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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttccaggtagaagttatgtactttagtgattgaggtatatgttggtctttattttgagtctgctttgtgatatttctttttatactatgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCAGTACCTCTGCTTAGGCACCAG

Basic information

species Oryza sativa
transcript LOC_Os08g08220.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g08220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G449355_T01 (Zea mays), 3'ss of exon 3
---attttccaggtagaagttatgtactttagtg-attgaggtatatgttggtctttattttgagtctgctttgtgatatttctttttatactatgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCAGTACCTCTGCTTAGGCACCAG
   |   |     |||  ||| | |  | || |  ||||     |  ||  ||| | ||| ||   |   |   |   ||| ||||| | | |||||||| ||||||||||  |  || ||||| ||||||||||||||||||||||| ||  |||||||||||||||| || |||
ggtaaactttgtttagctgttgtttgttatatttcattgtaccctgagt--gtcatcattctgctcca--tgaatatcattgcttttcaaaatatgttatgcagAATATTAGTCGCGAAAAAAGTGAAGATGATCTGCCTGAGGGTGTGCTAGCAGTACCTCTGCTTAGACATCAG
















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|58667760|gb|CK056446.1|CK056446
EST:     CCAGGAAGCACTACAG                         ACATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTC
genomic: CCAGGAAGCACTACAGgcatgtgttc ... tgttatacagA-ATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTC
EST: gi|29619028|gb|CB624040.1|CB624040
EST:     ATAGGATTATAGATTCTGACGAGAGAGCGGTGTACCAGGAAGCACTACAG                         AATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCA
genomic: ATAGGATTATAGATTCTGACGAGAGAGCGGTGTACCAGGAAGCACTACAGgcatgtgttc ... tgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCA
EST: gi|29619027|gb|CB624039.1|CB624039
EST:     ATAGGATTATAGATTCTGACGAGAGAGCGGTGTACCAGGAAGCACTACAG                         AATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCA
genomic: ATAGGATTATAGATTCTGACGAGAGAGCGGTGTACCAGGAAGCACTACAGgcatgtgttc ... tgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtctttattttgagtctgctttgtgatatttctttttatactatgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCAGTACCTCTGCTTAGGCACCAG
                         tgatatttctttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttccaggtagaagttatgtactttagtgattgaggtatatgttggtctttattttgagtctgctttgtgatatttctttttatactatgttatacagAATATTATCCAGGATAAAAGGGAAGATGATCTGCCTGAGGGTGTTCTGTCAGTACCTCTGCTTAGGCACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - gtgattg
- - - - - - - - - - - - - - - - - - - - tatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgcttt