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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtagctattctttgatctgtgtgactagactgaagtatgcataaattgtgaggttaaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG

Basic information

species Zea mays
transcript GRMZM2G132804_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 2
-cagtagctattctttgatctgtgtgactagactgaagtatgcataaattgtgaggt-taaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG
    ||  |  | ||||   | ||| || | ||  || ||   ||      | | || ||      |  |  |||  | ||      | ||||||  | ||||| |||||||||||||||| ||||||||||||||||| || |||||||||||  |||||||||||||||| ||||||||
tgcataaattgtgtttgtcttttgttaccacac--aattacaaatgctacttcatgtatatgctgctttatgatatgacattgctcaaatatcttattacagGTATGGTTGAGACAGACCCTGAGGGTGCACTTGCTGGCTTCGATCAAGTAGTACGTATGGAGCCTGAAAAGGCTGAATG

upper sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 2
cagtagctattctttgatctgtgtgac-tagactgaagtatgcataaattgtgaggtt-aaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG
 | |   ||   |    |   ||     | |||| | | ||   |   |||  |  || ||| ||||              |||  |  |   ||    |||||||||||||||| || ||||| |||||||||||||| |||| | |||||||  | ||||| || || || || || ||
-aatttgtaaattccagttattgccttgtggacttatggatttttgttttgcaaatttcaaatgaatggttttcctctggagctcat-ttcctttgtcacagGTTTGGTTGAGACTGATCCAGAAGGTGCACTTGCTGGCTTTGCTGAAGTAGTTCGCATGGAACCAGAGAAGGCAGAGTG
















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|32933387|gb|CF038199.1|CF038199
EST:     GCCGGAGGAGTAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|31664621|gb|CD573554.1|CD573554
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|29946668|gb|CB816265.1|CB816265
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|211131141|gb|FL290028.1|FL290028
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|9731371|gb|BE510123.1|BE510123
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|29946544|gb|CB816202.1|CB816202
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|9461676|gb|BE453849.1|BE453849
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
EST: gi|211131142|gb|FL290029.1|FL290029
EST:     GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAG                         GTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG
genomic: GCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAG

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: 246

ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 164

ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 118

ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 191

ATGCGGATATGGAGGACTACGGGTTCGAGTACTCAGACGAGGAGCCGGAGGAGCAGGATGTCGATATCGAGAACCAGTATTACAACTCTAAAGgttcggtctt ... ctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattgtgaggttaaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG
                                         ctatctttct  CT-rich tract
                 aatacaaaatagtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtagctattctttgatctgtgtgactagactgaagtatgcataaattgtgaggttaaaggaatacaaaatagtaaatgctattactatctttctgcagGTTTGGTTGAGACAGACCCAGAGGGTGCACTTGCTGGTTTTGATCAAGTAGTCAGTATGGAGCCTGAAAAAGCTGAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA