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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt...

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G176612_T01 (Zea mays), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt--
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||||||||||||||  | | | ||  | ||| | |  ||| |    |||   | |   ||||  | || |   || |  | | || |  ||       || | ||||  |    
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGCCCACCGCAGCCTCGGGGTCCACATCACCTTCGTCAGgtaccgtaccactactcctgcac-cccccacttgcgcattcacgtatcactcgctcagatctcggagctc-ccgttccagatctcgccatccctccgccccg

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G083546_T01 (Zea mays), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacat--ccgattcctttcctcatctt-
|||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||| || ||||||||||||||||||||||  |   | ||  |  || ||  || |||    | |   | |   ||| |   |      ||||| |  |   ||||    |||| |       | |     
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCGGCCGTCCACCGCAGCCTTGGGGTCCACATCACCTTCGTCAGgtaccaacc-actactactccc--tctcgacttgcacaatcgcgtatcagatcttgctgcttccgctccagatctcacgctcccgacttgcacaatgagggca

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA08G36700.2 (Glycine max), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacc--cccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt
| |||||||| |||||||| |||||||| || || ||||| |||||| |||| ||||||||||| |||||||| |||||||| ||||||| |||||| |||    ||| | |        || | ||   ||  ||            |     |               ||    | | ||| ||||   |  || ||   
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTTCTCTGCATCGATTGCTCCGCCGTACACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttcaatggtgaatcaatttgttaatttttctgtgcggaaattgtttgtaaccttttgaaatctgattgtgtggctgatt--

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G12340.1 (Glycine max), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacc--cccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt
| |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||| |||||||| |||||||| ||||||| |||||| |||    ||| | |        ||   ||   ||  |  |     |    |   | |  | | |||  |     |    || ||  ||||   |  || ||  |
CGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCGTGAGgcaagtttttgctgattttgtttgaatggtgaatc-tgtttgttgattttttatgtgcggaaatttgtatcggtttgca-atatgattgtgtggctgattct

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA01G12340.2 (Glycine max), 5'ss of exon 2
-----CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacc--cccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt
     | |||||||| |||||||| |||||||| || || |||||||||||| |||| ||||||||||| |||||||| |||||||| ||||||| |||||| |||    ||| | |        ||   ||   ||  |  |     |    |   | |  | | |||  |     |    || ||  ||||   |  ||      
CAATGCGAAGAACCCTACCTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGATTGCTCCGCCGTTCACCGCAGTCTCGGCGTGCACATCAGCTTCgtgaggcaagtttttgctgattttgtttgaatggtgaatc-tgtttgttgattttttatgtgcggaaatttgtatcggtttgca-atatgattgtgtggctg-----

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: AT2G35210.2 (Arabidopsis thaliana), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgt-----------ttctttctacccccccttcccatcccgatccacgccccctcccc-------------tcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt---
| |||||||| || ||||| ||||| || ||||| ||||| |||||| |||| ||||| || || || || || || ||||||||||| | |||||||||||           ||| |||     |  ||||  || |   |  |    |  | ||              | | |  ||||||  |    ||| |  ||    |     | | ||  |  | ||   
CGAAGAACCCAACATGGGCTTCCGTTACTTACGGGATCTTTCTCTGCATCGATTGCTCAGCTGTTCATCGGAGTCTTGGCGTCCACATTAGCTTCGTCAGgtcatttgattcattcattcattttcatcttctgattctattatagagacatttcctaataatctagggtttagagaatctgctttttagccaagaaattgtgttgatcttcattttttgtttttag

upper sequence: LOC_Os03g63710.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv02s0012g01330.t01 (Vitis vinifera), 5'ss of exon 2
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccat--cccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt----
| |||||||| || ||||| |||||||| || || |||||||||||| |||||||||||||||| ||  | || || || || ||||||| |||||||||||   |||| |       ||    |     |||||| |          |    || ||   |||  |   |    ||    | ||| |    |  | || |     
CGAAGAACCCGACTTGGGCGTCCGTCACGTATGGGATCTTCCTCTGCATCGACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtga-tttcaattttgagttttggtggtttgatccatgatttagggttttggcagttc---aatttggtgatttgata--tttcgactagggttttgatttaagat

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|88739668|gb|CI763176.1|CI763176
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAA
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAA
EST: gi|88364273|gb|CI612222.1|CI612222
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88302091|gb|CI667937.1|CI667937
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88826434|gb|CI776999.1|CI776999
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAG
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAG
EST: gi|428827|gb|D24983.1|D24983
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|58658150|gb|CK046830.1|CK046830
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTC
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|58664331|gb|CK053017.1|CK053017
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|66916299|gb|CX103147.1|CX103147
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88721612|gb|CI744911.1|CI744911
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88341494|gb|CI635692.1|CI635692
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|29645173|gb|CB650180.1|CB650180
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|58680319|gb|CK069006.1|CK069006
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|58677850|gb|CK066537.1|CK066537
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|87006728|gb|CI285762.1|CI285762
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCACGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|29677839|gb|CB674114.1|CB674114
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|29635513|gb|CB640522.1|CB640522
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88288415|gb|CI661620.1|CI661620
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|88723709|gb|CI747219.1|CI747219
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTC
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTC
EST: gi|88351379|gb|CI627395.1|CI627395
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|11443001|gb|BF430888.1|BF430888
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|29679055|gb|CB675330.1|CB675330
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
EST: gi|33654274|gb|CF276888.1|CF276888
EST:     GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAG                         GTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT
genomic: GACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTT

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: 75 (upstream exon), 75 (downstream exon)
Score: 56

CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttct ... ttttctatagGTCAACAAACCTAGATTCATGGACTCCAGATCAACTGAAGATGATGGCTTTTGGAGGCAACAATCGTGCCCATGCTTTCTTTAAACAGCACGGGTGGACA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAAGAACCCCACCTGGGCCTCCGTCACCTACGGCATCTTCCTCTGCCTCGACTGCTCCGCCGTCCACCGCAGCCTCGGCGTCCACATCACCTTCGTCAGgtttctttctacccccccttcccatcccgatccacgccccctcccctcacaagatctgcaatccgcccacgccatcacatccgattcctttcctcatctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccccccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccatcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccacgc