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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acggatactattttggaacggagggagtatatatttgtctaccgggacatgcagttgattcaagtgatcaagtctatcatgcttgcctcctttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAGAGCTTTGGAGAGAAA

Basic information

species Zea mays
transcript GRMZM2G039683_T02
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G039683_T01 (Zea mays), 3'ss of exon 12
lower sequence: LOC_Os02g54020.1 (Oryza sativa), 3'ss of exon 14
acggatactattttggaacggagggagtatatatttgtctaccgggacatgcagttgattcaagtgatcaagtctatcatgcttgcctcctttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAGAGCTTTGGAGAGAAA
   | | |  | |||  ||  |    | |   ||| ||||||     |||||||| ||||  |         | | |  | ||||| ||  ||||||||||| ||||| ||||| |||| ||||| |||||| || |||| |||||||||||||||||| ||||| 
gttggtgcactcttgctacctaacatgga---attggtctactatatcatgcagtagatttcat------gtttttttttacttgcatctcttgatgcagATAATTGATTACTGCGAAAATTCTACCTGCCGACGAAAAATGATCATTGAGAGCTTTGGGGAGAAG
















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|60399085|gb|DN231899.1|DN231899
EST:     CTTCCTCTTCAAATGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAG                         ATTATTGACTACTGTGAAATT
genomic: CTTCCTCTTCAAATGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAGgttcttactg ... tttgatgcagATTATTGACTACTGTGAAATT
EST: gi|60350164|gb|DN217137.1|DN217137
EST:     TTCCTCTTTCAA-TGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAG                         ATTATTGACTACT
genomic: TTCCTCTT-CAAATGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAGgttcttactg ... tttgatgcagATTATTGACTACT
EST: gi|89761057|gb|DY689223.1|DY689223
EST:     CTTCCTCTTCAAATGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAG                         ATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAG
genomic: CTTCCTCTTCAAATGAGCTTTCTGAGAAGGCTCTAGCTGACTTCAGTCAGgttcttactg ... tttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAG
EST: gi|91878619|gb|EB408576.1|EB408576
EST:     CTCTAGCTGACTTCAGTCAG                         ATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAG
genomic: CTCTAGCTGACTTCAGTCAGgttcttactg ... tttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacatgcagttgattcaagtgatcaagtctatcatgcttgcctcctttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAGAGCTTTGGAGAGAAA
                                            ctttgat  putative branch site (score: 5)
                                  tgcttgcctccttt  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acggatactattttggaacggagggagtatatatttgtctaccgggacatgcagttgattcaagtgatcaagtctatcatgcttgcctcctttgatgcagATTATTGACTACTGTGAAATTTCTAGCTGCCGGCGGAAAAAGATCATTGAGAGCTTTGGAGAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA