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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagcttgacttgtattcttgttttcgtcgattgaattctatttgcttctctgaattattccaatcaaaactaatacttgttgttctctgaataa...

Basic information

species Oryza sativa
transcript LOC_Os01g27210.1
intron # 2
splice site 5'
intron type U2

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|88335790|gb|CI647146.1|CI647146
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88290470|gb|CI665259.1|CI665259
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88570430|gb|CI661803.1|CI661803
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|86517182|gb|CI157388.1|CI157388
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCCTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|86831146|gb|CI295623.1|CI295623
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|454518|gb|D28287.1|D28287
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGNTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88336380|gb|CI648967.1|CI648967
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88742546|gb|CI766054.1|CI766054
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|55414863|gb|CV727239.1|CV727239
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88574439|gb|CI666208.1|CI666208
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|55414167|gb|CV726543.1|CV726543
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|33796153|gb|CF323942.1|CF323942
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88305839|gb|CI633419.1|CI633419
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGAACTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|29667780|gb|CB664055.1|CB664055
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|25799620|gb|CA755581.1|CA755581
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|287276|gb|D16078.1|D16078
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGNTCTATC                         AATCGCGAGCANTCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88348212|gb|CI637673.1|CI637673
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|86906390|gb|CI294513.1|CI294513
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88306238|gb|CI636623.1|CI636623
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88826284|gb|CI776849.1|CI776849
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88764479|gb|CI773597.1|CI773597
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAAAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|32948407|gb|BP184979.1|BP184979
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88828083|gb|CI778648.1|CI778648
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88350933|gb|CI620593.1|CI620593
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|3090514|gb|C93501.1|C93501
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCAAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88742188|gb|CI765696.1|CI765696
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88363216|gb|CI643074.1|CI643074
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|51946184|gb|CV152525.1|CV152525
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|32948287|gb|BP184859.1|BP184859
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88353725|gb|CI633116.1|CI633116
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88347219|gb|CI631299.1|CI631299
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88362614|gb|CI608763.1|CI608763
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|87027890|gb|CI276246.1|CI276246
EST:     CGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88575573|gb|CI669718.1|CI669718
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|55414769|gb|CV727145.1|CV727145
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
EST: gi|88326634|gb|CI658354.1|CI658354
EST:     CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATC                         AATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC
genomic: CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCC

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: 49 (upstream exon), 21 (downstream exon)
Score: 3

CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagc ... ttcttgtcagAATCGCGAGCAATCGCTAGGTACATCTTTCGCAAGTACAAACCAGAGTTCCTGGGACTCGGAGAAGGTGGAAGCCTGGAGGAGTCGGCAATGGTGGACGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCGTTCGGTGAGATTCCAGTACTGGAGGATGGCGACCTGACGCTCTATCgtaagcaagcttgacttgtattcttgttttcgtcgattgaattctatttgcttctctgaattattccaatcaaaactaatacttgttgttctctgaataa

- - - - - - - - - - - TGGAGG
- - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - GAGGAT
- - - - - - - - - - - -  AGGATG