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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTCGTTGGGGATCCTAAGGAGAAGATCTGCGAGGTGACGGCAAATCTCAAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggataataagcactctctctgcactggttagctaacttggcgtggtttgattctgtccacttaatagggaacagacctgcaattccgtagttttt...

Basic information

species Oryza sativa
transcript LOC_Os02g52314.1
intron # 3
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|87016957|gb|CI284291.1|CI284291
EST:     CGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: CGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88242125|gb|CI241974.1|CI241974
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGTTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|163925691|gb|EG714527.1|EG714527
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|427820|gb|D23959.1|D23959
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88956111|gb|CI092399.1|CI092399
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|86483041|gb|CI125674.1|CI125674
EST:     CCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAGTGTGGTCTGTCC
genomic: CCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88850698|gb|CI094963.1|CI094963
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|218783402|gb|GE329454.1|GE329454
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88994744|gb|CI036325.1|CI036325
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|86535500|gb|CI175706.1|CI175706
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88992889|gb|CI035851.1|CI035851
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88417716|gb|CI535875.1|CI535875
EST:     CGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: CGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88203912|gb|CI203761.1|CI203761
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|117227159|gb|CT846067.1|CT846067
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTGTGGCCCTCTCGAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACCATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|86434045|gb|CI094388.1|CI094388
EST:     AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: AAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
EST: gi|88507116|gb|CI434622.1|CI434622
EST:     ATCTGCTCGTCAT-GGGTGCCGNTGCTTTTGGCCCCCTCAAGAG                         AATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC
genomic: ATCTGCTCGTCATGGGGTGCCG-TGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCC

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: 74 (upstream exon), 28 (downstream exon)
Score: 4

TGGTCGTTGGGGATCCTAAGGAGAAGATCTGCGAGGTGACGGCAAATCTCAAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggata ... tgttctacagAATGTTCTTAGGAAGTGTGAGCAACTACTGCATCAACAATGTGGTCTGTCCAGTTGTTGTAATCAAAGGCACTTGAGCCATCTTCGATCAGTATTCTTTG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTCGTTGGGGATCCTAAGGAGAAGATCTGCGAGGTGACGGCAAATCTCAAGGCCGATCTGCTCGTCATGGGGTGCCGTGCTTTTGGCCCCCTCAAGAGgtaatggataataagcactctctctgcactggttagctaacttggcgtggtttgattctgtccacttaatagggaacagacctgcaattccgtagttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggcgtgg