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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaattttgctatcgcctttaaaatctgacttattctctgttcgcttgataaattaagttgttctgtcctattgtggctattcag

Basic information

species Oryza sativa
transcript LOC_Os11g47330.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G072216_T01 (Zea mays), 5'ss of exon 1
CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaattttgctatcgcctttaaaatctgacttattctctgttcgcttgataaattaagttgttctgtcctattgtggctattcag-------
 || |||||||||||||||| ||  ||||| |  || ||||| |||||| | ||| | | |||||||||||||||| | |||||| |||||||  ||||||||  | |  | ||||   |   | ||||    |||| | ||       | || || ||||  |  ||||||     ||||  |  |          
TGATATGCTGTTCGGGAAGCCTGAGAAGAGTGATCTCGTGGCTCTCAACTTGGATTTCGATCAAGTCAAGGAGTTTATCAAGGAGCGGCTGGGGATTGAGgta--taacatctgcttgtg---tgaaaaaaaaacttgtccttgag--acatgctacattacttgattctgtttc-ctgtgattcattgatttttag

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G340672_T01 (Zea mays), 5'ss of exon 2
CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaattttgctatcgcctttaaaatctga--cttattctctgttcgcttgataaattaagttgttctgtcctattgtggctattcag---------------------------------------------------------------------------------------------
 || |||||||||||||||| ||| ||||| || || ||||| |||||| | ||| | | |||||||||||||||| | |||||| |||||||  ||||||||   ||  | ||||   |     |||| ||    |||      || |   ||  |  |||  ||| | ||||  |    ||  | ||  |                                                                                             
TGATATGCTGTTCGGGAAGCATGGGAAGAGTGGTCTCGTGGCTCTCAACTTGGATTTCGATCAAGTCAAGGAGTTTATCAAGGAGCGGCTGGGGATTGAGgtatagca--tctgcttgtgtgaaaaaaaacttgtccttgagacatgctacattacttgattctgtt-tcctgtgattcattgatttttaggttgagatgggtggttgcaaggcttaaatcatgaccttcatcgtcgagccattcgtgtcacatgatcaagagtactacctttcgattatttcag

upper sequence: LOC_Os11g47330.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G107082_T01 (Zea mays), 5'ss of exon 2
CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaattttgctatcgcctttaaaatctgacttattctctgttc--gcttgataaattaagtt---gttctgtcctattgtggctattcag
 || |||||||||||||||||||| |||||||| || ||||| |||||| | ||| |   |||||||||||||||||| |||||| ||||||| |||||||||    | |  ||||   |    | |||  | || | | |||    |  |||  || | || | ||   ||  |||  |    |   | |||||
TGATATGCTGTTCGGGAAGCGTGGGAAGAGCGGCCTCGTGGCTCTCAACTTGGATTTCAATCAAGTCAAGGAGTTTGTCAAGGAGCGGCTGGGGGTTGAGgtatagtagt--tgcttgtg----tgaaaaataacctgtcctccagacatgctacatgagttgattttgtgtcatgtgatccattaatttttcag

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|88355914|gb|CI653324.1|CI653324
EST:     TAAATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCAC
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCAC
EST: gi|88690145|gb|CI734224.1|CI734224
EST:     GTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: GTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|38478269|gb|CF962402.1|CF962402
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|569081|gb|D39930.1|D39930
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGGAGCC
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGG-AGCC
EST: gi|117247393|gb|CT848567.1|CT848567
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|33670036|gb|CF298275.1|CF298275
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|33671919|gb|CF300158.1|CF300158
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|33657822|gb|CF280436.1|CF280436
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|88387140|gb|CI577926.1|CI577926
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGG
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGG
EST: gi|88690955|gb|CI735034.1|CI735034
EST:     GTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: GTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|38481987|gb|CF966050.1|CF966050
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
EST: gi|88423731|gb|CI617083.1|CI617083
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGG
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGG
EST: gi|88688256|gb|CI731832.1|CI731832
EST:     TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCT
genomic: TAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCT
EST: gi|88690505|gb|CI734584.1|CI734584
EST:     GTTTGTGAAGGAGAGGCTGGGAGTTGAG                         GTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA
genomic: GTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCA

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: 70 (upstream exon), 70 (downstream exon)
Score: 19

CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaat ... ggctattcagGTCGAGATGGGTGGCTGCAAGGCTCCAATCACCACCTTCATTGTGGAGCCATTTGTACCCCATGATCAAGAATACTACCTTTCTATTGTCTCGGAGAGGC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACATGCTGTTCGGGAAGCGTGGCAAGAGCGGACTTGTGGCCCTCAACCTAGATATTGCTCAAGTCAAGGAGTTTGTGAAGGAGAGGCTGGGAGTTGAGgtagttcaattttgctatcgcctttaaaatctgacttattctctgttcgcttgataaattaagttgttctgtcctattgtggctattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG