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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGTGACGTGACGACGCCCCTCTCCTCCTCCTCCGCTGCCGCATCCGAGTTCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagccccgcccccgcttcatcagttcggtcggattggatgaacgcccattttttgtggggacgttcagcgtgatgtatcaacgattcaatcgaa...

Basic information

species Oryza sativa
transcript LOC_Os04g58620.1
intron # 1
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|88428428|gb|CI564896.1|CI564896
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|29675207|gb|CB671482.1|CB671482
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88390266|gb|CI605719.1|CI605719
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88342055|gb|CI644392.1|CI644392
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88718872|gb|CI742382.1|CI742382
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88408041|gb|CI601519.1|CI601519
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCC-G                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88405756|gb|CI609655.1|CI609655
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88311360|gb|CI570434.1|CI570434
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88332274|gb|CI656143.1|CI656143
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88309606|gb|CI656347.1|CI656347
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88327165|gb|CI652205.1|CI652205
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCG
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCG
EST: gi|88388909|gb|CI592797.1|CI592797
EST:     CATAAACCCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCC-GCGGACGGGCTT
genomic: CATAAACC-TTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88353192|gb|CI654458.1|CI654458
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88310234|gb|CI659024.1|CI659024
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88761387|gb|CI770943.1|CI770943
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88313126|gb|CI592410.1|CI592410
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88301925|gb|CI667771.1|CI667771
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88394425|gb|CI603614.1|CI603614
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88377419|gb|CI602904.1|CI602904
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88412842|gb|CI576106.1|CI576106
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88407810|gb|CI607944.1|CI607944
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGTCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88336549|gb|CI656820.1|CI656820
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88573375|gb|CI664946.1|CI664946
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88299281|gb|CI572233.1|CI572233
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88401398|gb|CI585954.1|CI585954
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88372181|gb|CI641816.1|CI641816
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88726178|gb|CI749833.1|CI749833
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
EST: gi|88572069|gb|CI663640.1|CI663640
EST:     TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCG                         GGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT
genomic: TCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTT

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: 68 (upstream exon), 75 (downstream exon)
Score: 40

CGGTGACGTGACGACGCCCCTCTCCTCCTCCTCCGCTGCCGCATCCGAGTTCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagc ... gttcgtacagGGGGCGCGTGGGGATGGATTTGTCTAGGTTTACTGCCCCGCGGCCGGGCTTGCAGATCGGCGCCGCCGGGAATGGCTTCCGGGCATGCTCCCTGCGGCGT




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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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGTGACGTGACGACGCCCCTCTCCTCCTCCTCCGCTGCCGCATCCGAGTTCATAAACCTTCGTCCCTTCCGCCCCGCCATCCGTCTTCCCGGAATCCCGgtatgtaagccccgcccccgcttcatcagttcggtcggattggatgaacgcccattttttgtggggacgttcagcgtgatgtatcaacgattcaatcgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccccgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggggacg