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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtacgcgtctctaggcccccctctctctctcgatttgatcggtttgatctgtggtgccctaggtttgatctgtggatttattttttttcttgttttgtgggggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG

Basic information

species Oryza sativa
transcript LOC_Os04g57220.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g57220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G102471_T04 (Zea mays), 3'ss of exon 1
gtcggtacgcgtctctaggcccccctctctctctcgatttgatcggtttgatctgtggtgccctaggtttgatctgtggatttattttttttcttgttttgtgggggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG
                  |  |  |   ||| ||||||| ||| || |  | ||  ||  |||||   | | |     |||||  | | |   || ||  | |    || |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||| |||||||| ||||||||||
------------------gtacggccacctccctcgattcgattggctctaactacggaaccctaccctaggttc---gatttgatctgtggatt-ttgggggattttgtttagGGTTTGATCGATGGCGTCGAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCGCCCACCTCCTGCAGCGCAG

upper sequence: LOC_Os04g57220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv19s0015g01190.t01 (Vitis vinifera), 3'ss of exon 1
----gtcggtacgcgtctctaggcccccctctctctctcgatttgat-cggtttgatctgtggtgccctagg----tttgatctgtggat-ttattttttttcttgttttgtgggggtgattagGGTTTGATCGAT-------GGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG
      |  |     ||| | |  |    |   | |||      ||   | |||  |   |  | | || |     ||| || | ||  | ||  |      |   |  |      ||  | |   |||| || ||       ||| || ||| | ||    ||||||||||||||||||||||||||||||||||| ||           
attttgcattgtctttctatggaacttgtttgatatcttatggagaagtgatttagttattcttactcttgacattttttatttatgcgtattgctgcagCACGAATCCTTCAACTGTATTGAAACTTTGGTCAATCTGTAATGGCTTCAAAGCGAATTAACAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACTTC-----------

upper sequence: LOC_Os04g57220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: EDO98738 (Chlamydomonas reinhardtii), 3'ss of exon 1
gtcggtacgcgtctctaggcccccctctctctctcgatttgatcggtttgatctgtggtgccctaggtttgatc-tgtggatttattttttttcttgttttgtggg--ggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG
                 ||    |  |   |   ||  ||| |  |  ||    |     | | |||    |   |   ||      | |   |  |   |||     | | |  |||   ||  |    |   ||       || || ||    ||  || ||||| |  |       |  || |  ||||     
-----------------ggatgtcagcaaccagccgccttgttgaggctgtgtagaaccacgcgaggcccaacaattcagacgcgcatctgccccggccctgtcatccgctcaacagGACCTG--CAGAAGGACCCGCCCACCTCGTGCAG----TGCGGGCCCTGCGGGCGATGATCTCTTCCACTGGCAG-----

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|218504761|gb|FG960866.1|FG960866
EST:     TCGCCGGAGCGCCCCGTCGCCG                         GGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
genomic: TCGCCGGAGCGCCCCGTCGCCGgtcggtacgc ... gggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
EST: gi|86599825|gb|CI255987.1|CI255987
EST:     CGGAGCGCCCCGTCGCCGGTCG                      
genomic: CGGAGCGCCCCGTCG-C---CGgtcggtacgc ... gggtgat
EST: gi|218488112|gb|FG949877.1|FG949877
EST:     CGCCGGAGCGCCCCGTCGCCGGTCG                      
genomic: CGCCGGAGCGCCCCGTCG-C---CGgtcggtacgc ... gggtgat
EST: gi|218482001|gb|FG956573.1|FG956573
EST:     TCGCCGGAGCGCCCCGTCGCCG                         GGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
genomic: TCGCCGGAGCGCCCCGTCGCCGgtcggtacgc ... gggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
EST: gi|58599461|gb|CK009989.1|CK009989
EST:     TCGCCGGAGCGCCCCGTCGCCG                         GGTTTGATCGATGGCGTCCAAGAGG-TCCTGAAGGAGTTGAAGGACCTGCA
genomic: TCGCCGGAGCGCCCCGTCGCCGgtcggtacgc ... gggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
EST: gi|218491681|gb|FG954119.1|FG954119
EST:     TCGCCGGAGCGCCCCGTCGCCG                         GGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
genomic: TCGCCGGAGCGCCCCGTCGCCGgtcggtacgc ... gggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCA
EST: gi|29680725|gb|CB677000.1|CB677000
EST:     TCGCCGGAGCGCCCCGTCGCCGGTCG                      
genomic: TCGCCGGAGCGCCCCGTCG-C---CGgtcggtacgc ... gggtgat
EST: gi|3763269|gb|AU030021.1|AU030021
EST:     TCGCCGGAGCGCCCCGTCGCCGG                         T
genomic: TCGCCGGAGCGCCCCGTCGCC-Ggtcggtacgc ... gggtgattag-
EST: gi|3763269|gb|AU030021.1|AU030021
EST:     TCGCCGGAGCGCCCCGTCGCCGG                         T
genomic: TCGCCGGAGCGCCCCGTCGCC-Ggtcggtacgc ... gggtgattag-
EST: gi|3763269|gb|AU030021.1|AU030021
EST:     TCGCCGGAGCGCCCCGTCGCCGG                         T
genomic: TCGCCGGAGCGCCCCGTCGCC-Ggtcggtacgc ... gggtgattag-
EST: gi|1632631|gb|C20360.1|C20360
EST:     CGGAGCGCCCCGTCGCCGGTCG                      
genomic: CGGAGCGCCCCGTCG-C---CGgtcggtacgc ... gggtgat
EST: gi|86592570|gb|CI253251.1|CI253251
EST:     TCGCCGGAGCGCCCCTTCGCCGGTCG                         GGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGC
genomic: TCGCCGGAGCGCCCCGTCG-C---CGgtcggtacgc ... gggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccctaggtttgatctgtggatttattttttttcttgttttgtgggggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG
       gtttgat  putative branch site (score: 5)
                    atttattttttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcggtacgcgtctctaggcccccctctctctctcgatttgatcggtttgatctgtggtgccctaggtttgatctgtggatttattttttttcttgttttgtgggggtgattagGGTTTGATCGATGGCGTCCAAGAGGATCCTGAAGGAGTTGAAGGACCTGCAGAAGGACCCTCCCACCTCATGCAGCGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG