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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgtcaagcaatgtgctttagtgcttgcaagtttcaagggtctgcttcgttacgtatgagatacaggaacttcaacttgtgtttcttttcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT

Basic information

species Zea mays
transcript GRMZM2G014066_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014066_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g48190.1 (Oryza sativa), 3'ss of exon 4
tgctgtcaagcaatgtgctttagtgcttgcaagtttcaa----gggtctgcttcgttacgtatgagatacaggaacttcaacttgtgtttcttttcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT
|   ||| |   |||||||     | | | | |||||||    |   ||  |    | | || ||||||    ||  | || |  | | | ||||| ||||||| || || ||||| ||||| || ||||||||||| |||||||||||||| ||||| | |||||||||||||||||||||||| |||||||||||| |||||
tcaggtctatatatgtgctca---gttagtatgtttcaaaccagcagcttataaactccttaagagatatgcaaatatgaaat-atttattttttccatggcagGATCGACTCATCGCTCACGAGTGAGGAAAGGGAACAAAAGCGGAAACAAGCCACTGACAGAGCAACCTTTGTGCAAGGCCTGGTGCTCTCCACTTTATTT
















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|60351166|gb|DN218139.1|DN218139
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|71305273|gb|DR788770.1|DR788770
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|93283598|gb|EB675862.1|EB675862
EST:     CCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: CCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|78074874|gb|DV503308.1|DV503308
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|32809740|gb|CD961974.1|CD961974
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|32827729|gb|CD967407.1|CD967407
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAGGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|211484732|gb|FL156866.1|FL156866
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
EST: gi|211538730|gb|FL481471.1|FL481471
EST:     GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAG                         TATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC
genomic: GATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGC

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: 45 (upstream exon), 46 (downstream exon)
Score: 71

TCTCACCATCAGATGCACCAGAACCATCAAAATCGGCGTCTTCTATTCCAGATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT


Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 101

TCTCACCATCAGATGCACCAGAACCATCAAAATCGGCGTCTTCTATTCCAGATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 105

TCTCACCATCAGATGCACCAGAACCATCAAAATCGGCGTCTTCTATTCCAGATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 59

TCTCACCATCAGATGCACCAGAACCATCAAAATCGGCGTCTTCTATTCCAGATGGCGCCTCAATACGTAAGGAGACACCGGTTCAGCCTTGGGAGTCGAGgtatatataa ... tcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcttcgttacgtatgagatacaggaacttcaacttgtgtttcttttcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT
                                cttgtgtttcttttc  CT-rich tract
                                      tttctttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgtcaagcaatgtgctttagtgcttgcaagtttcaagggtctgcttcgttacgtatgagatacaggaacttcaacttgtgtttcttttcgatggcagTATTGATTCATCTCTCACAAGCGAGGAAAGGGAGCAAAAGCGGAAACAGGCCACCGGCAGAGCAACCTTTGTGCAAGGCCTAGTGCTCTCCACTCTATTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
tgctgtc
- - - - - - -tgtgctt
- - - - - - - - - - - -tgcttgc
- - - - - - - - - - - - - - - - - - - - - -ctgcttc