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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgaaatcgatcaaagaacttgaaatcaagtgccaaacaagctctcgcacattagcactacgttttaatttcgttcttacaattctctccttgattaattttggttcaattttctgtctgaaaaaaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATCGACGATAGCCAGATCCCGGATACGTTGGGCGGGAAGCTGGCACCGGTTT

Basic information

species Oryza sativa
transcript LOC_Os01g70210.1
intron # 5
splice site 3'
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|88469981|gb|CI407252.1|CI407252
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|33665932|gb|CF296899.1|CF296899
EST:     AGGCCTGGAAGATGATTTACCCTTTCATCGACAATGTCACCAGGGGCAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|89176897|gb|CI013470.1|CI013470
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88847573|gb|CI016066.1|CI016066
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|86525746|gb|CI165952.1|CI165952
EST:     AAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88269525|gb|CI380823.1|CI380823
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88203980|gb|CI203829.1|CI203829
EST:     AGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|27577459|gb|CB000154.1|CB000154
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88200125|gb|CI199975.1|CI199975
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|33666129|gb|CF297096.1|CF297096
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGGCAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88258593|gb|CI361179.1|CI361179
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|33677265|gb|CF305504.1|CF305504
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGGCAAG                         TTCGTGTTCGT
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGT
EST: gi|86601296|gb|CI251670.1|CI251670
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|86413397|gb|CI067802.1|CI067802
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|33662282|gb|CF293249.1|CF293249
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGGCAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|88985097|gb|CI011948.1|CI011948
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|11565074|gb|AU165710.1|AU165710
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
EST: gi|18385341|gb|BM418540.1|BM418540
EST:     AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAG                         TTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC
genomic: AGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATC

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: 66 (upstream exon), 72 (downstream exon)
Score: 52

GGAGAGGCTCGGCAAGGCCCTGATGATCCATGTACCCTACATGTTCATGAAGGCCTGGAAGATGATCTACCCTTTCATCGACAATGTCACCAGGGACAAGgtaatgaaat ... aaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATCGACGATAGCCAGATCCCGGATACGTTGGGCGGGAAGCTGGCACCGGTTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caattctctccttgattaattttggttcaattttctgtctgaaaaaaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATCGACGATAGCCAGATCCCGGATACGTTGGGCGGGAAGCTGGCACCGGTTT
             gattaat  putative branch site (score: 52)
                                     tctgaaaaaaaaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgaaatcgatcaaagaacttgaaatcaagtgccaaacaagctctcgcacattagcactacgttttaatttcgttcttacaattctctccttgattaattttggttcaattttctgtctgaaaaaaaaatgcagTTCGTGTTCGTGGACGACAAGAGCTTGCAAGAGGTGCTGCACCAGGAGATCGACGATAGCCAGATCCCGGATACGTTGGGCGGGAAGCTGGCACCGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG