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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgtttatgcttgtgatttagtctagatagcaatttagtcctctttttacttagcaaatctagttctgagtgagcactaatgtttggaacactaactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG

Basic information

species Zea mays
transcript GRMZM2G063851_T05
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 18
----gtatgtttatgcttgtgatttagtctag----atagc-aatttagtcctctttttact------tagcaaatctagttct-gagtgagcactaatgtttggaacactaactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG
    || | | | |  | || |   | ||||     ||  | |||||| || |    |||        |||||||||||  | | ||  ||| ||| | |       | ||||||| ||||||||||||||||  | ||||| |||||||| ||||| || ||||||||||||
gtatgtttatctgtattggttaaacaatctaatgccatgtctaatttaatcttgaacttatgatagagtagcaaatctaactttagaacgagtacttaagaaaacttctctaactgcgcagGTATTACACTGTTCTTTTCGGAGTTTCAAGGAGCATTGGAATAGGATCTCAG
















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|33100125|gb|CF060085.1|CF060085
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|40335071|gb|CK369141.1|CK369141
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|84908305|gb|DW404183.1|DW404183
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|111433800|gb|EE298053.1|EE298053
EST:     GTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGGGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|89248619|gb|DY620405.1|DY620405
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|148929642|gb|EC876096.2|EC876096
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|76010584|gb|DT937754.1|DT937754
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|31363851|gb|CD448206.1|CD448206
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|149100798|gb|EE186892.2|EE186892
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATTTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|6973552|gb|AW438288.1|AW438288
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCTATGGGGATAGGATCTC
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGC-ATGGGGATAGGATCTC
EST: gi|110202089|gb|EC883986.1|EC883986
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|71771088|gb|DR969025.1|DR969025
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|78021514|gb|DV489901.1|DV489901
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|37380261|gb|CF626924.1|CF626924
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|5901109|gb|AW042209.1|AW042209
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|241994796|gb|GR421149.1|GR421149
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGCGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|110954440|gb|EE174492.1|EE174492
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATTTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATTTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|148991805|gb|EE033386.2|EE033386
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|93284645|gb|EB676909.1|EB676909
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|37376636|gb|CF624868.1|CF624868
EST:     GATGCTCACAGTGGAGTTTTGTTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|149082973|gb|EE172210.2|EE172210
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
EST: gi|60395299|gb|DN228168.1|DN228168
EST:     GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACG                         GTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA
genomic: GATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCA

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), 48 (downstream exon)
Score: 82

GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 541

GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 614

GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 303

GTCAAGAACCCATGGCCAAATGTTGATGCTCACAGTGGAGTTTTGCTGAACCACTTTGGACTATCTGAAGCACGgtatgtttat ... aactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acttagcaaatctagttctgagtgagcactaatgtttggaacactaactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG
                                         cactaac  putative branch site (score: 303)
                             taatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgtttatgcttgtgatttagtctagatagcaatttagtcctctttttacttagcaaatctagttctgagtgagcactaatgtttggaacactaactgtgcagGTATTACACTGTCTTGTTCGGTGTTTCAAGAAGCATGGGGATAGGATCTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC