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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC

Basic information

species Oryza sativa
transcript LOC_Os03g20310.4
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 9
------------------------------------------tg-tgttccctttcttatttg------------tgct-tttgatcccgagcaagttctgcaagttttaga----tgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
                                          || |||| |  || ||   ||            ||   |||||| |    ||  |||  ||  ||| |||    ||    |   | | |||||| | ||||  |||  || |   |||||||||||| | || |||||||| || ||||| ||||| || || |||||||| |||||||| || || || || ||||||||||| || ||||| ||||
gtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatgtatgtagctctgtctgaatacttctgttctatttgcc-tcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GRMZM2G056099_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------------------------------tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaagagttctaatcttctttc--tgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
                                                                              |||  |    |||       |   | |  |    || ||  | || | ||      ||    ||  |   |||||||| || |  | |||| |    |  ||||||||||| | || |||||||| |||||||| ||||| || || |||||||||||||||||||| ||||| || |||||||| ||||| ||||| ||||
gtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtg-ttcctagctctgaagacttttggtgttctattatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA20G39050.1 (Glycine max), 3'ss of exon 11
----------------------------------tgtgttccctttcttatttgtgcttttgatcccgagcaagttct----gcaagttttagatgaccctttttttttctgaag------agttctaatcttctttctgcc-----------agGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
                                  |  ||||  |||  |    |    |    |  |   ||   | |    |||  || | |||  |     |   |  | ||       || |||  || | ||| ||             |||||||||||||||| ||||||||||| || ||||| || || ||  ||||||  || ||| | || ||||| ||||||||||||||||| ||||| ||  
gtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA19G31050.2 (Glycine max), 3'ss of exon 9
-tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
 ||||    |      |  ||  | |    |       |  |  || |     |     |   | ||  | |        ||||  || | || || | ||||||||||| ||||||||||||| ||||| |||||||  |||||  | || | | | ||| | || || ||||| || || ||   |||||| |||||||
atgtgcatgcacgaaaaactggacctaaactattccagacatgatggattcactcatcaatattattaatcttctgttcattctt-tcgtgttactactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCAGCTCGAGCTCTTCTCGCCATCAGTGATTATTTCTCAC

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: GLYMA03G28320.1 (Glycine max), 3'ss of exon 11
tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaag----agttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
     |    | | |           ||| ||  | | | | | |  |   |    | || | |     || | ||     || ||     ||| |  | | ||||||||||| ||||||||||||| ||||| |||||||  |||||  | || | | | ||| | || |||||||| ||||| ||   |||||| |||||||
----atgatgtgcatgcacaaaaaactgaacctaaactattccagacatgatggattcactcatcaaaattattaatcttcagctcattctttcgtgttactagGCTGACAATCTGCGGCAGCAGACATTACAACAAATGCTTCGAATATTAACGACCAGGCAATCGGCTCGTGCTCTTCTTGCCATCAGTGATTATTTCTCAC

upper sequence: LOC_Os03g20310.4 (Oryza sativa), 3'ss of exon 8
lower sequence: AT5G06950.3 (Arabidopsis thaliana), 3'ss of exon 9
tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
 ||    |  || | || |    ||  |||        ||||  | |   | || ||    |  |   ||  | |     |||    ||  |  || |||||||| |||||| | |  || || || || || |||    || |  | ||||   ||||  | || |||||||||||||||||||| |||||||||||||
-gtacaacacttgtgatgt---tttgagatgatatcttagttaag-agtatatatatatatcaataggttaataatcgtctcttgg-ttggtggtggcagGCTGATAATTTGAGACTACAAACATTGCAACAGATGATAAGAGTATTAACAACGAGACAGTCAGCACGTGCTCTACTTGCAATACACGATTACTTCTCAC

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|86432768|gb|CI086379.1|CI086379
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88989568|gb|CI107315.1|CI107315
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|89183025|gb|CI003089.1|CI003089
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTGCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|29657288|gb|CB653563.1|CB653563
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|29671390|gb|CB667665.1|CB667665
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86492952|gb|CI135585.1|CI135585
EST:     GACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: GACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88248322|gb|CI248171.1|CI248171
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86827348|gb|CI270985.1|CI270985
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88279357|gb|CI399842.1|CI399842
EST:     GGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACCATTTGCGGCACCAGACTTTACATCAAATGCAGCGAATTCTGACC
genomic: GGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86871462|gb|CI342062.1|CI342062
EST:     TGGCTATGGCCATGGGCAAACTT-GGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|29687728|gb|CB684003.1|CB684003
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTTTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88226191|gb|CI226107.1|CI226107
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|29662680|gb|CB658955.1|CB658955
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86489560|gb|CI132193.1|CI132193
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86492378|gb|CI135011.1|CI135011
EST:     CTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: CTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88908128|gb|CI090724.1|CI090724
EST:     TGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|89196645|gb|CI400815.1|CI400815
EST:     AGAATTTCCTCCGTCAG                         GCTGACAAGTTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGAC
genomic: AGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAA-TTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGAC
EST: gi|113931025|gb|DQ884119.1|DQ884119
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCA
EST: gi|88274806|gb|CI388264.1|CI388264
EST:     TATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88215878|gb|CI215727.1|CI215727
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88220386|gb|CI219946.1|CI219946
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88277103|gb|CI397905.1|CI397905
EST:     GCAAACTT-GGACCCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: GCAAACTTGGGA-CCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|29671391|gb|CB667666.1|CB667666
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|86834069|gb|CI340208.1|CI340208
EST:     GGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: GGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|88227827|gb|CI227307.1|CI227307
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
EST: gi|38476672|gb|CF960805.1|CF960805
EST:     TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAG                         GCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA
genomic: TGGCTATGGCCATGGGCAAACTTGGGACCCTTGAGAATTTCCTCCGTCAGgtaagcgtct ... tttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caagttttagatgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC
                                  ttctaat  putative branch site (score: 2)
                                  ttctaatcttctttct  CT-rich tract
                 tttttttttctgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgttccctttcttatttgtgcttttgatcccgagcaagttctgcaagttttagatgaccctttttttttctgaagagttctaatcttctttctgccagGCTGACAATTTGCGGCAGCAGACTTTACATCAAATGCAGCGAATTCTGACAATCCGACAAGCTGCCCGTGCTCTACTTGCAATACATGATTACTTCTCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- tgttccc
- - - - - - - - tttgtgc
- - - - - - - - - - - - - tgatccc
- - - - - - - - - - - - - - - - - - - - ttctgca