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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCCAACGAGGCCTGAATGTTTCCCTGTCAACGGATGATCCATTGCAAATTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctctttccctctcccctcaccctattcatcttatgcagacactaatgtacatacttatgtttatatatgtgcatgtacaagacatacatgaat...

Basic information

species Oryza sativa
transcript LOC_Os05g28180.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G416667_T03 (Zea mays), 5'ss of exon 17
TTTCCAACGAGGCCTGAATGTTTCCCTGTCAACGGATGATCCATTGCAAATTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctctttccctctcccctcaccctattcatcttatgcagacactaatgtacatacttatgtttatatatgtgcatgtacaagacatacatgaat-------------------------------------------------------------------------
 ||||||||||| |||||||| ||  | || |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||||||||||||| |||||| ||  ||||||| |   |   |   ||    || | |   |||  |  | ||     |  ||| | |    |  | | ||  ||| || |  |                                                                          
CTTCCAACGAGGTCTGAATGTCTCATTATCTACGGATGACCCTTTGCAAATTCACCTGACAAAAGAACCATTGGTGGAAGAATACAGCATTGCTGCTTCGgtactcgctacttccctcgcttttttgcgccttttgattgttctttcac--acatgcagcacgagctttgtgtgcacgtgtatgcagcacacacctttacgcatagatactattgtacccacgccaaaagggacgagtgactaatgtccattactccattttgattgtttcag

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv08s0105g00570.t01 (Vitis vinifera), 5'ss of exon 16
TTTCCAACGAGGCCTGAATGTTTCCCTGTCAACGGATGATCCATTGCAAATTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctctttccctctcccctcaccctattcatct---tatgcagacactaatgtacatacttatgtttat-atatgtgcatgtacaagacatacatgaat
|||||  || ||||| ||||||||||| || || ||||||||| | ||||| ||||| |||||||| || |||||||||||||||||||| |||||||| |||  | |||| || ||||| |     |   | ||||    |||  ||  | | || |   ||||| ||||||| |||  | |   |     |           
TTTCCTTCGGGGCCTCAATGTTTCCCTCTCTACAGATGATCCACTACAAATCCACCTAACAAAAGAACCCTTGGTGGAAGAATACAGCATAGCTGCTTCTgtaagctctctctctctctctctctctctcttccatcagggtat-tagggattgatctg-gtactt-tgtttatgataattcctcatcttgcag----------

upper sequence: LOC_Os05g28180.3 (Oryza sativa), 5'ss of exon 8
lower sequence: PP1S307_76V6.1 (Physcomitrella patens), 5'ss of exon 16
TTTCCAACGAGGCCTGAATGTTTCCCTGTCAACGGATGATCCATTGCAAATTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctctttccctctcccctcaccctattcatcttatgcagacactaatgtaca--tacttatgtttatatatgtgcatgtacaagacatacatgaat--
|||   |||||| || || || | | |||| |||||||||||||||||||| ||||| || ||||||||  | |||||||| ||  |||||||||||   ||     |||  |  |  | | | || |  ||| | |  | | | | |  | |  |    | ||| ||| | ||| | || ||||| |    ||| |  | |  
TTTTGCACGAGGGCTCAACGTATGCTTGTCTACGGATGATCCATTGCAAATACACCTCACCAAAGAGCCTCTTGTGGAAGAGTATGGCATTGCTGCTCAGgtggcttctcccttaccttgctcccatctcattta-cgaaggaaaataaaattaaaagagtgcttgtgtgtgtatgtatgtatgtata---tatataccactct

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|29675538|gb|CB671813.1|CB671813
EST:     TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCA                         CTCTGGAAGGTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
genomic: TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctc ... tttgtttcagCTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
EST: gi|27548799|gb|CA767547.2|CA767547
EST:     TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCA                         CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
genomic: TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctc ... tttgtttcagCTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
EST: gi|29638453|gb|CB643462.1|CB643462
EST:     TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCA                         CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
genomic: TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctc ... tttgtttcagCTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
EST: gi|29637475|gb|CB642484.1|CB642484
EST:     TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCA                         CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
genomic: TTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctc ... tttgtttcagCTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
EST: gi|87022773|gb|CI269709.1|CI269709
EST:     AAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCA                         CTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC
genomic: AAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctc ... tttgtttcagCTCTGGAAGCTCAGTTCTTGTGATTTATGTGAAATAGCTAGAAACTCTGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCCAACGAGGCCTGAATGTTTCCCTGTCAACGGATGATCCATTGCAAATTCACCTGACAAAAGAGCCATTGGTGGAAGAATACAGCATTGCTGCTTCAgtactccctctttccctctcccctcaccctattcatcttatgcagacactaatgtacatacttatgtttatatatgtgcatgtacaagacatacatgaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT