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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag

Basic information

species Oryza sativa
transcript LOC_Os09g36710.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G042604_T01 (Zea mays), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacc----cccatagatctcatctcgc----cggtgggggattcgattcgcag---------
|||||||||||||||||||||||||||| |||||||||||| | ||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||| | | | |||||   |  ||| |||  ||    |||    | |      |||  |||      |  |    ||  ||| |  | |         
AGGCCGTCCGCAAGGGCAACGCCGCCGTGGGCGTCCGCGGCACGGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACACCCAAGCTCCAGGACTCCAGgtagcaaacccctccgtccctcctttctatcctccgaccagatctcgcgatcctcgcctcaaactactatctctgacccgagtttccgtctccctag

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G138128_T01 (Zea mays), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacc---tcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag---------------
||||||||||||||||||||||||||||||||||||||||| | ||||||||||||||||| || ||||||||||| |||||||||||||||||||||||||| | | | |    |||   | | |  ||  || |      | |     || |  |||     |      |  ||  |  |                
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACGGACACCGTCGTCCTCGGTGTGGAGAAGAAGTCAACCCCCAAGCTCCAGGACTCCAGgtagcaaaccctccgtccctcccatcgatcctccgaccagatctcgcgattcccgactcaa-actaatatctctgaccccgaattcatgtctccccag

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA02G05190.1 (Glycine max), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag--------------------
| ||||||||||||||||||||||||||||||||||||||| |||||| |||||||||||||||||||||||| |||||| |||||||||| |||||||||||||  |   ||  ||    || | ||  || | | |       | | |    ||| |    |    ||   || ||||                    
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAACGTCGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAGCTCCAAGACTCCAGgtaccactactcttatcaattcccccctttcctttcccttattaggttttttaatcggcaaatgttagttttgttagcagagaggattttccctcttccc

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GLYMA16G23580.1 (Glycine max), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccata-cacccccatagatctcatctcgccggtgggggattcgattcgcag----------------------
| ||||||||||||||||||||||||||||||||||||||| ||||||  || |||||||||||||||||||| |||||| |||| ||||| ||||||||||||   |   ||  ||    |   || | || |  ||   || |   |  |   |||       ||||||      | |                       
AAGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACAATGTTGTCCTCGGCGTCGAGAAGAAATCCACCGCCAAACTCCAAGACTCCAGgtactactactcttttcaattcaattccctccgtttcagatccct---ttccccttcgattactagggattaaccaagaaaactacgtgttataaggagaagg

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT5G66140.1 (Arabidopsis thaliana), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtggg-ggattcgattcgcag--------------------
| |||||||||||||| |||||||||||||| ||||||||  |||||||||| ||||||| ||||||||||||||||||||||||||| ||||| || ||||    ||  ||  |||   || | | ||     ||      | |||  |   ||| |   |    |||| |   | |                       
AAGCCGTCCGCAAGGGTAACGCCGCCGTCGGTGTCCGCGGTACCGACACCGTTGTCCTCGCCGTCGAGAAGAAGTCCACCCCCAAGCTTCAGGATTCTAGgt-tttatttccatctcttcacttttatcatggcaccaattaacagacttgccctctctacttattggatcctgcttggtttactctcagttgctagttga

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: AT3G51260.1 (Arabidopsis thaliana), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacc-catcacctcctcgcgac--------ctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag------------
| |||||||| ||||| |||||||||||||| ||||||||| | || || |||||||||| |||||| ||||| |||||||| ||||||||||| ||||||||   |  |     ||  |||         ||    ||  ||  |  ||  |   | |  | ||  |  |  |   || | ||   ||            
AAGCCGTCCGAAAGGGTAACGCCGCCGTCGGAGTCCGCGGCACAGATACTGTCGTCCTCGCCGTCGAAAAGAAATCCACCCCTAAGCTCCAGGATTCCAGgtattgctccgatctctaccgatacaagatgcttaaaccggatttagtccatttacttttgtttctgcactttgat-tttggttttaagcttcacctggat

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv03s0038g02300.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag----------------------
| |||||||| |||||||||||||||||||||||||||||| |||||||| |||||||||||||||| |||||||||||| | ||||||||||||||  ||||||  || | ||||| | ||   |   |   | ||        | | | |  |||    |   |  |  | ||   |                       
AAGCCGTCCGTAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTCCTCGGCGTCGAAAAGAAGTCCACCGCTAAGCTCCAGGACTCTCGgtacc--tctcttcctctctacgattacgcattttcagtgattgtggtttaagatcgtgaattctgagtcagcttttgaacctatctgatggtttctgtggc

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: Vv04s0023g03690.t01 (Vitis vinifera), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccat--agatctcatctcgccggtgggg----gattcgat----tcgcag----------
| |||||||| || ||||||||||||||||||||||||||| |||||||| |||| |||||||||||||| ||||||||| |||| ||||| || |||||||  || |       |    |  | | |   | |     |   |  | ||  ||    |  ||| |||    | || |||    | | ||          
AAGCCGTCCGTAAAGGCAACGCCGCCGTCGGCGTCCGCGGCACCGACACCATCGTTCTCGGCGTCGAGAAAAAGTCCACCGCCAAACTCCAAGATTCCAGgtctccttttttcatttttcatttttattttctttttttcttgtgtaaataccaaaatgaaggtagggttagggtttgatggttttggagacatccatgt

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ31080 (Selaginella moellendorffii), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag
||||||| ||||||||||||||||||||||||||||||||| | |||||  |||| |||||||| |||||||| |||||| |||||||||||||| | ||||     ||   |||    || ||||        | ||| |  ||||| ||      | | |   | | ||  |   |||
AGGCCGTGCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACAATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-----tcgtttccctctgatctct--------agacctc--tagatttctagctcctgattccgaaatctctgtccag

upper sequence: LOC_Os09g36710.1 (Oryza sativa), 5'ss of exon 1
lower sequence: EFJ34636 (Selaginella moellendorffii), 5'ss of exon 1
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag
||||||| || |||||||||||||||||||||||||||||| | |||||  |||| |||||||| |||||||| |||||| |||||||||||||| | ||||     ||   |||    || ||||        | ||| |  ||||| ||      | | |   | | ||  |   |||
AGGCCGTGCGAAAGGGCAACGCCGCCGTCGGCGTCCGCGGCACTGACACGATCGTGCTCGGCGTGGAGAAGAAATCCACCGCCAAGCTCCAGGACGCGAGgt-----tcgtttccctctgatctct--------agacctc--tagatttctagctcctgattccgaaatctctgtccag

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|88731285|gb|CI754898.1|CI754898
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|88345796|gb|CI631064.1|CI631064
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|32948053|gb|BP184625.1|BP184625
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|29671436|gb|CB667711.1|CB667711
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|88414494|gb|CI698593.1|CI698593
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|112785395|gb|EE590608.1|EE590608
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|88432778|gb|CI690627.1|CI690627
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|86907553|gb|CI296562.1|CI296562
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|88738735|gb|CI762243.1|CI762243
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC
EST: gi|88572717|gb|CI664288.1|CI664288
EST:     GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAG                         GTCGGTGCGCAAGATCGCTACCCTGGACACCCACATCGCGCTGGCGTGCGC
genomic: GTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGC

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), 74 (downstream exon)
Score: 12

AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatca ... cgattcgcagGTCGGTGCGCAAGATCGCTAGCCTGGACACCCACATCGCGCTGGCGTGCGCGGGGCTCAAGGCGGACGCCCGCGTGCTCATCAACCGCGCGCGGGTCGAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCCGTCCGCAAGGGCAACGCCGCCGTCGGCGTCCGCGGCTCCGACACCGTCGTCCTCGGCGTCGAGAAGAAGTCCACCCCCAAGCTCCAGGACTCCAGgtacccatcacctcctcgcgacctctctccccatacacccccatagatctcatctcgccggtgggggattcgattcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT