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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtttcttttgttgtaactttgctcagtagggcattgaattagatggtttctatatcatttttcttctatgatatacaatctgaaacatatggtcgtactgtcag

Basic information

species Oryza sativa
transcript LOC_Os02g19510.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G119725_T01 (Zea mays), 5'ss of exon 5
TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtttcttttgttgtaactttgctcagtagggcattgaattagatggtttctatatcatttttcttctatgatatacaatctgaaacatatggtcgtactgtcag
|||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||||||||||| ||| || ||| | ||||||||||||||||||||| ||||||  |      |  | |||  |||  |  || |||||||       || | || ||| |||  | ||   | ||   ||| |||||||||  | |    ||||
TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgtt-----agccattttcttcaaaactgccttgaattt-----cttttttaacatattttatatacactctatgttcttaaacatatg-ccat-tcatcag

upper sequence: LOC_Os02g19510.1 (Oryza sativa), 5'ss of exon 5
lower sequence: GRMZM2G006507_T02 (Zea mays), 5'ss of exon 5
TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtttcttttgttgtaactttgctcagtagggcattgaattagatggtttctatatcatttttcttctatgatatacaatctgaaacatatggtcgtactgtcag
|||||| |||||||| ||||||||||| || || |||||||||||||| || |||||||||||||||| ||| || ||| | ||||||||||||||||||||| ||||||  |      |  |||||  |||  |     |||||||    |  || | || ||| | || | ||  || ||   ||| |||||||||  | |    ||||
TGTTCCTACAAACCCAAAAGGTGCTGAGAGACTTCCACCAGGCATTGTAGTGTCTGAAACAGATCTTTATCCCCGAAGACTATGGGGTGATCCTAGTGAGgttcgtggttgtt-----agccacttt-ttcaacactaacttgaatt----gccttttttaacatctatcatatacaatctatgttcttaaacatatg-ccat-tcatcag
















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|428327|gb|D24475.1|D24475
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|88360895|gb|CI625201.1|CI625201
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACT
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|428279|gb|D24427.1|D24427
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|29646523|gb|CB651530.1|CB651530
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|428340|gb|D24488.1|D24488
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|29673248|gb|CB669523.1|CB669523
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|29624841|gb|CB629852.1|CB629852
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|29676038|gb|CB672313.1|CB672313
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGGTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|29673598|gb|CB669873.1|CB669873
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGT
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGT
EST: gi|29640936|gb|CB645943.1|CB645943
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|58670226|gb|CK058912.1|CK058912
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATCGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAA
EST: gi|58691339|gb|CK080026.1|CK080026
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|66913022|gb|CX099870.1|CX099870
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
EST: gi|87006680|gb|CI285714.1|CI285714
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGGTTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGT
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGT
EST: gi|33675555|gb|CF303794.1|CF303794
EST:     TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAG                         GACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA
genomic: TTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACA

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: 75 (upstream exon), 57 (downstream exon)
Score: 29

TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtt ... gtactgtcagGACCTGAGTAGCGAACCACGGTACCTTGTTACTTTTACAGTTGGAATTACACAGAAGGCTAATATTGATGCTGCTGTCAAAAAG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTCCCACAAACCCTAAAGGTGCTGAAAGGCTCCCACCAGGCATTGTTGTTTCTGAAACAGATCTTTTTCCACGGAGATTGTGGGGTGATCCTAGTGAGgtttgtggtttcttttgttgtaactttgctcagtagggcattgaattagatggtttctatatcatttttcttctatgatatacaatctgaaacatatggtcgtactgtcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT