Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgttaactccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC

Basic information

species Oryza sativa
transcript LOC_Os03g11970.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G64740.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacgttaactccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgt--gtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC
    || ||   | |||     ||    |       || |  |   ||       | |  |        ||  |  || || |||     | ||||| || || || |||||||||||||||||||||||||||||  | |  || || || || |||||||| |||||     | ||||| ||||||||||||
----gtaaagagc-tcacactactagtgtttct---ttctctcttaagtctccttctactacacatttcaaatctttggtcatgttaaaattagGTGCCCAACTGGATTCAAGTGCGGGATAAACTACCAGCCGCCTTCCGTTGTTCCAGGTGGTGACCTGGCTAAGGTTCAACGAGCGGTTTGCATGATCAGC

upper sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S341_23V6.2 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------gtacgtta-actccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgtgtttc----agGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC
                                                               |  ||    | |  |    |  |  || |      |    |   ||   ||| ||  |  |  |  || |   || |||   | ||  | |    ||||||||||| || ||||||||||| || ||||||||||| || |||| |||||| || || ||||| |||||||||  | ||||||||||||||||||||
gtaagcggaggggggtgaggttgggattgcgtgttgtgggtgaggggcgggaatgcgtagtaggggcgagggagtgtaggcgcgaggggagtgggcatgtgcatgtgcgtgcatgttggtgggggcg-cgatgtgaacagtggagtggtaatgcgtgcagGTGTCCGACGGGTTTCAAGTGCGGAATCAACTACCAGCCACCAACGGTGGTGCCCGGCGGCGACCTTGCGAAGGTGCAGCGGGCGGTGTGCATGATCAGC

upper sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S215_52V6.1 (Physcomitrella patens), 3'ss of exon 2
------------------------------------------gtacgttaactccatcatctcgctgaattccagagattttagccggagatga--tgacgatgatgatgacgaagacggtgatcttgtgttt-cagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC
                                          |   | | | |       |  || |      ||   |  |||  |  |  |      |||  | |  |   |    || | |||  ||| |  |||||||| || || |||||||||||||| ||||||||||| || || | |||||| || || || || || |||||     ||||||||||||||||||||
gtaagcagagtggtggtttcagtggtgttgttttagatggtggagtggtgagttggatggcaggcggtgcggtaggtgtgataggtgctggcgcatctccgacaacgccgttaactgtggagttctgatgtgtgtagGTGTCCAACTGGTTTCAAGTGCGGGATTAACTACCAGCCACCAACCGTGGTGCCCGGCGGTGATCTTGCCAAGGTCCAACGGGCGGTGTGCATGATCAGC

upper sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ09935 (Selaginella moellendorffii), 3'ss of exon 4
gtacgttaactccatcatctcgctgaattccagagattttagccggagatga-tgacgatgatgatgacgaagacggtgatcttgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC
                     |      |||| || ||   ||    | ||  |  | ||     | ||      | | |   |   |   ||||||||||| || |||||||| || |||||||||||||||||||||||||| ||    || || |||||||  |||| | | || ||||| |||||||||
---------------------gtaaggctccaaagcttc--gcttttgctggctttcaatcgatctaacttttttgctca--ctacttccaagGTGTCCGACTGGATTCAAGTGTGGCATAAACTACCAGCCGCCGACGGCGGTTCCAAACGGAGATCTGGCGAGAGTGAAGCGCGCAGTGTGTATGATCAGC

upper sequence: LOC_Os03g11970.1 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ23680 (Selaginella moellendorffii), 3'ss of exon 4
gtacgttaactccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC
                     |      |||| || ||     |||   ||    ||||     | ||      | | |   |   |   ||||||||||| || |||||||| || |||||||||||||||||||||||||| ||    || || |||||||  |||| | | || ||||| |||||||||
---------------------gtaaggctccaaagctt-----cggttttgcaatcgatc----taacttttttgctca--ctacttccaagGTGTCCGACTGGATTCAAGTGTGGCATAAACTACCAGCCGCCGACGGCGGTTCCAAACGGAGATCTGGCGAGAGTGAAGCGCGCAGTGTGTATGATCAGC

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|86904672|gb|CI321580.1|CI321580
EST:     ACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGGCCCCCGACGGCGG
genomic: ACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCA-GCCGCCGACGGCGG
EST: gi|86414971|gb|CI069374.1|CI069374
EST:     CAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: CAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|58687898|gb|CK076585.1|CK076585
EST:     GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|86528593|gb|CI168799.1|CI168799
EST:     GAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: GAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|29638415|gb|CB643424.1|CB643424
EST:     GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|11565038|gb|AU165674.1|AU165674
EST:     GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88216555|gb|CI214731.1|CI214731
EST:     GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88843928|gb|CI008509.1|CI008509
EST:     CTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: CTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|4880618|gb|AU064917.1|AU064917
EST:     GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACG-CGGT
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|4715112|gb|AU056229.1|AU056229
EST:     GCCGCCNTCCACTCCATCAAGACCAGGAGGACTGTNCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCANGCC-CCGACGGCGG
genomic: GCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCA-GCCGCCGACGGCGG
EST: gi|86254625|gb|CI059352.1|CI059352
EST:     CACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: CACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|89194272|gb|CI116709.1|CI116709
EST:     ATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: ATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88905964|gb|CI089550.1|CI089550
EST:     CACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: CACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88849236|gb|CI087758.1|CI087758
EST:     CCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: CCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88206699|gb|CI206548.1|CI206548
EST:     TGTGCAGTTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: TGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
EST: gi|88845601|gb|CI084526.1|CI084526
EST:     TTCGTCGACTG                         GTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT
genomic: TTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 67 (upstream exon), 65 (downstream exon)
Score: 32

TGGCCTGCTGCCTGATGTACCGCGGCGACGTCGTCCCCAAGGACGTCAACGCCGCCGTCCACTCCATCAAGACCAGGAGGACTGTGCAGTTCGTCGACTGgtacgttaac ... tgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgttaactccatcatctcgctgaattccagagattttagccggagatgatgacgatgatgatgacgaagacggtgatcttgtgtttcagGTGTCCGACAGGGTTCAAGTGCGGGATAAACTACCAGCCGCCGACGGCGGTGCCGGGAGGGGACCTGGCGAAGGTGAGGAGGGCGGTGTGCATGATCAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG