb|EB406102.1|EB406102
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|74233408|gb|DT641322.1|DT641322
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211230918|gb|FL222487.1|FL222487
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211230908|gb|FL222477.1|FL222477
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|149109143|gb|EE190035.2|EE190035
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211228853|gb|FL222474.1|FL222474
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTCTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|89251153|gb|DY622939.1|DY622939
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211230914|gb|FL222483.1|FL222483
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTCTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAGTTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|71434207|gb|DR815257.1|DR815257
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|78117239|gb|DV535626.1|DV535626
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
EST: gi|211230917|gb|FL222486.1|FL222486
EST:     AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAG                         GCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA
genomic: AGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGA

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: 48 (upstream exon), 48 (downstream exon)
Score: 128

CGAGTGGATTGATTTGGACGCGGAGGACGAGCGGCTCCGGCTGGACTCCGAGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT


Block sizes: 47 (upstream exon), 43 (downstream exon)
Score: 76

CGAGTGGATTGATTTGGACGCGGAGGACGAGCGGCTCCGGCTGGACTCCGAGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 120

CGAGTGGATTGATTTGGACGCGGAGGACGAGCGGCTCCGGCTGGACTCCGAGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT


Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 77

CGAGTGGATTGATTTGGACGCGGAGGACGAGCGGCTCCGGCTGGACTCCGAGCTCACGCTGAAGCAGGAGATCGCTTGGGCATCTCACGTTTCGCTGCAGgtccagttgt ... gtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcagcgttttccttttcgaagaaacaaaatgaattttggtgcacgtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT
                      aaacaaaatgaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggattttgatggtagctcaaaactttgttagcttgactgtctcatgcagcgttttccttttcgaagaaacaaaatgaattttggtgcacgtccatgcagGCATGTGTTATTCCTGCCCCCAGGAGATCTTTTTGCGGCAATTATGCCAGAGTTGTGAATCAAATTTTGCAAGGCCTGACCAATATGAAT

- - -tttgatg
- - - - - - - - - - - - - - - - - - - - - tcatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgcac