Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgcacttttcatcacctcttgccttgaaagttttctgtataagttccaggttttttttttaccccaatgatttcgataatttccatgcacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT

Basic information

species Oryza sativa
transcript LOC_Os02g58020.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G013890_T01 (Zea mays), 3'ss of exon 3
------------------------------------------------------ctttgcacttttcatcacctcttgccttgaaagttttctgtataagttccaggttttttttttaccccaatgatttcgataatttccatgcac--acttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT
                                                      ||  | |  || |||   |  ||   || | |  | ||| || |||||   | ||    |  ||||| |    ||| |  | ||   ||  ||    |||||| |||||||||||||| || || ||||| || |||||||||||||| |||||  ||||||| |||||||| ||||| |||||||||||||||||||||||
gtgagtactctgtggtgtttggtagttttcagtagataaaactgtggccggggcctgggaagcttgcatgttcagtt-tatttatacatatctataaaagttttcg-ttgaaatgctaccctacaagttttggaatttcttatttacttgtttcagGACTTGTTGGAAGAAACGGGACTGGGAAGACATCTTTTCTCAGAGCGATGGCATTGCATGCAATTGATGGTATTCCTAAGAACTGCCAGATATTGCATGT

upper sequence: LOC_Os02g58020.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv02s0025g02160.t01 (Vitis vinifera), 3'ss of exon 3
------ctttgcacttttcatcacctcttgccttgaaagttttctgtataagttccaggttttttttttaccccaatgatttcgataatttccatgcacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT
      ||||| |  ||   | |  |||  ||    |   |     ||  | ||     ||  ||||||     | |  |  |    | ||   |  |||     || ||||| |||||||||||||| || |||||  |||| || ||    ||||| |||||||| |||||||| ||||| ||||||||||||||||| |||||
gaacttctttg-atgttatctaatgtctatccaatcataatagtaataataatttggatttggttttttgatgtattactgccatatacttttgtataca-----gGCCTTGTAGGAAGAAATGGTACTGGCAAAACAACTTTCCTTAGGTACATGGCTATGCATGCTATTGATGGTATTCCTAAGAACTGCCAGATATTACATGT
















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|29623430|gb|CB628441.1|CB628441
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|157651259|gb|EX450893.1|EX450893
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTAC
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTAC
EST: gi|29664091|gb|CB660366.1|CB660366
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|29644366|gb|CB649373.1|CB649373
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|66915780|gb|CX102628.1|CX102628
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGA
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGA
EST: gi|29627492|gb|CB632503.1|CB632503
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|117239285|gb|CT849366.1|CT849366
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGG
EST: gi|157651253|gb|EX450887.1|EX450887
EST:     TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATG                         GTCTTGTTGGAAGAAATGGTAC
genomic: TGATCTCATTCAAGATTGCACTGTAACACTTGCTTTTGGGAGGCACTATGgtgagttaca ... cacacttcagGTCTTGTTGGAAGAAATGGTAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttccaggttttttttttaccccaatgatttcgataatttccatgcacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT
     aggtttttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgcacttttcatcacctcttgccttgaaagttttctgtataagttccaggttttttttttaccccaatgatttcgataatttccatgcacacttcagGTCTTGTTGGAAGAAATGGTACAGGGAAAACCTCTTTTCTCAGAGCTATGGCGATGCATGCGATTGATGGGATTCCCAAGAACTGCCAGATATTGCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC