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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattttgcaccctgcacaattcaatttcattatattctgtgctgcattttcgaggctggaatgttgcaaatagaaagtttcttacataatttgggaattctgatgtacag

Basic information

species Oryza sativa
transcript LOC_Os07g12250.1
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|88581534|gb|CI698528.1|CI698528
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|325493082|gb|JG457606.1|JG457606
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCA
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCA
EST: gi|88348866|gb|CI653910.1|CI653910
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|33670740|gb|CF298979.1|CF298979
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|24468910|gb|CA305859.1|CA305859
EST:     GTAAGGAGGCATCGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCTGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88381633|gb|CI682300.1|CI682300
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAAGGGTA
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGG-AAGGGTA
EST: gi|88348364|gb|CI639023.1|CI639023
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88388417|gb|CI683189.1|CI683189
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGGAAGGGTA
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCA-GGGAAGGGTA
EST: gi|88592045|gb|CI710122.1|CI710122
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88571275|gb|CI662648.1|CI662648
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|218483042|gb|FG956499.1|FG956499
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAA-ATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCA-GGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|86898740|gb|CI296058.1|CI296058
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|3767629|gb|AU031656.1|AU031656
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|55441469|gb|CV734055.1|CV734055
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88763039|gb|CI772595.1|CI772595
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCNAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|163927854|gb|EG713502.1|EG713502
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|112787065|gb|EE591987.1|EE591987
EST:     GTAAGGAGGCATCGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCTGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88290337|gb|CI665126.1|CI665126
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88739146|gb|CI762654.1|CI762654
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
EST: gi|88574546|gb|CI666315.1|CI666315
EST:     GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAA                         GACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT
genomic: GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTAT

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: 47 (upstream exon), 70 (downstream exon)
Score: 52

GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattt ... tgatgtacagGACAGAGCTGTGCCGTTTCAGCGGCGCCAAGATTTACCCAGGGAAGGGTATCAGATTCATCCGTGCAGACTCCCAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGGAGGCATTGAAGGTTTGGTGAGGCAGCGAAGATGGTTCTCAAgtatgtattttgcaccctgcacaattcaatttcattatattctgtgctgcattttcgaggctggaatgttgcaaatagaaagtttcttacataatttgggaattctgatgtacag

- AAGGAG
- - - - -  TTGAAG
- - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - -  AAGATG