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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctgggtgctcttcagcttattttgggttcataagtatgcattatctcagtttgttcttatgtattcacatccatgaggaatgttattctgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG

Basic information

species Zea mays
transcript GRMZM2G387076_T02
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g64650.1 (Oryza sativa), 3'ss of exon 5
ttctgggtgctcttcagctta---ttttgggttcataagtatg--cattatctcagtttgttcttatgtattcacatccatgaggaatgttattctgt-ctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGG-CTCTTCACTCATGGTTGCAAG--------
    ||   || || | ||||   |||| | ||  ||||| |   | | ||  | ||||||    | | |||    |  | |   | |||| |||| | ||| |||||||||||||||||||||||||| |||||||||||||| || ||||| | || ||||| || | |  || |       |         
----ggaccctttttaacttacattttttgtttgttaagttttatcttgattaccgtttgtctcca-gaattt-tgttgagggatattgtttttcttttcttccagATGTTCTACAAGCAGGCAAAGAAAACAAACCAATGCTGTACTATACTCTGAAGTTTGGACTTTCCTGTCCTTAAGATGAAGACTCCAG

upper sequence: GRMZM2G387076_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os01g64650.2 (Oryza sativa), 3'ss of exon 5
ttctgggtgctcttcagctta---ttttgggttcataagtat--gcattatctcagtttgttcttatgtattcacatccatgaggaatgttattctgt-ctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGG-CTCTTCACTCATGGTTGCAAG--------------------
    ||   || || | ||||   |||| | ||  ||||| |   | | ||  | ||||||    | | |||    |  | |   | |||| |||| | ||| |||||||||||||||||||||||||| |||||||||||||| || ||||| | || ||||| || | |  || |       |                     
----ggaccctttttaacttacattttttgtttgttaagttttatcttgattaccgtttgtctcca-gaattt-tgttgagggatattgtttttcttttcttccagATGTTCTACAAGCAGGCAAAGAAAACAAACCAATGCTGTACTATACTCTGAAGTTTGGACTTTCCTGTCCTTAAGATGAAGACTCCAGGTTAATTTTGCT
















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|74235349|gb|DT643263.1|DT643263
EST:     GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG                         ATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
genomic: GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
EST: gi|211460687|gb|FL127589.1|FL127589
EST:     GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG                         ATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
genomic: GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
EST: gi|60354098|gb|DN221071.1|DN221071
EST:     GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG                         ATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
genomic: GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
EST: gi|149057998|gb|EE156679.2|EE156679
EST:     GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG                         ATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
genomic: GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
EST: gi|44681914|gb|CK786962.1|CK786962
EST:     GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAG                         ATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA
genomic: GATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAA

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: 85

CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 129

CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 150

CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG


Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 61

CATAAAACTATTGAGAGTGTCCTTGCCAGAGGAGAGAGATTGGATAGCTTGGTTGAGAAAAGCTCTGATCTGAGTGCTGCTTCTCAGgtaaccctat ... tgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcagtttgttcttatgtattcacatccatgaggaatgttattctgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG
                                       ttattctgtctttc  CT-rich tract
             ttatgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctgggtgctcttcagcttattttgggttcataagtatgcattatctcagtttgttcttatgtattcacatccatgaggaatgttattctgtctttcagATGTTCTACAAGCAGGCAAAGAAGACAAACCAATGCTGCACAATACTGTAAATTTTGGCTCTTCACTCATGGTTGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - gggtgct
- - - - - -cttcagc
- - - - - - - - - - - - - - - - - -gtatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atccatg