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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatccatcatttctactatgctgttt...

Basic information

species Oryza sativa
transcript LOC_Os10g39220.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G174286_T03 (Zea mays), 5'ss of exon 7
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgctttt---cctctccagcaattcata--tgttttaagtgaacataggaaattta-gggcatatgcatcc-atcatttctactatgctgttt
|||||  ||||| ||||| | |||||||||||||||||| ||||| |||||||||| ||||||||||||||||||  |||  ||||||  ||||   | |||||| ||||  ||   | | | |  |  ||   ||||| | | |||||| ||||||    ||||  |    ||      
ATAATCCTATGGTTGGTTTTGTGGTGGAAACCAGTTCGAATTATGGTCATCTTGTCAAAGATGTTCTTTGCAGgt--aatccatgtttaattttttccttctccatcaatctatccctatatcactttgactgcggaaaatcatgggcatgtgcatcttggcattgatgaagtgt-----

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G003076_T02 (Zea mays), 5'ss of exon 6
--------------------ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgt--ttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatcc-atcatttctactatgctgttt
                    |||||  ||||| ||||| |||||||||||||||||||||||||| |||| ||| | |||||||||||||||||||     | | |  ||  ||    |||||| ||||   |   ||||| ||    ||   |   | ||  |||  |||||    ||||| ||   |||  || 
TTGACATCAATGTATTTCAGATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAGgtattccatgtttcattaattcatttctccatcaatctct---ttttatgtccctatgacagcatgagatcatgggcatcttgccatttataaagtgcgatta

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G003076_T03 (Zea mays), 5'ss of exon 6
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgt--ttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatcc-atcatttctactatgctgttt
|||||  ||||| ||||| |||||||||||||||||||||||||| |||| ||| | |||||||||||||||||||     | | |  ||  ||    |||||| ||||   |   ||||| ||    ||   |   | ||  |||  |||||    ||||| ||   |||  || 
ATAATTCTATGGTTGGTTTTATGGTGGAAACCAGTTCGAGTTATGGTCATTTTGCCAAAGATGTTCTTTGCAGgtattccatgtttcattaattcatttctccatcaatctct---ttttatgtccctatgacagcatgagatcatgggcatcttgccatttataaagtgcgatta

upper sequence: LOC_Os10g39220.1 (Oryza sativa), 5'ss of exon 6
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 5'ss of exon 6
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatccatcatttctactatgctgttt
||     ||||| ||||| | |||||||| || |||||||||||| | ||| | || |||||||||||||||||||    |||  || | |   ||| || |   | || |    | |||   |   |       | |   |   |||     | || | | |          
ATTGCTCTATGGTTGGTTTTGTGGTGGAAGCCTGTTCGAGTTATGGTAATCCTATCTAAGATGTTCTTTGCAGgtaa---ttagcttcgat---cctatcgatacactctttctatataatccatagtgcctgtctcacctctcttgcgaattttatatttgcag--------

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|89176193|gb|CI043214.1|CI043214
EST:     ATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTT-CGGCTTTTGGG-TTCTTCTCTACGGTGGGAG
genomic: ATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|218492361|gb|FG955401.1|FG955401
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|218502314|gb|FG958985.1|FG958985
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTTTTCTTTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|5002917|gb|AU068026.1|AU068026
EST:     GTGGAACCCAGTNCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|87035694|gb|CI190316.1|CI190316
EST:     GTGGAGACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|3768123|gb|AU032150.1|AU032150
EST:     TTATGATCATCTTGTCNAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: TTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|87035709|gb|CI190331.1|CI190331
EST:     GTGGAGACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|29664023|gb|CB660298.1|CB660298
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|218501789|gb|FG963428.1|FG963428
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|11118168|gb|AU163356.1|AU163356
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGC-GGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|29663945|gb|CB660220.1|CB660220
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|11173257|gb|AU164690.1|AU164690
EST:     GTGGAAACCANTTCGAGTTATGATCATCTTGTCGAAGATGTNCTTTGCAG                         GTGTATCACTGTTTNCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|87035720|gb|CI190342.1|CI190342
EST:     AGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: AGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|44666590|gb|CR280024.1|CR280024
EST:     GAAACCAGTTCGAGTTAAGATCATCTTGTCGAAGATGGTCTTTGCAG                         GTGTATCACTGTTTACGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|218483378|gb|FG949318.1|FG949318
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|87035684|gb|CI190306.1|CI190306
EST:     GTGGAGACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|29663981|gb|CB660256.1|CB660256
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTATACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|86854988|gb|CI263055.1|CI263055
EST:     AGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTGTCTTCTCTACGGTGGGAG
genomic: AGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
EST: gi|29659575|gb|CB655850.1|CB655850
EST:     GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAG                         GTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG
genomic: GTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG

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: 71 (upstream exon), 46 (downstream exon)
Score: 39

ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaattta ... taatttttagGTGTATCACTGTTTGCGGCTTTTGGGTTTCTTCTCTACGGTGGGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATAATATTATGGATGGTTCTATGGTGGAAACCAGTTCGAGTTATGATCATCTTGTCGAAGATGTTCTTTGCAGgtagaatttatgtttgcttttcctctccagcaattcatatgttttaagtgaacataggaaatttagggcatatgcatccatcatttctactatgctgttt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctctcc